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Commits on Apr 21, 2011
  1. skip # off

    Chris Fields
    Chris Fields committed Apr 21, 2011
  2. hack in a workaround for version(), which conflicts with the -version…

    Chris Fields
    Chris Fields committed Apr 21, 2011
    … parameter for BLAST+
  3. a few last additions

    Chris Fields
    Chris Fields committed Apr 21, 2011
Commits on Apr 20, 2011
  1. some more Changes

    Chris Fields
    Chris Fields committed Apr 20, 2011
  2. add comment on the required BLAST+ version, refs #3213

    Chris Fields
    Chris Fields committed Apr 20, 2011
  3. get SABlast tests passing with v 2.2.24+ and up

    Chris Fields
    Chris Fields committed Apr 20, 2011
  4. BLAST+ tests passing so far, refs #3213

    Chris Fields
    Chris Fields committed Apr 20, 2011
  5. changes to deal with indexing of FASTA with dup ID failing with lates…

    Chris Fields
    Chris Fields committed Apr 20, 2011
    …t BLAST+
Commits on Apr 14, 2011
  1. get MAFFT working

    Chris Fields
    Chris Fields committed Apr 14, 2011
  2. latest samtools needs a sorted BAM for indexing

    Chris Fields
    Chris Fields committed Apr 14, 2011
  3. update for EMBOSS 6.2.0

    Chris Fields
    Chris Fields committed Apr 14, 2011
Commits on Apr 13, 2011
Commits on Apr 4, 2011
  1. Revert "test hook from run (issue might be CGI params)"

    Chris Fields
    Chris Fields committed Apr 4, 2011
    This reverts commit 08f7bed.
  2. test hook from run (issue might be CGI params)

    Chris Fields
    Chris Fields committed Apr 4, 2011
Commits on Apr 1, 2011
  1. Update Bowtie module for 0.12.7

    kortschak
    kortschak committed Apr 1, 2011
  2. Update BEDTools module for v2.10.1

    kortschak
    kortschak committed Apr 1, 2011
Commits on Mar 27, 2011
  1. bugzilla -> redmine

    hyphaltip committed Mar 27, 2011
  2. use the 1a file -- still problem in parsing the trailing score in the…

    hyphaltip committed Mar 27, 2011
    … tree file, needs to e fixed at the parser level I think
  3. test for bug #3085

    hyphaltip committed Mar 27, 2011
  4. don't need this lib include

    hyphaltip committed Mar 27, 2011
Commits on Nov 5, 2010
  1. remove cruft, gunge, and implement searchio()

    Chris Fields
    Chris Fields committed Nov 5, 2010
  2. allow other SearchIO formats and parameters (though axt and sim4 are …

    Chris Fields
    Chris Fields committed Nov 5, 2010
    …not working as expected)
  3. tests for regions, require a .2bit database so only run when present …

    Chris Fields
    Chris Fields committed Nov 5, 2010
    …(may generate this on the fly later)
  4. add an uppercase alias for db, tests pass

    Chris Fields
    Chris Fields committed Nov 5, 2010
  5. initial checkin of revamped Blat wrapper

    Chris Fields
    Chris Fields committed Nov 5, 2010
Commits on Aug 12, 2010
  1. StandaloneBlastPlus: don't automatically add ./ to remote database names

    Kai Blin
    Kai Blin committed Aug 12, 2010
    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
    Chris Fields committed Aug 5, 2010
Commits on Jul 23, 2010
  1. Revert "add dots param"

    Chris Fields
    Chris Fields committed Jul 23, 2010
    This reverts commit 4b82f66543326d8afd13cd4a585e9552eca2ab5b.
  2. add dots param

    Chris Fields
    Chris Fields committed Jul 23, 2010
  3. [RT 58464] patching to allow file names with spaces

    Chris Fields
    Chris Fields committed Jul 23, 2010