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Commits on Sep 13, 2016
Commits on Jul 17, 2016
  1. add a few more vetted dists

    cjfields committed Jul 17, 2016
  2. remove bad character

    cjfields committed Jul 17, 2016
  3. try triggering travis

    cjfields committed Jul 17, 2016
  4. gotta install bioperl first!

    cjfields committed Jul 17, 2016
  5. add travis-ci file

    cjfields committed Jul 17, 2016
Commits on Jul 7, 2016
  1. Merge pull request #40 from hettling/fast-bootstrap

    adding support for RAxML's rapid bootstrap
    cjfields committed on GitHub Jul 7, 2016
  2. Merge pull request #39 from hettling/master

    Making Raxml test run
    cjfields committed on GitHub Jul 7, 2016
Commits on May 28, 2015
  1. Merge pull request #15 from adsj/master

    Supply TEMPLATE and SUFFIX for temporary query sequence files.
    cjfields committed May 28, 2015
Commits on May 26, 2015
  1. Supply TEMPLATE and SUFFIX for temporary query sequence files.

    This avoid the problem of query sequence file names randomly ending
    in _Z, which makes (at least) wublastp (3.0SE-AB) try to unzgip the
    non-gzipped temporary file, resulting in an error.
    adsj committed May 26, 2015
Commits on Feb 20, 2015
  1. Raxml: use File::Spec->devnull() instead of our own code and do not i…

    …mport extra stuff into namespace
    carandraug committed Feb 20, 2015
  2. Merge pull request #13 from hettling/master

    yes, seems good.
    carandraug committed Feb 20, 2015
Commits on Jan 31, 2015
Commits on Jan 28, 2015
  1. removed obsolete whitespace

    hettling committed Jan 28, 2015
Commits on Dec 18, 2014
  1. StandAloneBlastPlus: Improved 'db_info' Algorithm ID regex,

    which was failing in a test, and adjusted the mask maker programs
    (windowmasker, segmasker and dustmasker) to use 'maskinfo_asn1_text'
    output format, so it can be used with makeblastdb (all other formats
    fails). Removed the TODOs from the test file now that masking works.
    fjossandon committed Dec 18, 2014
Commits on Oct 29, 2014
  1. Added -d option (random starting tree) to raxml run, because raxml

    complained about starting tree. Added test for -w option with tempdir().
    Test runs now.
    hettling committed Oct 29, 2014
  2. (1) when -w option was provided with a custom directory, 'run' always

    returned undef. This is now fixed. (2) When -quiet was set, redirection
    to /dev/null messed up the outfile name. This is also fixed.
    hettling committed Oct 29, 2014
Commits on Sep 1, 2014
  1. WBCommandExts.t: Fixed a pending TODO related to

    "->_translate_params" with the solution applied recently
    to BWA.t, Bowtie.t, Maq.t and Samtools.t
    fjossandon committed Sep 1, 2014
Commits on Aug 26, 2014
Commits on Aug 24, 2014
  1. no dependencies on any of the Test::* or Sub::Uplevel in any test (ex…

    …cept 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.
    majensen committed Aug 24, 2014
  2. fixed translate_params tests according to discussion at commit a6d0dc2;…

    … removed TODO around translate_params test
    majensen committed Aug 24, 2014
Commits on Aug 23, 2014
Commits on Aug 22, 2014
  1. Removed empty file Bio/Tools/Run/hmmer3.pm, which seems

    to have been added by mistake
    fjossandon committed Aug 22, 2014