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Commits on Jan 28, 2009
  1. forgot to change versioning, will retag

    cjfields authored
    svn path=/bioperl-run/branches/branch-1-6/; revision=15460
  2. sync with run trunk

    cjfields authored
    svn path=/bioperl-run/branches/branch-1-6/; revision=15456
Commits on Jan 13, 2009
  1. @fangly

    Bio::Tools::TigrAssembler improvement to allow to submit quality scor…

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

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

    cjfields authored
    svn path=/bioperl-run/trunk/; revision=15359
  4. Add DEPENDENCIES file.

    cjfields authored
    svn path=/bioperl-run/trunk/; revision=15358
  5. Remove Pise-related examples (moved into bioperl-pise)

    cjfields authored
    svn path=/bioperl-run/trunk/; revision=15356
  6. Remove Pise-related module (moved into bioperl-pise)

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

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

    cjfields authored
    svn path=/bioperl-run/trunk/; revision=15351
Commits on Jan 12, 2009
  1. @sendu

    removed this stub now that people have had time to adjust

    sendu authored
    svn path=/bioperl-run/trunk/; revision=15341
  2. @sendu

    revert mistaken commit

    sendu authored
    svn path=/bioperl-run/trunk/; revision=15338
  3. @sendu

    removed extraneous use lib lines

    sendu authored
    svn path=/bioperl-run/trunk/; revision=15337
  4. @sendu

    removed syntactical nonsense that broke the test

    sendu authored
    svn path=/bioperl-run/trunk/; revision=15336
  5. @sendu

    test_output_file() creates an empty file, but it must be unlinked bef…

    sendu authored
    …ore hmmbuild will work
    
    svn path=/bioperl-run/trunk/; revision=15335
  6. @sendu

    corrected number of tests; output to a temp file

    sendu authored
    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 authored
    …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 authored
    … tests abort prematurely)
    
    svn path=/bioperl-run/trunk/; revision=15327
  3. TODO failing test (problem with SOAP protocol)

    cjfields authored
    svn path=/bioperl-run/trunk/; revision=15326
  4. * finish up bioperl-run conversion

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

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

    cjfields authored
    svn path=/bioperl-run/trunk/; revision=15317
  4. * convert to Bio::Root::Test

    cjfields authored
    * 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. @sendu

    Don't todo tests that work for other people - it causes test failure;…

    sendu authored
    … 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 authored
    …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 authored
    …0, fo instance)
    
    svn path=/bioperl-run/trunk/; revision=15313
Commits on Dec 31, 2008
  1. @sendu

    the distribution name is BioPerl, not bioperl; version bump for trunc…

    sendu authored
    …, try2
    
    svn path=/bioperl-run/trunk/; revision=15275
  2. @sendu

    the distribution name is BioPerl, not bioperl; version bump for trunc

    sendu authored
    svn path=/bioperl-run/trunk/; revision=15273
Commits on Dec 18, 2008
  1. @sendu

    test script and data for semphy wrapper

    sendu authored
    svn path=/bioperl-run/trunk/; revision=15210
  2. @sendu

    added new params and switches for semphy 2

    sendu authored
    svn path=/bioperl-run/trunk/; revision=15209
Commits on Dec 17, 2008
  1. @sendu

    test script and data for Pal2Nal wrapper

    sendu authored
    svn path=/bioperl-run/trunk/; revision=15205
  2. @sendu

    test script and data for match wrapper

    sendu authored
    svn path=/bioperl-run/trunk/; revision=15204
  3. @sendu

    corrected ENV setting, fixed file location bug

    sendu authored
    svn path=/bioperl-run/trunk/; revision=15203
  4. @sendu

    test script for the Ensembl wrapper

    sendu authored
    svn path=/bioperl-run/trunk/; revision=15202
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