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Commits on Feb 24, 2009
  1. bump version

    svn path=/bioperl-run/branches/branch-1-6/; revision=15567
    cjfields committed Feb 24, 2009
  2. sync with trunk

    svn path=/bioperl-run/branches/branch-1-6/; revision=15564
    cjfields committed Feb 24, 2009
Commits on Feb 11, 2009
  1. sync with trunk

    svn path=/bioperl-run/branches/branch-1-6/; revision=15521
    cjfields committed Feb 11, 2009
Commits on Feb 1, 2009
  1. branch-specific versioning

    svn path=/bioperl-run/branches/branch-1-6/; revision=15487
    cjfields committed Feb 1, 2009
  2. syc with trunk

    svn path=/bioperl-run/branches/branch-1-6/; revision=15486
    cjfields committed Feb 1, 2009
Commits on Jan 28, 2009
  1. forgot to change versioning, will retag

    svn path=/bioperl-run/branches/branch-1-6/; revision=15460
    cjfields committed Jan 28, 2009
  2. sync with run trunk

    svn path=/bioperl-run/branches/branch-1-6/; revision=15456
    cjfields committed Jan 28, 2009
Commits on Jan 13, 2009
  1. Bio::Tools::TigrAssembler improvement to allow to submit quality scor…

    …es that are not in the same object as the sequences
    
    svn path=/bioperl-run/trunk/; revision=15371
    fangly committed Jan 13, 2009
  2. * small updates

    svn path=/bioperl-run/trunk/; revision=15360
    cjfields committed Jan 13, 2009
  3. Remove Pise-related stuff, update with other dependencies

    svn path=/bioperl-run/trunk/; revision=15359
    cjfields committed Jan 13, 2009
  4. Add DEPENDENCIES file.

    svn path=/bioperl-run/trunk/; revision=15358
    cjfields committed Jan 13, 2009
  5. Remove Pise-related examples (moved into bioperl-pise)

    svn path=/bioperl-run/trunk/; revision=15356
    cjfields committed Jan 13, 2009
  6. Remove Pise-related module (moved into bioperl-pise)

    svn path=/bioperl-run/trunk/; revision=15354
    cjfields committed Jan 13, 2009
  7. Remove Pise modules and tests (moved into bioperl-pise)

    svn path=/bioperl-run/trunk/; revision=15352
    cjfields committed Jan 13, 2009
  8. Remove Pise modules and tests (moved into bioperl-pise)

    svn path=/bioperl-run/trunk/; revision=15351
    cjfields committed Jan 13, 2009
Commits on Jan 12, 2009
  1. removed this stub now that people have had time to adjust

    svn path=/bioperl-run/trunk/; revision=15341
    sendu committed Jan 12, 2009
  2. revert mistaken commit

    svn path=/bioperl-run/trunk/; revision=15338
    sendu committed Jan 12, 2009
  3. removed extraneous use lib lines

    svn path=/bioperl-run/trunk/; revision=15337
    sendu committed Jan 12, 2009
  4. removed syntactical nonsense that broke the test

    svn path=/bioperl-run/trunk/; revision=15336
    sendu committed Jan 12, 2009
  5. test_output_file() creates an empty file, but it must be unlinked bef…

    …ore hmmbuild will work
    
    svn path=/bioperl-run/trunk/; revision=15335
    sendu committed Jan 12, 2009
  6. corrected number of tests; output to a temp file

    svn path=/bioperl-run/trunk/; revision=15334
    sendu committed Jan 12, 2009
Commits on Jan 10, 2009
  1. Don't TODO the test, actually attempt to run it and check for an erro…

    …r, then report the error if it fails.
    
    svn path=/bioperl-run/trunk/; revision=15328
    cjfields committed Jan 10, 2009
  2. Actually make tests complete (not skipped if there is a job error, so…

    … tests abort prematurely)
    
    svn path=/bioperl-run/trunk/; revision=15327
    cjfields committed Jan 10, 2009
  3. TODO failing test (problem with SOAP protocol)

    svn path=/bioperl-run/trunk/; revision=15326
    cjfields committed Jan 10, 2009
  4. * finish up bioperl-run conversion

    * will need to add a Bio::Root::Test test_cleanup method for unlinking some files
    
    svn path=/bioperl-run/trunk/; revision=15323
    cjfields committed Jan 10, 2009
Commits on Jan 8, 2009
  1. requires not required

    svn path=/bioperl-run/trunk/; revision=15320
    cjfields committed Jan 8, 2009
  2. * convert over to Bio::Root::Test and update some to use new test_ski…

    …p parameters
    
    svn path=/bioperl-run/trunk/; revision=15319
    cjfields committed Jan 8, 2009
  3. * convert to Bio::Root::Test

    svn path=/bioperl-run/trunk/; revision=15317
    cjfields committed Jan 8, 2009
  4. * convert to Bio::Root::Test

    * tests now pass if Phyml isn't installed
    * Phyml.pm : ensure version() is defined before comparisons are made
    
    svn path=/bioperl-run/trunk/; revision=15316
    cjfields committed Jan 8, 2009
Commits on Jan 7, 2009
  1. Don't todo tests that work for other people - it causes test failure;…

    … reverted and changed test to handle presumed difference in Bio::EnsEMBL versions
    
    svn path=/bioperl-run/trunk/; revision=15315
    sendu committed Jan 7, 2009
  2. Getting a failed test using latest EnsEMBL perl API; TODO'ing the fai…

    …led test for now.
    
    svn path=/bioperl-run/trunk/; revision=15314
    cjfields committed Jan 7, 2009
  3. Catch version, skip tests if version isn't supported yet (Clustalw 2.…

    …0, fo instance)
    
    svn path=/bioperl-run/trunk/; revision=15313
    cjfields committed Jan 7, 2009
Commits on Dec 31, 2008
  1. the distribution name is BioPerl, not bioperl; version bump for trunc…

    …, try2
    
    svn path=/bioperl-run/trunk/; revision=15275
    sendu committed Dec 31, 2008
  2. the distribution name is BioPerl, not bioperl; version bump for trunc

    svn path=/bioperl-run/trunk/; revision=15273
    sendu committed Dec 31, 2008
Commits on Dec 18, 2008
  1. test script and data for semphy wrapper

    svn path=/bioperl-run/trunk/; revision=15210
    sendu committed Dec 18, 2008