Run 1.1.0 1.2.0 delta

From BioPerl
Jump to: navigation, search

These are detailed notes on changes made between bioperl-release-1-1-0 and bioperl-run-release-1-2-0.

Bio::Factory::EMBOSS
Moving from bioperl-live CVS module
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
Bio::Tools::Run::Alignment::Clustalw
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
Bio::Tools::Run::Alignment::DBA
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
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
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
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
Bio::Tools::Run::Alignment::TCoffee
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
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
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
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
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 :-)
Bio::Tools::Run::AnalysisFactory::soap
Added a general Analysis client together with its incarnation as a SOAP client
Changes in Soaplab API
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
Bio::Tools::Run::EMBOSSApplication
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
Bio::Tools::Run::EMBOSSacd
No more warnings under perl 5.8.0
Bio::Tools::Run::Eponine
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
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
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
Bio::Tools::Run::Genscan
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
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
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::Phylo::Molphy::ProtML
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
Bio::Tools::Run::Phylo::PAML::Codeml
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
Bio::Tools::Run::Phylo::PAML::Yn00
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
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
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
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
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
Bio::Tools::Run::Phylo::Phylip::Neighbor
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.
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
Bio::Tools::Run::Phylo::Phylip::ProtDist
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
Bio::Tools::Run::Phylo::Phylip::ProtPars
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
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
Bio::Tools::Run::PiseApplication
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 :-)
Bio::Tools::Run::PiseApplication::Puzzle
Puzzle interface update : - Add missing amino-acid substitution models. - Alignment file is now set on the command line.
Bio::Tools::Run::PiseApplication::clustalw_convert
Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).
Bio::Tools::Run::PiseApplication::dialign2
Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).
Bio::Tools::Run::PiseApplication::genscan
- 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 :-)
Bio::Tools::Run::PiseApplication::grailclnt
Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).
Bio::Tools::Run::PiseApplication::neighbor
Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).
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).
Bio::Tools::Run::PiseApplication::prot_nucml
Bug fixes in PiseJob.pm (as found by make test). Updated some applications (changed parameters or bug fixes). Added a new program (pdbsearch).
Bio::Tools::Run::PiseApplication::quicktree
Pise: added quicktree, bug fix in PiseJob.pm
Bio::Tools::Run::PiseApplication::toppred
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
Bio::Tools::Run::PiseJob
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 :-)
Bio::Tools::Run::PiseJobParser
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.
Bio::Tools::Run::Primate
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
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
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
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
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
Bio::Tools::Run::RemoteBlast
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
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
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
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
Bio::Tools::Run::StandAloneBlast
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
Bio::Tools::Run::TribeMCL
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
Bio::Tools::Run::Vista
Vista wrapper taking in SimpleAlign object and generate pdfs
Support more options
Bug, don't reverse seq
More docs
Makefile.PL
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
examples/pise/blast2.pl
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
Pise: added data for examples
examples/pise/clustalw.pl
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
examples/pise/dnadist.data
Pise: added data for examples
examples/pise/dnadist.pl
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
Pise: added data for examples
examples/pise/genscan.pl
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
Pise: added data for examples
examples/pise/needle.pl
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
examples/pise/toppred.pl
Bioperl Pise: moving Bio::Factory::Pise to bioperl-run
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
scripts/papplmaker.PLS
Added a general Analysis client together with its incarnation as a SOAP client
Changes in Soaplab API
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
Personal tools
Namespaces
Variants
Actions
Main Links
documentation
community
development
Toolbox