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Commits on Jan 28, 2009
  1. sync with run trunk

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    cjfields
    cjfields committed Jan 8, 2009
    * 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
Commits on Jan 7, 2009
  1. Don't todo tests that work for other people - it causes test failure;…

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

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

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

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

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

    sendu committed Dec 18, 2008
    svn path=/bioperl-run/trunk/; revision=15210
  2. added new params and switches for semphy 2

    sendu committed Dec 18, 2008
    svn path=/bioperl-run/trunk/; revision=15209
Commits on Dec 17, 2008
  1. test script and data for Pal2Nal wrapper

    sendu committed Dec 17, 2008
    svn path=/bioperl-run/trunk/; revision=15205
  2. test script and data for match wrapper

    sendu committed Dec 17, 2008
    svn path=/bioperl-run/trunk/; revision=15204
  3. corrected ENV setting, fixed file location bug

    sendu committed Dec 17, 2008
    svn path=/bioperl-run/trunk/; revision=15203
  4. test script for the Ensembl wrapper

    sendu committed Dec 17, 2008
    svn path=/bioperl-run/trunk/; revision=15202
  5. added POD

    sendu committed Dec 17, 2008
    svn path=/bioperl-run/trunk/; revision=15201