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::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::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::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::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

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