Run 1.4.0 1.5.1 delta

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These are detailed notes on changes made between bioperl-run-devel-1-4-0 and bioperl-run-release-1-5-1.

Bio::Factory::EMBOSS
Moving from bioperl-live CVS module
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Installer::Clustalw
Adding class
Bio::Installer::EMBOSS
Added
Changing from hardcoded version to EMBOSS-latest
EMBOSS-latest version bug
Added FIXME
Less spam - more ham
Bio::Installer::Generic
Added
Less spam - more ham
Bio::Installer::PAML
Added
Updating to 3.14a version
Updating directory_name to version 3.14
Less spam - more ham
Bio::Installer::Probcons
Adding a probcons installer - watch out for newer releases than 'PACKAGE_NAME' => 'probcons_v1_09.tar.gz'
Less spam - more ham
Bio::Installer::TCoffee
Added
Less spam - more ham
Bio::Tools::Run::AbstractRunner
Proposed fundamental classes for other specific classes
Bio::Tools::Run::Alignment::Blat
Moving to Bio::Tools::Run::Alignment Namespace
Some code cleanup to avoid warnings and insure filehandles are properly closed, etc
Well, at least it runs the blat program now, although it isn't seemingly able to find the output tempfile to retrieve the results
Various fixes to get blat runnable in line with bioperl-live 1.2.3 all tests now pass.
This still needs an overhaul but fix minor doc bugs in naming the module
Stan's fix
Executable is the string to run
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Alignment::Clustalw
Migrated code that runs tools to Bio::Tools::Run
Renaming packages for new dir structure
Fixed to PROPER usage of tempfile
More intelligent detection of installed modules (File::Spec) and cleanup of .dnd files
Quoted unquoted string literals used as hash keys.
Migrated to new Bio::Root::RootI chained new
Changed to adopt Bio::Root::IO.
Properly removing tempfiles
Io was not initialized, meaning tempfiles were not cleaned up
Intitialize io -- facilitate tempfile cleanup
The module was requiring input sequences to eq Bio::Seq, changed that to isa->Bio::PrimarySeqI. Clustalw chrashes if the the sequence does not have id() set, undef id() now throws an error.
Checks that seq is a Bio::PrimarySeq and seq->id() is set
Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.
The code for setting the path to binary was in BEGIN block making it impossible to change from a calling perl script. Moved it into new(). $ENV{CLUSTALDIR} = '/path/to/clustalwdir/'; now works.
The code for setting the path to binary was in BEGIN block making it impossible to change from a calling perl script. Moved it into new(). $ENV{CLUSTALDIR} = '/path/to/clustalwdir/'; now works.
Changed exists_clustal() to use new Bio::Root::IO->exists_exe().
Sweeping change: Bio::Root::RootI is now a pure abstract interface and cannot be inherited from unless you implement several of its abstract methods. Most people will want to inherit from Bio::Root::Root. This change was necessary in order to support Bioperl objects that were not based on hashrefs.
More quiet warning so tests are less chatty
Check to insure defined object before calling ISA
Use the updated PROGRAM exe location information to set the PROGRAM variable
Added method version() $self->isa('Bio::Factory::ApplicationFactoryI')
Debug message now uses the debug method
Verbosity=-1 is same as quiet()
Params should be appended not overwriting
No need for the dir variable
Now can take a program path as arg on the new method, aboids need for ENV variable (ENV still in not to break other people's scripts,etc)
Tweak to clustalw test for falling over correctly
Turn of clustalw debugging
Slightly more intelligent checking for clustalw exe
Merged exe checking from branch
Minor documentation fixes
Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)
Allow phylip output format to be set
Make sure we cleanup tempfiles before each run
Make sure we've closed temporary file handles
Some changes to deal with dec_osf bug
Moving executable method to Wrapper base, removing global TMP variables where possible
Closing AlignIO to avoid too many open files error
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Nathan's version of the module
More, better tests for the new implementation for tree/bootstrap -- still some things to fix
Issue #1646; This should go with msf if gcg format is requested
Some Documentation fixes to clarify how to set the env variables so that it shows up in the perldoc not just as comments
Adhere to the style that makes sense to me
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Alignment::DBA
Wrapper object for Ewan Birney's Dna Block Aligner
Changed to use PAML template for find executable insated of ClustalW way
Fixed tempdir, inherit from wrapperbase
Doh left out tempdir bug
Moving executable method to Wrapper base, removing global TMP variables where possible
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
To Quieten declaration warnings
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Alignment::Exonerate
Wrapper for exonerate
Doc fix
Properly run Exonerate
Bio::Tools::Run::Alignment::Lagan
Poh. Lagan being a MSA program, it belongs into the Bio::Tools::Run::Alignment namespace
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Swapping order so that it won't fail on an isa of an array
Small fixes and addition of options
Really should include the program name
Added the right credits.
Allowing of setting of outfile
Can't declare are expect a variable at the same time
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Alignment::MAFFT
More, better tests for the new implementation for tree/bootstrap -- still some things to fix
Update link
Tcoffee --> MAFFT, version stuff removed, allow percent ID to waver a little
Bio::Tools::Run::Alignment::Muscle
Bare Bones MUSCLE wrapper and tests
Adding params to be able to run refine option
Added maxiters and tree1 options
Test more muscle args, fix new {} _rearrage with mixed args
Support for the soon-to-be-released update cmdline option '-scorefile'
Bio::Tools::Run::Alignment::Probcons
Probcons wrapper -- first try!!!
Adding params and switches
Uppercase params and switches
FIXME: last line switches - dunno how to set them
Fixing double dashes and equal signs
Bio::Tools::Run::Alignment::Sim4
Sim4 wrapper
Housekeeping for open files
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
To Quieten declaration warnings
Michael's patch
Allow alignment methods (A=[01234]) to be specified, default to A=0 as before
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Alignment::StandAloneFasta
Committing first port of StandAloneFasta from Tiequan, may not be fully functional
Fix bug
Argh left out program_dir
Small fixes for linux and setting of program param correctly
Need to override executable to store multiple program namesTempfile cleanup may not be correct - need to verify
Support -S and a place to put the 'output' data - although not used yet
Bug which was not caught before
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Alignment::TCoffee
Migrated code that runs tools to Bio::Tools::Run
Renaming packages for new dir structure
Fixed to PROPER usage of tempfile
Extra documentation
More intelligent detection of installed modules (File::Spec) and cleanup of .dnd files
Quoted unquoted string literals used as hash keys.
Migrated to new Bio::Root::RootI chained new
Fixed several doc format bugs.
Correct authors + email for consistency
Changed to adopt Bio::Root::IO.
Fixed TCoffee changes to properly output seqs to temp file when passing in array of seqs
Io was not initialized, meaning tempfiles were not cleaned up
Intitialize io -- facilitate tempfile cleanup
Checks that seq is a Bio::PrimarySeq and seq->id() is set
Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.
The code for setting the path to binary was in BEGIN block making it impossible to change from a calling perl script. Moved it into new(). $ENV{TCOFFEEDIR} = '/path/to/clustalwdir/'; now works.
The code for setting the path to binary was in BEGIN block making it impossible to change from a calling perl script. Moved it into new(). $ENV{TCOFFEEDIR} = '/path/to/clustalwdir/'; now works.
Changed exists_tcoffee() to use new Bio::Root::IO->exists_exe().
Sweeping change: Bio::Root::RootI is now a pure abstract interface and cannot be inherited from unless you implement several of its abstract methods. Most people will want to inherit from Bio::Root::Root. This change was necessary in order to support Bioperl objects that were not based on hashrefs.
StandAloneBlast now checks for ecoli.nt (is this right?) and TCoffee is a little more verbose
Use the updated PROGRAM exe location information to set the PROGRAM variable
Added version() Implementaion might print an annoying string "FATAL error..." on non-UNIX platforms. Post 1.37 versions of t_coffee will have an explicit -version argument.
Verbosity=-1 is same as quiet()
Version determining regexp protected
Use proper Tools::WrapperBase now
Codeml --> tcoffee copy+paste silliness
More robust parameter handling, matrix is not a required parameter (default of blosum), generic run method now
Make sure we've closed temporary file handles
Moving executable method to Wrapper base, removing global TMP variables where possible
Cleaned docs for cleanup()
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Adding null matrix capability and score_ascii
small docu fixes
Some Documentation fixes to clarify how to set the env variables so that it shows up in the perldoc not just as comments
Albert's patch
Small cosmetic changes
Profile align expects 1st arg to be profile, second to be seq
Adhere to the style that makes sense to me
Bio::Tools::Run::Analysis
Added a general Analysis client together with its incarnation as a SOAP client
Added -timeout parameter to the SOAP-based Analysis client
Binary input added
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Fix revision string problems
Default location for SOAP analysis services at EBI has changed
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Analysis::soap
Added a general Analysis client together with its incarnation as a SOAP client
Added -timeout parameter to the SOAP-based Analysis client
Changes in Soaplab API
Changes in Soaplab API
Binary input added
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Fix revision string problems
Default location for SOAP analysis services at EBI has changed
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::AnalysisFactory
Added a general Analysis client together with its incarnation as a SOAP client
Added -timeout parameter to the SOAP-based Analysis client
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Default location for SOAP analysis services at EBI has changed
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::AnalysisFactory::Pise
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
Email not mandatory anymore in Pise
Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT and SEE ALSO parts.
- Piseapplication.pm, AnalysisFactory/Pise.pm and PiseJob.pm: -remote parameter to -location to conform to Bio::Tools::Run::AnalysisFactory interface - PiseApplication/genscan.pm: The documentation of all PiseApplication/*.pm files is going to change: in addition to COPYRIGHT, FEEDBACK SEE ALSO section, the DESCRIPTION section now contains *only* the parameters that can be set by the client. "Fake" parameters such as "Results" or "Paragraph" are no longer displayed here. => I commit only genscan.pm to let bioperl core see if it's ok :-)
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::AnalysisFactory::soap
Added a general Analysis client together with its incarnation as a SOAP client
Changes in Soaplab API
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Fix revision string problems
Default location for SOAP analysis services at EBI has changed
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Blat
Wrapper for blat...still under dev
Wrapper for Blat
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Changes in align subroutine taking only one argument
Moving to Bio::Tools::Run::Alignment Namespace
Bio::Tools::Run::Coil
Wrapper for coil
Added quiet param, moving executable method to base class
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::EMBOSSApplication
Classes for wrapping EMBOSS suite
Claning. Needs code to compare input and ACD options
EMBOSS more runnable and w/ tests
Sweeping change: Bio::Root::RootI is now a pure abstract interface and cannot be inherited from unless you implement several of its abstract methods. Most people will want to inherit from Bio::Root::Root. This change was necessary in order to support Bioperl objects that were not based on hashrefs.
Handle cmd line arguments pointing to a Bio::PrimarySeqI object or array or Bio::PrimarySeqI
Added ability to dump alignments as well as sequences when running an EMBOSS application
Cleanup before each run of an application
Merged changes from trunk to branch
Handle some weird boundary cases
Added ACD parsing and modified EMBOSS modules to check parameters if verbose() is set over zero
Explicitly closing some filehandles appears to do a better job freeing resources
No more warnings under perl 5.8.0
Added a missing semicolon to make the synopsis runnable
Use debug to print out the dumper info
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
No need for this debugging
Allow 0 value attributes per Susan Miller's bug report
Debugging enabled
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::EMBOSSacd
Added ACD parsing and modified EMBOSS modules to check parameters if verbose() is set over zero
No more warnings under perl 5.8.0
Stephen's patch
EMBOSS 3.0.0 testing passes
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Eponine
wrapper for Eponine.. fixed bug
Inherit from WrapperBase
Cleanup of tempfiles works
Fixed Eponine test and runnable
Trying to add sanity to bioperl-run, added checks and pretty failures in the tests... will get there one day
Make sure resources are freed
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
More standardized way of running Eponine
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::FootPrinter
First wrapper for Blanchette's FootPrinter for Phylogenetic Footprinting Todo, take in Bio::Tree for tree_of_life Smarter handling of seq ids
Close file handles
Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)
Moving executable method to Wrapper base, removing global TMP variables where possible
Cleaned docs for cleanup()
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Write the files properly
Mark Wagner's enhancements Issue #1399
Fix stupidity with tempfilehandle and outfh not being closed properly as reported by Ben Westover
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Genewise
First addition of Genewise wrapper module
Few small fixes to Genewise runnable and test
Uses the parser in Bio::Tools::Genscan instead of internal parsing
Refactor wrapper
Added -trev option
Remove Fugu system stuff and insure that File tmp handles are closed -- this is what creates the problems of running out of filehandles
Make sure resources are freed
Support -u and -v settings, support passing in file instead of Bio::Seq object (trust user to do the right thing here and passing fastafile
Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)
Support HMMER filetype parameter
Oops - meant to set the HMMER param in the right place, also support another set of GENEWISE parameters
Let's create one less temporary file -- also - let's use the filehandle that was created for us, one less open call, support quiet operation
Quiet properly
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.
Clarified HMM support. Added checks & exception. Added docs
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Added more options
Docfix, an array of genes can be returned
Genewise tests should pass now on 2.2.3 and 2.2.0
Test for wise 2.2.0 and 2.2.3
Bio::Tools::Run::Genscan
Wrapper for Genscan executable
POX fixes
Fixing wrapper to be in line with ProtML + WrapperBase
Dumb print statement cuzing failed test
Allow suppression of stderr
Make sure resources are freed
Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Doc fix
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Hmmer
Hmmer wrapper factory, currently supports hmmsearch, hmmalign,hmmpfam, hmmbuild and hmmcalibrate
Fixes option to allow -n and also allow -arguments
Cleanup code for debugging
Fix filehandle problem without using IO::String -- problem before was FH was getting closed because it went out of scope
Scott Markel's additions + some tweaking for hmmalign; Added many more cmd-line options plus support for doubledash arguments and force -q option on hmmalign
Switch flag per Issue #1775
Bio::Tools::Run::Hmmpfam
Wrapper module for hmmpfam
Check for options
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Updated to set params properly and return searchio object
Hmmpfam deprecated, replacted by Hmmer
Bio::Tools::Run::JavaRunner
Proposed fundamental classes for other specific classes
Bio::Tools::Run::Lagan
Moved from bioperl-live. Note: name change: Bio::Tools::Lagan -> Bio::Tools::Run::Lagan
Poh. Lagan being a MSA program, it belongs into the Bio::Tools::Run::Alignment namespace
Bio::Tools::Run::Mdust
Moved Mdust.pm from Bio::Tools to Bio::Tools::Run, added test script and data file.
Some minor changes. Also, I think 'use warnings' has been removed for back-compatibility
Modified documentation to conform to bioperl format
Modified to inherit Bio::Tools::Run::WrapperBase, use Bio::Root::IO to build up paths
Use save_tempfiles, use PROGRAMNAME as a variable, use tempfile instead of randomly generating filename
Modified call to io->tmpfile to get file name as well as handle
Bio::Tools::Run::Phrap
Phrap wrapper
Teeny code cleanup
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::Forester::SDI
SDI in Forester package. it should be announced that you need to modify the source code of SDI to stop the popup window, if you only need the output file of it, before using this module
More document
Bio::Tools::Run::Phylo::LVB
Adding Daniel's LVB wrapper
LVB changes by Daniel
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::Molphy::ProtML
Added ProtML wrapper - part of Molphy packager for ML tree building
Codeml->protml doc fixes
Code formatting
Cleanup of tempfiles works
Synopsis doc
Moving executable method to Wrapper base, removing global TMP variables where possible
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Align the code
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::PAML::Baseml
Add Baseml
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::PAML::Codeml
PAML package -- codeml wrapper and test committed
Small doc tweaks and added runnable synopsis
POX fixes
Little fixes: catdir -> catfile, better error matching regexp
Migrate from PAMLBase to WrapperBase
Fix internal parameter name
Copy+paste error
Added additions of .exe for on windows, allow alignment to be specified as a file as well as Bio::Align::AlignI object
API changed a little bit with new parser
Cleanup of tempfiles works
Whoops,one more time, cleanup tempfiles and dirs
Cosmetic code fix
Handle exe apps
Default should be F3X4
Respect the original cwd
Refer to the correct base class
Moving executable method to Wrapper base, removing global TMP variables where possible
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Default should be an arrayref
George Hartzell fixes
What is that underscore in there for?
Stupid jason - it saves a syscall
Docu fix
Let alpha be more free - don't try and restrict it
Support more models
Allow alignment to be specified in run()
Some docu update
Update doc
Allow omega to varied
Adding allowed fix_blength = 1
Added no_param_checks getter-setter -- added no_param_checks condition in set_parameter
Silence undef warning
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::PAML::PAMLBase
PAML package -- codeml wrapper and test committed
Migrate from PAMLBase to WrapperBase
Bio::Tools::Run::Phylo::PAML::Yn00
Yn00 wrapper for PAML
Return the values as hash of hashes as they are all pairwise calculations - nei and yang results are returned as 2 separate arrays- this is all going to be improved when we abstract the parsing to a separate parser class
POX fixes
Remove debug copyfile
Migrate from PAMLBase to WrapperBase
Handle windows exes
Fixed to work with new base object and use bioperl PAML parser
Add some debugging support
Moving executable method to Wrapper base, removing global TMP variables where possible
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Issue #1507, SYNOPSIS is runnable now with API changes
Issue #1507 add MSwin .exe extension where appropriate
Wait -this isn't necessary , we already pad the PROGRAMNAME with the .exe when appropriate
George Hartzell fixes
Catfile not catdir
Allow alignment to be passed in to run()
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::Phylip::Base
Should read correct filename for output, and allows one to programatically set the output and treefiles for phylip apps
Tree drawing modules
Use tempdir to run things
First stab at configuration files for managing version difference of phylip
Moving executable method to Wrapper base, removing global TMP variables where possible
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Protdist works for me on phylip 3.61
DrawTree Basically works
Bio::Tools::Run::Phylo::Phylip::Consense
Wrapper for consense
Allow outgroups to be set using names
Changes to allow multiple alignments, matrices
Moving executable method to Wrapper base, removing global TMP variables where possible
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
No more "Using a hash as a reference is deprecated" warnings
Do the right thing that I wanted you to do (you know that thing)
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::Phylip::DrawGram
Tree drawing modules
Use tempdir to run things
Oops - use class state not class variable for the tempdir -- simplify protdist matrix parsing slightly
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming to run method
Don't need to cat tempdir if its an absolute path
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Drawgram works
DrawTree Basically works
Bio::Tools::Run::Phylo::Phylip::DrawTree
Tree drawing modules
Use tempdir to run things
Oops - use class state not class variable for the tempdir -- simplify protdist matrix parsing slightly
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming to run method
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
DrawTree Basically works
Bio::Tools::Run::Phylo::Phylip::Neighbor
Added Neighbor-Joining wrapper
Fix warnings
Update some of the docs
Move towards wrapperbase type wrappers
Skip if ret val is 0
Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)
Should read correct filename for output, and allows one to programatically set the output and treefiles for phylip apps
Tree drawing modules
Use tempdir to run things
Oops - use class state not class variable for the tempdir -- simplify protdist matrix parsing slightly
First stab at configuration files for managing version difference of phylip
Allow outgroups to be set using names
Changes to allow multiple alignments, matrices
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming to run method
Require jumble parameter to be odd or we get ina bad infinite loop
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Check for multiple data sets and set parameter accordingly. Caught by Vladimir.
Properly get the hash value
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::Phylip::PhylipConf
First stab at configuration files for managing version difference of phylip
Added seqboot
Added consense
Changes to allow multiple alignments, matrices
JIT should be JTT
Bug fix, shouldn't writing Y to change MODEL type
No more "Using a hash as a reference is deprecated" warnings
Protdist works for me on phylip 3.61
Indent some code
Drawgram works
DrawTree Basically works
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::Phylip::ProtDist
Wrapper for phylip program protdist which calculates a distance matrix based on amino acid substitution
Removed superfluous variables
Update some of the docs
Doc fix
Brought in line with WrapperBase
Move towards wrapperbase type wrappers
Doh left out tempdir bug
Consistency
Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)
Small formatting changes
Should read correct filename for output, and allows one to programatically set the output and treefiles for phylip apps
Tree drawing modules
Use tempdir to run things
Oops - use class state not class variable for the tempdir -- simplify protdist matrix parsing slightly
First stab at configuration files for managing version difference of phylip
Changes to allow multiple alignments, matrices
Moving executable method to Wrapper base, removing global TMP variables where possible
Formatting
Renaming to run method
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Get rid of deprecation warning
Protdist works for me on phylip 3.61
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::Phylip::ProtPars
New wrapper for the phylip program protpars for creating of phylogenetic trees from a multiple alignment
Removed superfluous variables
Move towards wrapperbase type wrappers
Doh left out tempdir bug
Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)
Tree drawing modules
Use the new Phylip base wrapper
Doc + code formatting cleanup
Use tempdir to run things
Oops - use class state not class variable for the tempdir -- simplify protdist matrix parsing slightly
First stab at configuration files for managing version difference of phylip
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming to run method
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
No more "Using a hash as a reference is deprecated" warnings
Do the right thing that I wanted you to do (you know that thing)
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Phylo::Phylip::SeqBoot
Seqboot wrapper, only working with v3.5 currently
Changes to allow multiple alignments, matrices
Moving executable method to Wrapper base, removing global TMP variables where possible
Handle interleaved output from phylip 3.6, handle 3.6 in general
Remove debugging code
Allow more than one alignment
No more "Using a hash as a reference is deprecated" warnings
Support new exported Menu variable
Bio::Tools::Run::PiseApplication
Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
Email not mandatory anymore in Pise
Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT and SEE ALSO parts.
- Piseapplication.pm, AnalysisFactory/Pise.pm and PiseJob.pm: -remote parameter to -location to conform to Bio::Tools::Run::AnalysisFactory interface - PiseApplication/genscan.pm: The documentation of all PiseApplication/*.pm files is going to change: in addition to COPYRIGHT, FEEDBACK SEE ALSO section, the DESCRIPTION section now contains *only* the parameters that can be set by the client. "Fake" parameters such as "Results" or "Paragraph" are no longer displayed here. => I commit only genscan.pm to let bioperl core see if it's ok :-)
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::CSR
Pise Factory and Application classes : files associated with each program defined in Pise.
Bio::Tools::Run::PiseApplication::Puzzle
Pise Factory and Application classes : files associated with each program defined in Pise.
Puzzle interface update : - Add missing amino-acid substitution models. - Alignment file is now set on the command line.
Bio::Tools::Run::PiseApplication::abiview
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::addquart
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::align2model
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::alistat
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::antigenic
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::assp
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::backtranseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::bambe
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::banana
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::bionj
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::biosed
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::bl2seq
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::blast2
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::blimps
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::blimps_block
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::blimps_matrix
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::boxshade
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::btwisted
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::cai
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::cap
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::cds
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::chaos
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::charge
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::checktrans
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::chips
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::cirdna
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::clique
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::clustalw
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::clustalw_convert
Pise Factory and Application classes : files associated with each program defined in Pise.
Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::codcmp
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::coderet
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::codnocod
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::codontree
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::codonw
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::comalign
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::combat
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::compseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::con_filter
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::confmat
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::cons
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::consense
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::consensus
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::cpgplot
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::cpgreport
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::cusp
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::cutseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dan
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dca
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::decorate
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::degapseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::descseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dialign2
Pise Factory and Application classes : files associated with each program defined in Pise.
Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::diffseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::digest
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::distmat
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::distquart
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dnadist
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dnapars
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dollop
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::domainer
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dotmatcher
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dotpath
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dottup
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::drawgram
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::drawpyr
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::drawtree
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dreg
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::druid
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dsc
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::dssp
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::einverted
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::emma
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::emowse
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::environ
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::eprimer3
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::equicktandem
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::est2genome
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::etandem
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::extractfeat
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::extractseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fasta
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fastdnaml
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fastrna
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::filtersites
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::findkm
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fitch
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fmtseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::freak
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fuzznuc
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fuzzpro
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::fuzztran
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::gb2xml
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::geecee
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::genscan
Pise Factory and Application classes : files associated with each program defined in Pise.
- Piseapplication.pm, AnalysisFactory/Pise.pm and PiseJob.pm: -remote parameter to -location to conform to Bio::Tools::Run::AnalysisFactory interface - PiseApplication/genscan.pm: The documentation of all PiseApplication/*.pm files is going to change: in addition to COPYRIGHT, FEEDBACK SEE ALSO section, the DESCRIPTION section now contains *only* the parameters that can be set by the client. "Fake" parameters such as "Results" or "Paragraph" are no longer displayed here. => I commit only genscan.pm to let bioperl core see if it's ok :-)
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::getblock
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::getorf
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::gff2ps
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::gibbs
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::gibbs_scan
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::golden
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::grailclnt
Pise Factory and Application classes : files associated with each program defined in Pise.
Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::gruppi
Pise Factory and Application classes : files associated with each program defined in Pise.
Pise files update for program beginning with d, e, f and g.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::helixturnhelix
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmalign
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmbuild
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmcalibrate
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmconvert
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmemit
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmer2sam
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmfetch
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmpfam
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmscore
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmmsearch
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::hmoment
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::homology
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::html4blast
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::iep
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::infoalign
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::infoseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::interface
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::isochore
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::kitsch
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::lassap
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::lgicsearch
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removing application LGICSEARCH upon request of the author
Bio::Tools::Run::PiseApplication::lindna
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::listor
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::loadseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::lvb
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::makehist
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::map
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::marscan
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::maskfeat
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::maskseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::matcher
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::megamerger
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::melting
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::merger
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::mfold
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Pise/bioperl module for a recent version of mfold (3.1.2).
Mfold version change (3.1.2)
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::mix
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::modelfromalign
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::most
Pise Factory and Application classes : files associated with each program defined in Pise.
Bio::Tools::Run::PiseApplication::mreps
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::msa
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::msbar
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::mspcrunch
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::mview_alig
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::mview_blast
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::mwfilter
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation updates, as well as location parameter, continuing with programs starting by h, i, k, l and m.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::needle
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::neighbor
Pise Factory and Application classes : files associated with each program defined in Pise.
Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::newcpgreport
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::newcpgseek
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::newseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::njdist
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::nnssp
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::notseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::nrscope
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::nthseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::octanol
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::oddcomp
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::palindrome
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pam
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::parciquart
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pars
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pasteseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::patmatdb
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::patmatmotifs
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::patser
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pdbsearch
Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pepcoil
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pepinfo
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pepnet
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pepstats
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pepwheel
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pepwindow
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pepwindowall
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pestfind
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pftools
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::phiblast
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pima
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::plotcon
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::plotorf
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::plsearch
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::polydot
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pratt
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::predator
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::preg
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prettyalign
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prettyplot
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prettyseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::primersearch
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::primo
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prodom
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::profit
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prophecy
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prophet
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prose
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::prot_nucml
Pise Factory and Application classes : files associated with each program defined in Pise.
Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::protal2dna
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::protdist
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::protpars
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pscan
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::psiblast
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::psort2
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pyramids
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::pyreval
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::qstar
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::quicktree
Pise: added quicktree, bug fix in PiseJob.pm
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::readnexus
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::readseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::recoder
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::redata
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::remap
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::repeats
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::restover
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::restrict
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::revseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnadistance
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnaeval
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnafold
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnaga
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnaheat
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnainverse
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnapdist
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::rnasubopt
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation + location parameter update. Programs from n to r.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::sam2hmmer
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::sampleseqs
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::saps
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::satellites
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::scan_for_matches
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::scope
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::scopparse
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::seqboot
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::seqgen
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Changes in parameters: - added options invar_site (-i), random_seed (-z), write-ancest (-wa), write-sites (-wr), partition_numb (-p) - fixed bug in Phylip option: it was -p now it's a vlist: -op, -or, -on - changed type of some options type from integer to float (scale_branch, scale_tree, rate123, shape, freqACGT, transratio)
- pb in some variable names: changed '-' to '_'
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::seqmatchall
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::seqsblast
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::seqstat
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::showalign
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::showfeat
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::showorf
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::showseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::shuffleseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::sigcleave
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::siggen
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::sigscan
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::silent
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::sirna
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::splitter
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::sreformat
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::stretcher
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::stride
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::stssearch
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::supermatcher
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::syco
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::tacg
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::tfscan
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::tipdate
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::tmap
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::toppred
Pise Factory and Application classes : files associated with each program defined in Pise.
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::tranalign
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::transeq
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::treealign
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::trimest
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::trimseq
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::trnascan
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::twofeat
Starting to add new interfaces versions (letters a, b and c). Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::unroot
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::vectorstrip
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::water
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::weighbor
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::whichdb
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::wise2
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::wobble
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::wordcount
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::wordmatch
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::wublast2
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::xblast
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseApplication::xpound
Pise Factory and Application classes : files associated with each program defined in Pise.
Documentation update and location parameter. Programs from s to z.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseJob
Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page
Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).
Clean up to make -w clean
User agent version and job stdout/stderr mtd name
Pise: added quicktree, bug fix in PiseJob.pm
Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT and SEE ALSO parts.
- Piseapplication.pm, AnalysisFactory/Pise.pm and PiseJob.pm: -remote parameter to -location to conform to Bio::Tools::Run::AnalysisFactory interface - PiseApplication/genscan.pm: The documentation of all PiseApplication/*.pm files is going to change: in addition to COPYRIGHT, FEEDBACK SEE ALSO section, the DESCRIPTION section now contains *only* the parameters that can be set by the client. "Fake" parameters such as "Results" or "Paragraph" are no longer displayed here. => I commit only genscan.pm to let bioperl core see if it's ok :-)
Removed module specific $VERSION, all modules now use global one from Bio::Root::Version
Reverting change for VERSION for 1.2.2 release
Sub fh(): the test to compare the requested file and the url in the list of results was not appropriate.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseJobParser
Source code for Pise Factory and Application classes. Bio/Factory/Pise.pm: factory Bio/Tools/Run/PiseApplication.pm: base class for all programs Bio/Tools/Run/PiseJob.pm: class for a launched job Bio/Tools/Run/PiseJobParser.pm: XML parser for a job result page
Pise: added warning handling in parser
Clean up to make -w clean
Added code in the SYNOPSIS, as well as the FEEDBACK, COPYRIGHT and SEE ALSO parts.
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::PiseWorkflow
PiseWorkflow is a module for building and running a workflow on top of PiseApplication instances.
Bio::Tools::Run::Primate
Wrapper for Primate, Guy Slater's exact match finder
Modified how target and queries are fed
Fix tempdir bug
Make sure resources are freed
Changed to seqname to seq_id
Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Primer3
Porting Rob Edwards extension of Primer3 wrapper and parser
Changed Bio::Tools::Run::Primer3 to allow get/set of program name and directory
Attempted cleanup of code for Issue #1657
Patch applied
Some code formatting
Let's put the new new() example up top so no one misses it
6th inning, 6th game, Sox up by 4! Can't do much else but hit the tab key.
Minor change to program_dir in Bio::Tools::Run::Primer3 which could never be set and then checked later
Minor change to included_region in Bio::Tools::Run::Primer3 to make default set correctly
George Hartzell's excellent code fixes
Bio::Tools::Run::Prints
Make sure resources are freed
Executable name change
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Profile
Wrapper module for Profile
Make sure resources are freed
Name of program is pfscan
Add an Id header
Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Use seq_id
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Promoterwise
Initial check in for promoterwise
Group hsps together as subseqfeatures
Using parser
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Bio::Tools::Run::Pseudowise
Added fixes and executable checking
Make sure resources are freed
Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)
Changed the parser to store the ka/ks ratio
Make quieten test work
Remove Kiran's hardcoded path to exe
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
An hour of my life gone... pseudowise wrapper is now better suited to actually work and separate parsing from running
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::RemoteBlast
Pure perl (via HTTP) Remote blast submission and retrieval -- see test script for example usage
Quieter tests when verbose == 0, use tempfile for HTML -> text cleanup
Fixed tempfile filehandle handling in retrieve_blast().
Updated to use ncbi Blast.cgi script rather than blast.cgi Text formatting done by cgi rather than HTML tag stripping in module code
Status set to invalid on a failed retrieval
Documentation for retrieve_blast method
Sweeping change: Bio::Root::RootI is now a pure abstract interface and cannot be inherited from unless you implement several of its abstract methods. Most people will want to inherit from Bio::Root::Root. This change was necessary in order to support Bioperl objects that were not based on hashrefs.
Better synopsis and doc update
Merge main trunk changes which include using SearchIO by default and a better SYNOPSIS
SYNOPSIS needed -readmethod argument
Added example to set MATRIX_NAME and NCBI URL for CGI parameters
Matthew's Changes committed: Add support to save_output. Add fix to put fasta header into QUERY line so query output has Query name. Add support to accept PROGRAM, DATABASE, EXPECT vars like MATRIX_NAME, etc.
Fix synopsis example for save_output, doesn't take rid.
Update SYNOPSIS code so that it runs
Change QUERY to use sequence display_id rather than primary_id
Remove commented lines, minor cleanup of header
Free resources
Moving remote blast into core
Bio::Tools::Run::RepeatMasker
Alpha Wrapper for RepeatMasker
Use the determined path to RP when attempting to find the version
Doc fix
POX fixes
Returns SeqFeature::Generic aot FeaturePair
Brought module in-line with new WrapperBase
Returns FeaturePairs now
Dump tempdir bug
Fixed nasty bug coming from Ensembl missing the first line of repeatmasker output file
Tiny extra curly brace
Moving parsing code out of wrapper
Make sure resources are freed
Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)
Move quiet to a wrapper param
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.
Cleaned docs for cleanup()
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Operate happily with new open-version
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Seg
Wrapper module for seg program
Wrapper module for Seg(Documentation changes)
Make sure resources are freed
Can run tests if we let executeable find the exe
Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Initial commit
Previous commit on this module by mistaken. reverted in this commit
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Signalp
wrapper for signalp
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Bug fix caught by david, truncate sequence to 50 aa
Fixed truncation bug
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::StandAloneBlast
Migrated code that runs tools to Bio::Tools::Run
Renaming packages for new dir structure
Fixed to PROPER usage of tempfile
Migrated to new Bio::Root::RootI chained new
Fixed several doc format bugs. (Why is an unprotected -p in the DESCRIPTION section disallowed and somewhere else it is not? Anyway, perldoc is quiet now.)
Fixed inclusion of 'use Bio::Root::RootI' instead of Bio::Root::Object. Fixed exists_blast() (didn't work due to missing braces).
Updated bptutorial and other documentation
BPlite changes to make BPlite a SeqAnalysisParserI object BPbl2seq now requires named input parameter (no longer can just pass in filehandle reference, must pass in -fh => $filehandle) Assundry changes made to related files to handle these changes
Changed to adopt Bio::Root::IO.
Io was not initialized, meaning tempfiles were not cleaned up - better argument matching
Intitialize io -- facilitate tempfile cleanup
Enabled BPbl2seq to read multiple HSPs. Also various documentation fixes.
Rewrote exists_blast(). Should now work properly on both Unix and MSWin.
Merged over exists_blast() rewrite and other fixes from the main trunk.
Fix to avoid bark in File::Spec.
Small fix to shut up File::Spec.
Sweeping change: Bio::Root::RootI is now a pure abstract interface and cannot be inherited from unless you implement several of its abstract methods. Most people will want to inherit from Bio::Root::Root. This change was necessary in order to support Bioperl objects that were not based on hashrefs.
Nice message printing when blast is not runnable
Find blast executeable in the PATH if possible -- bl2seq might still fail if one does not have .ncbirc set correctly
Use SearchIO not Tools::Blast
Call cleanup upon _setinput call
Io cleanup called at outset of an analyses -- from branch
Merge cleanup io from main trunk
StandAlone tests will detect that data dir is not set and exit test nicely
Remove debug code and tests for blastinstalled more efficiently
Merge changes from branch
Minor documentation fixes
Explicitly closing some filehandles appears to do a better job freeing resources
Convert StandAloneBlast to WrapperBase (finallyperl -I. -w t/StandAloneBlast.t) -- need to test in different environments now
Fixed Issue #1354 from bugzilla, improved test to report more error details
This is really what I meant by splitting up these conditionals - careful about blindly committing submitted patches
Made docs slightly more clear (still long ways to go IMHO)
Deal with changes needed as seen by Issue #1359, mostly this is just a needed map_chars call in StandAloneBlast but have cleaned up the code some in other places
Moving standaloneblast from bioperl-run
Bio::Tools::Run::Tmhmm
Wrapper module for Tmhmm(Documentation changes)
Insure filehandles are closed
Phylip works with 3.6a version now. Small tweaks and fixes to win back the good name of Fugu ;)
Moving executable method to Wrapper base, removing global TMP variables where possible
Renaming all the various factory run methods to factory->run to make them in line with WrapperBase.
Rework tempfile handling to explicitly close a filehanle - assigning it to undef leaves it open and causes the left-open filehandle errors we've seen
Tcoffee --> MAFFT, version stuff removed, allow percent ID to waver a little
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::TribeMCL
Wrapper for tribemcl program for protein family clustering using markov flow simulation based on blast scores
Modified the way input is fed.
Takes in HSP as well
More robust program finding
Print data to file right away rather than holding array in memory - there appeared to be a memory leak otherwise anyways with the simple blast file parsing returning an array ref.
Inherit from WrapperBase, inline with ProtML
Added consensus description generation, with dependency on Algorith::Diff
Brought up to spec with the new Objects and seqname --> seq_id transition Don't use my %hash = undef; we get warnings, initialize to () Also insuring that tmp filehandles are closed to insure freeing of resources
Forgot to commit
Separated parameters for tribe-matrix and mcl in MATRIXPROGRAM_PARAMS and MCLPROGRAM_PARAMS. To discriminate upper and lower case parameters, in particular for mcl, AUTOLOAD is case sensitive when for unallowed parameters. Changed as consequences the way to build the command line in _run_matrix and _run_mcl methods. in _consensifier make sure that UNKNOWN has confidence_annotation_score equal to 0.
Checks to quieten tests
Do require for Algorithm::Diff
Moving executable method to Wrapper base, removing global TMP variables where possible
Jump out of parser loop when we hit the stats at the bottom of the report (I think this did not used to be there)
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Bio::Tools::Run::Vista
Vista wrapper taking in SimpleAlign object and generate pdfs
Support more options
Bug, don't reverse seq
More docs
Added java param to allow setting of java parameters, for example to set higher heap sizes..
Major bug, need to project aligmnents, basically need to remove position in pairwise aligmnet if both are gap characters, else vista will count wrongly
Allow more than one references to be selected
Fix from Jonathan Manning
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
Makefile.PL
Makefile
Prompt user when Makefile.PL is run
Makefile.PL with sub_test option
Skipping Pise tests if XML::Parser::SAX not installed, added dependency in Makefile
SAX/Sax -> PerlSAX
Added dependency to HTML::PArser which caused Pise tests to fail if not present
Added Algorithm::Diff dependency for TribeMCL
VERSION to 1.2.2
George Hartzell fixes
Version updates
examples/pise/blast-kun.pl
Added examples for running blast2 and phylogeny on a non-default Pise server.
examples/pise/blast2.pl
Added t and examples directories together with Pise files
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
Pise: added data for examples
examples/pise/clustalw.pl
Added t and examples directories together with Pise files
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
examples/pise/dnadist.data
Pise: added data for examples
examples/pise/dnadist.pl
Added t and examples directories together with Pise files
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
Pise: added data for examples
examples/pise/genscan.pl
Added t and examples directories together with Pise files
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
Pise: added data for examples
examples/pise/needle.pl
Added t and examples directories together with Pise files
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
examples/pise/phylo-kun.pl
Added examples for running blast2 and phylogeny on a non-default Pise server.
examples/pise/toppred.pl
Added t and examples directories together with Pise files
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
scripts/bioperl_application_installer.PLS
Changed name of file installer.PLS to bioperl_application_installer.PLS
Less spam - more ham
scripts/installer.PLS
Adding installer.PLS
Changed name of file installer.PLS to bioperl_application_installer.PLS
scripts/panalysis.PLS
Added a general Analysis client together with its incarnation as a SOAP client
Added -timeout parameter to the SOAP-based Analysis client
Changes in Soaplab API
Patched, thank you Albert
Revision string fix
Default location for SOAP analysis services at EBI has changed
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
scripts/papplmaker.PLS
Added a general Analysis client together with its incarnation as a SOAP client
Changes in Soaplab API
Revision string fix
Default location for SOAP analysis services at EBI has changed
Removed all references to submitting bugs using email to the bugs list. All links to http://bioperl.org/bioperl-bugs/ were replaced with http://bugzilla.bioperl.org/.
scripts/run_neighbor.PLS
Some scripts for running protdist and neighbor, for easy use in the bsub world
scripts/run_protdist.PLS
Some scripts for running protdist and neighbor, for easy use in the bsub world
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