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Commits on Jul 8, 2003
  1. @heikkil

    VERSION to 1.2.2

    svn path=/bioperl-run/trunk/; revision=13476
    heikkil committed Jul 8, 2003
  2. @heikkil

    release number 1.2.2; reformatting

    svn path=/bioperl-run/trunk/; revision=13475
    heikkil committed Jul 8, 2003
Commits on Jul 7, 2003
  1. @heikkil

    in preparation for 1.2.2 relase, added collected changes from cvs log

    svn path=/bioperl-run/trunk/; revision=13474
    heikkil committed Jul 7, 2003
Commits on Jul 4, 2003
  1. Reverting change for VERSION for 1.2.2 release

    svn path=/bioperl-run/trunk/; revision=13473
    shawnh committed Jul 4, 2003
  2. Fix test to work with make

    svn path=/bioperl-run/trunk/; revision=13472
    shawnh committed Jul 4, 2003
Commits on Jul 2, 2003
  1. Bug fix caught by david, truncate sequence to 50 aa

    svn path=/bioperl-run/trunk/; revision=13471
    shawnh committed Jul 2, 2003
Commits on Jun 28, 2003
  1. @hyphaltip

    Mark Wagner's enhancements bug #1399

    svn path=/bioperl-run/trunk/; revision=13470
    hyphaltip committed Jun 28, 2003
Commits on Jun 14, 2003
  1. Documentation update and location parameter.

    Programs from s to z.
    
    svn path=/bioperl-run/trunk/; revision=13469
    letondal committed Jun 14, 2003
Commits on Jun 11, 2003
  1. Added examples for running blast2 and phylogeny on a non-default Pise…

    … server.
    
    svn path=/bioperl-run/trunk/; revision=13468
    letondal committed Jun 11, 2003
  2. Documentation + location parameter update. Programs from n to r.

    svn path=/bioperl-run/trunk/; revision=13467
    letondal committed Jun 11, 2003
Commits on Jun 10, 2003
  1. Documentation updates, as well as location parameter, continuing with…

    … programs starting by h, i, k, l and m.
    
    svn path=/bioperl-run/trunk/; revision=13466
    letondal committed Jun 10, 2003
Commits on Jun 9, 2003
  1. Modified to inherit Bio::Tools::Run::WrapperBase, use Bio::Root::IO t…

    …o build up paths
    
    svn path=/bioperl-run/trunk/; revision=13465
    djackson committed Jun 9, 2003
  2. Renamed mdust.t to Mdust.t for consistency with rest of test suite

    svn path=/bioperl-run/trunk/; revision=13464
    djackson committed Jun 9, 2003
Commits on Jun 6, 2003
  1. Added the right credits.

    svn path=/bioperl-run/trunk/; revision=13463
    smontgom committed Jun 6, 2003
  2. Pise files update for program beginning with d, e, f and g.

    svn path=/bioperl-run/trunk/; revision=13462
    letondal committed Jun 6, 2003
Commits on Jun 5, 2003
  1. Starting to add new interfaces versions (letters a, b and c).

    Added 3 programs: sirna, tranalign, twofeat (from EMBOSS 2.6).
    
    svn path=/bioperl-run/trunk/; revision=13461
    letondal committed Jun 5, 2003
Commits on Jun 4, 2003
  1. @heikkil

    removed module specific $VERSION, all modules now use global one from…

    … Bio::Root::Version
    
    svn path=/bioperl-run/trunk/; revision=13460
    heikkil committed Jun 4, 2003
  2. Modified documentation to conform to bioperl format

    svn path=/bioperl-run/trunk/; revision=13459
    djackson committed Jun 4, 2003
Commits on Jun 2, 2003
  1. @heikkil

    runnable SYNOPSIS & POD fixes

    svn path=/bioperl-run/trunk/; revision=13458
    heikkil committed Jun 2, 2003
Commits on May 30, 2003
  1. @hyphaltip

    POD fixes

    svn path=/bioperl-run/trunk/; revision=13457
    hyphaltip committed May 30, 2003
  2. binary input added

    svn path=/bioperl-run/trunk/; revision=13456
    senger committed May 30, 2003
Commits on May 28, 2003
  1. Some minor changes. Also, I think 'use warnings' has been removed for…

    … back-compatibility
    
    svn path=/bioperl-run/trunk/; revision=13455
    bosborne committed May 28, 2003
Commits on May 27, 2003
  1. Moved Mdust.pm from Bio::Tools to Bio::Tools::Run, added test script …

    …and data file.
    
    svn path=/bioperl-run/trunk/; revision=13454
    djackson committed May 27, 2003
Commits on May 26, 2003
  1. Write the files properly

    svn path=/bioperl-run/trunk/; revision=13451
    shawnh committed May 26, 2003
  2. Add Vista

    svn path=/bioperl-run/trunk/; revision=13450
    shawnh committed May 26, 2003
  3. More docs

    svn path=/bioperl-run/trunk/; revision=13449
    shawnh committed May 26, 2003
  4. Add Vista

    svn path=/bioperl-run/trunk/; revision=13448
    shawnh committed May 26, 2003
  5. Use seq_id

    svn path=/bioperl-run/trunk/; revision=13447
    shawnh committed May 26, 2003
Commits on May 25, 2003
  1. *** empty log message ***

    svn path=/bioperl-run/trunk/; revision=13446
    senger committed May 25, 2003
  2. bug, don't reverse seq

    svn path=/bioperl-run/trunk/; revision=13445
    shawnh committed May 25, 2003
Commits on May 23, 2003
  1. Really should include the program name

    svn path=/bioperl-run/trunk/; revision=13444
    shawnh committed May 23, 2003
  2. Support more options

    svn path=/bioperl-run/trunk/; revision=13443
    shawnh committed May 23, 2003
Commits on May 22, 2003
  1. Vista wrapper taking in SimpleAlign object and generate pdfs

    svn path=/bioperl-run/trunk/; revision=13442
    shawnh committed May 22, 2003
Commits on May 21, 2003
  1. @hyphaltip

    some code cleanup to avoid warnings and insure filehandles are proper…

    …ly closed, etc
    
    svn path=/bioperl-run/trunk/; revision=13441
    hyphaltip committed May 21, 2003
  2. @hyphaltip

    more modern use of hit/query instead of feature1/feature2. Support ne…

    …w quiet parameter to BLAT
    
    svn path=/bioperl-run/trunk/; revision=13440
    hyphaltip committed May 21, 2003