Run 1.5.1 1.5.2 delta

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These are detailed notes on changes made between bioperl-run-release-1-5-1 and bioperl-run-release-1-5-2.

Bio::Factory::EMBOSS
Emboss version number parsing -- could have sworn I already checked this in per-1.5.1, apparently not
Prog, not factory
Bio::Installer::Muscle
First version
Bio::Installer::PAML
Updated to 3.15 and http dir
Bio::Installer::TCoffee
Updated to 4.45
Bio::Tools::Run::Alignment::Amap
Copy/pasted from probcons -- see FIXMEs
Fixing version method
Adding switches and params
Adding amap options -- not extensively checked though
Let Bio::Tools::Run::WrapperBase handle error_string
Bio::Tools::Run::Alignment::Kalign
Adding Kalign.pm from a copy/paste of Muscle.pm -- havent tested all the options and switches yet
Bio::Tools::Run::Alignment::Lagan
Expected envvariable changed to LAGAN_DIR to match that used by lagan itself, work-around for sort sytax bug in lagan script
LAGAN_DIR is now required, files are cleaned up
Bio::Tools::Run::Alignment::MAFFT
Fixed parsing of version number while keeping backward compatibility
Use rel2abs from File::Spec not Bio::Root::IO. Also, compily with some Bioperl best practices
Bio::Tools::Run::Alignment::Muscle
Added GAPOPEN option -- havent tested at all
Adding KBAND in MUSCLE_PARAMS -- beware that this option only works for the discontinued version 6 of muscle
Recommend usage of v3.6, tests only run with >= 3.6
Adding profile option -- does not work for 3.6 but 3.52 -- please shout if you see something wrong
V3.6 profile comment
Bio::Tools::Run::Alignment::Probalign
First version of the probalign wrapper -- modified from Probcons.pm
Bio::Tools::Run::Alignment::Probcons
Probcons is a bit inconsistent with this flag
Some modes of operation do no generate an output alignment
Bio::Tools::Run::Alignment::TCoffee
Profile-related bug fixed, general issue with special characters causing failure or warnings solved
-no_warning only works and is only needed on certain versions of TCoffee
Bio::Tools::Run::Cap3
Add Marc's module
Bio::Tools::Run::Coil
Some clarification of COILSDIR
Bio::Tools::Run::EMBOSSApplication
Add executable(), program_dir(), program_path()
Write executable() method, t/EMBOSS.t tests pass now
Bio::Tools::Run::Eponine
Now correct usage for EPONINEDIR if it is a dir or pointing at the actual jar file
Bio::Tools::Run::FootPrinter
FOOTPRINTER_DIR env var is required
Bio::Tools::Run::Phylo::PAML::Baseml
Codeml -> baseml, but still doesn't quite work, baseml is VERY picky about sequence file input format and I can't figure out what is being written wrong. I moved to using wrapped sequential rather than whole line, I tried moving ids to their own line, and I tried with or without lots of padding at end of id string. Very frustrating....
Bio::Tools::Run::Phylo::PAML::Codeml
This prepare function is very similar to run -- should split run in the future
Allow output filename to be specified
Email addr mangle; don't double write outfile, quiet when not defined
Bio::Tools::Run::Phylo::PAML::Evolver
WARNING - only a skeleton - C-s FIXME in emacs
Start some fleshing in prepare method -- some FIXMEs need consideration
Back from the bus -- still not functional at all
Prepare method needs codonfreqs stuff and some newick love
Some more clear FIXME tags
It will prepare the stuff with codonfreqs now -- problem with trees -- still a lot of FIXMEs to solve
No internal ids in the tree - this needs nointernalids.patch in newick.pm
Adding rootseq fixme
Some more comments
This is still very rudimentary -- wear you seatbelt at all times
Adding alignment method and indel getset -- a bit of cleaning
Bio::Tools::Run::Phylo::PAML::Yn00
Email addr mangle; don't double write outfile, quiet when not defined
Bio::Tools::Run::Phylo::Phylip::DrawTree
Issue #1928
Issue #2040
Bio::Tools::Run::PiseApplication::Puzzle
Phyml is a program for estimating large phylogenies by maximum likelihood. New version of Puzzle (5.2).
Bio::Tools::Run::PiseApplication::phyml
Phyml is a program for estimating large phylogenies by maximum likelihood. New version of Puzzle (5.2).
Bio::Tools::Run::PiseJob
Added CLOSE() tied filehandle method (Issue #2126) to properly close tied filehandle. Still has redef'd sub warnings.
Bio::Tools::Run::Primer3
Let's try this
Mention release 1 compatibility
_set_variable() was in Bio/Tools/Primer3.pm but was unused by that module, actually used only by Bio/Tools/Run/Primer3.pm so move it there
I was wrong, better testing shows that _set_variable is better kept here
Small code/doc cleanup
Bio::Tools::Run::Tmhmm
TMHMMDIR is required
Enabled TMHMMDIR envvar requirment
Remove directory generated by tmhmm during run
Fixed to set -basedir properly and to use tempdir for working directory
Bio::Tools::Run::TribeMCL
Sane Species creation
Bio::Tools::Run::Vista
Update some errors in doc
Build.PL
New Build.PL install system, Makefile.PL still works but warns
Makefile.PL
Now using %packages for WriteMakefile
Check Bioperl is installed before proceeding with makefile
Better test for existing Bioperl installation
New-style with added features and implementation of the pise email question
Removed unneccessary use, corrected email question
Clearer version checking
Good style for ¬$VERSION
Do not die, just warn when required things are missing
Some modules don't define VERSION, default to 0
New Build.PL install system, Makefile.PL still works but warns
ModuleBuildBioperl.pm
New Build.PL install system, Makefile.PL still works but warns
Update fix from core
scripts/multi_hmmsearch.PLS
Add Mauricio's script
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