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Commits on Apr 21, 2011
  1. skip # off

    Chris Fields committed
  2. hack in a workaround for version(), which conflicts with the -version…

    Chris Fields committed
    … parameter for BLAST+
  3. a few last additions

    Chris Fields committed
Commits on Apr 20, 2011
  1. some more Changes

    Chris Fields committed
  2. add comment on the required BLAST+ version, refs #3213

    Chris Fields committed
  3. get SABlast tests passing with v 2.2.24+ and up

    Chris Fields committed
  4. BLAST+ tests passing so far, refs #3213

    Chris Fields committed
  5. changes to deal with indexing of FASTA with dup ID failing with lates…

    Chris Fields committed
    …t BLAST+
Commits on Apr 14, 2011
  1. get MAFFT working

    Chris Fields committed
  2. latest samtools needs a sorted BAM for indexing

    Chris Fields committed
  3. update for EMBOSS 6.2.0

    Chris Fields committed
Commits on Apr 13, 2011
  1. @hyphaltip
Commits on Apr 4, 2011
  1. Revert "test hook from run (issue might be CGI params)"

    Chris Fields committed
    This reverts commit 08f7bed.
  2. test hook from run (issue might be CGI params)

    Chris Fields committed
Commits on Apr 1, 2011
  1. Update Bowtie module for 0.12.7

    kortschak committed
  2. Update BEDTools module for v2.10.1

    kortschak committed
Commits on Mar 27, 2011
  1. @hyphaltip

    bugzilla -> redmine

    hyphaltip committed
  2. @hyphaltip

    use the 1a file -- still problem in parsing the trailing score in the…

    hyphaltip committed with hyphaltip
    … tree file, needs to e fixed at the parser level I think
  3. @hyphaltip

    test for bug #3085

    hyphaltip committed with hyphaltip
  4. @hyphaltip

    don't need this lib include

    hyphaltip committed with hyphaltip
Commits on Nov 5, 2010
  1. remove cruft, gunge, and implement searchio()

    Chris Fields committed
  2. allow other SearchIO formats and parameters (though axt and sim4 are …

    Chris Fields committed
    …not working as expected)
  3. tests for regions, require a .2bit database so only run when present …

    Chris Fields committed
    …(may generate this on the fly later)
  4. add an uppercase alias for db, tests pass

    Chris Fields committed
  5. initial checkin of revamped Blat wrapper

    Chris Fields committed
Commits on Aug 12, 2010
  1. @kblin

    StandaloneBlastPlus: don't automatically add ./ to remote database names

    kblin committed
    Thanks to Paul Cantalupo for reporting and testing this.
Commits on Aug 5, 2010
  1. [bug 2987] remove warning (patch courtesy Adam Witney

    Chris Fields committed
Commits on Jul 23, 2010
  1. Revert "add dots param"

    Chris Fields committed
    This reverts commit 4b82f66543326d8afd13cd4a585e9552eca2ab5b.
  2. add dots param

    Chris Fields committed
  3. [RT 58464] patching to allow file names with spaces

    Chris Fields committed
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