Tracking Git commits

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Core commits

Recent Commits to bioperl-live:master

Merge pull request #128 from dk/master
Merge pull request #79 from Buuntu/master
don't enforce strict line length for FASTA, it's good practice but not canonical and breaks things
Merge branch 'master' of
Add a sentence about the current version
Fix #129. Send 'missed line' messages to STDERR. hmmer.t test suite passes.
Merge pull request #136 from bioperl/feat-travis-containers
feat(travis-containers) : whitelist master again
feat(travis-containers) : mods for containers
fix #134 : do apt-get **update** first
fix #134 : do apt-get update first
Merge branch 'master' of
Updated INSTALL.WIN with the recent changes made in
Merge branch 'master' of
Remove ctrl M
phd: Fixed new "unescaped left brace in regex" warning from Perl 5.22
Build.PL: Removed duplicated dependency 'HTML::TableExtract'
Restriction::IO.t: REBASE ftp database is not responding properly,
hmmer.t: Added test case for the recent \Q\E fix for HMMer3 parsing
Run commits

Recent Commits to bioperl-run:master

Merge pull request #15 from adsj/master
Supply TEMPLATE and SUFFIX for temporary query sequence files.
Raxml: use File::Spec->devnull() instead of our own code and do not import extra stuff into namespace
Merge pull request #13 from hettling/master
convert to markdown for consistency
convert to markdown for consistency
removed obsolete whitespace
StandAloneBlastPlus: Improved 'db_info' Algorithm ID regex,
Added MYMETA.json to .gitignore
Added -d option (random starting tree) to raxml run, because raxml
(1) when -w option was provided with a custom directory, 'run' always
WBCommandExts.t: Fixed a pending TODO related to
Update Build.PL, MYMETA.json with build dependencies
no dependencies on any of the Test::* or Sub::Uplevel in any test (except maybe through Bio::Root::Test; in any case should not be frozen in the distro, but tests that break due to updates should instead be updated themselves.
Update Build.PL with config_requires and build_requires; add MANIFEST
Merge branch 'master' into topic/move_WrapperBase
fixed translate_params tests according to discussion at commit a6d0dc2; removed TODO around translate_params test
move StandAloneBlast* and WrapperBase* from root/Bio... to root/lib/Bio...
Merge branch 'master' of ../move_WrapperBase/bioperl-wb into topic/move_WrapperBase
test parameters independent of their order as issued on command line
Ext commits

Recent Commits to bioperl-ext:master

markdown-ize README
moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got them compiling cleanly. tests not passing yet
use UPPPER_TOL to catch the case when the expectation maximization step
fixed Vitebi typo
Fixed the typemap and also a memory bug in viterbi function in HMM.xs
adding FEEDBACK:Support section to pod
Bump to 1.007 (similar to trunk)
ext patches (courtesy Thomas Jahns)
get rid of some unended comment warnings from C compiler
-fPIC needed for lib construction
include errno definition
removed DEBUG=1
IUPAC DNA support
IUPAC DNA test case
Add some helper code and tests to demo evalue oddities (bug 1857); casting issue?
Add cast to correct pointer type (get rid of warnings)
update version to last bioperl release
bug 2329
bug 2074/2329
Removed Aaron's old test script (now in t/staden_read.t). Do we modify master ext makefile to account for this?
Bioperl-DB (BioSQL)

Recent Commits to bioperl-db:master

Merge pull request #9 from dvs/master
add_association - bugfix, sort the SQL arguments
Merge pull request #1 from dvs/master
_find_by_unique_key - bugfix
Fix various Taxonomy values that are tested. Yes, this will break again.
Run perltidy on this, add some documentation
Minor POD edits and reformatting
Add some useful example code
updates since last release
update skipped files
buzgilla -> redmine
[RT 44466] remove corba-related scripts, now obsolete
squash perl 5.12 warning
ignore conf file
add minimal .gitignore file
weird duplication removed
committing patch for bug #2958
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