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Commits on Dec 3, 2003
  1. updated using info from maintanence/authors.pl script

    svn path=/bioperl-run/trunk/; revision=13505
    heikkil committed Dec 3, 2003
Commits on Nov 25, 2003
  1. Patched, thank you Albert

    svn path=/bioperl-run/trunk/; revision=13504
    bosborne committed Nov 25, 2003
Commits on Nov 19, 2003
  1. George Hartzell fixes

    svn path=/bioperl-run/trunk/; revision=13503
    hyphaltip committed Nov 19, 2003
Commits on Oct 3, 2003
  1. Modified call to io->tmpfile to get file name as well as handle

    svn path=/bioperl-run/trunk/; revision=13502
    djackson committed Oct 3, 2003
Commits on Sep 30, 2003
  1. use save_tempfiles, use PROGRAMNAME as a variable, use tempfile inste…

    …ad of randomly generating filename
    
    svn path=/bioperl-run/trunk/; revision=13501
    hyphaltip committed Sep 30, 2003
  2. typo

    svn path=/bioperl-run/trunk/; revision=13500
    hyphaltip committed Sep 30, 2003
Commits on Sep 18, 2003
  1. various fixes to get blat runnable in line with bioperl-live 1.2.3

    all tests now pass.
    
    svn path=/bioperl-run/trunk/; revision=13499
    allenday committed Sep 18, 2003
  2. well, at least it runs the blat program now, although it isn't seemin…

    …gly able
    
    to find the output tempfile to retrieve the results
    
    svn path=/bioperl-run/trunk/; revision=13498
    allenday committed Sep 18, 2003
Commits on Sep 8, 2003
  1. default should be an arrayref

    svn path=/bioperl-run/trunk/; revision=13497
    hyphaltip committed Sep 8, 2003
  2. POD fixes

    svn path=/bioperl-run/trunk/; revision=13496
    heikkil committed Sep 8, 2003
Commits on Sep 3, 2003
  1. wait -this isn't necessary , we already pad the PROGRAMNAME with the …

    ….exe when appropriate
    
    svn path=/bioperl-run/trunk/; revision=13495
    hyphaltip committed Sep 3, 2003
  2. bug #1507 add MSwin .exe extension where appropriate

    svn path=/bioperl-run/trunk/; revision=13494
    hyphaltip committed Sep 3, 2003
  3. bug #1507, SYNOPSIS is runnable now with API changes

    svn path=/bioperl-run/trunk/; revision=13493
    hyphaltip committed Sep 3, 2003
Commits on Sep 1, 2003
  1. fix typo reported in bug #1505

    svn path=/bioperl-run/trunk/; revision=13492
    heikkil committed Sep 1, 2003
Commits on Aug 28, 2003
  1. typo

    svn path=/bioperl-run/trunk/; revision=13491
    shawnh committed Aug 28, 2003
Commits on Aug 27, 2003
  1. PiseWorkflow is a module for building and running a workflow on top o…

    …f PiseApplication instances.
    
    svn path=/bioperl-run/trunk/; revision=13490
    letondal committed Aug 27, 2003
  2. Major bug, need to project aligmnents, basically need to remove posit…

    …ion in pairwise aligmnet if both are gap characters, else vista will count wrongly
    
    svn path=/bioperl-run/trunk/; revision=13489
    shawnh committed Aug 27, 2003
Commits on Aug 25, 2003
  1. Pise/bioperl module for a recent version of mfold (3.1.2).

    svn path=/bioperl-run/trunk/; revision=13488
    letondal committed Aug 25, 2003
Commits on Aug 14, 2003
  1. can't declare are expect a variable at the same time

    svn path=/bioperl-run/trunk/; revision=13487
    hyphaltip committed Aug 14, 2003
  2. no need for this debugging

    svn path=/bioperl-run/trunk/; revision=13486
    hyphaltip committed Aug 14, 2003
  3. fix stupidity with tempfilehandle and outfh not being closed properly…

    … as reported by Ben Westover
    
    svn path=/bioperl-run/trunk/; revision=13485
    hyphaltip committed Aug 14, 2003
  4. Allowing of setting of outfile

    svn path=/bioperl-run/trunk/; revision=13484
    shawnh committed Aug 14, 2003
Commits on Aug 10, 2003
  1. Added java param to allow setting of java parameters, for example to …

    …set higher heap sizes..
    
    svn path=/bioperl-run/trunk/; revision=13483
    shawnh committed Aug 10, 2003
Commits on Jul 30, 2003
  1. test for Hmmer

    svn path=/bioperl-run/trunk/; revision=13482
    shawnh committed Jul 30, 2003
  2. Hmmer wrapper factory, currently supports hmmsearch, hmmalign,hmmpfam…

    …, hmmbuild and hmmcalibrate
    
    svn path=/bioperl-run/trunk/; revision=13481
    shawnh committed Jul 30, 2003
Commits on Jul 11, 2003
  1. align the code

    svn path=/bioperl-run/trunk/; revision=13480
    hyphaltip committed Jul 11, 2003
  2. properly get the hash value

    svn path=/bioperl-run/trunk/; revision=13479
    hyphaltip committed Jul 11, 2003
  3. Porting Rob Edwards extension of Primer3 wrapper and parser

    svn path=/bioperl-run/trunk/; revision=13478
    shawnh committed Jul 11, 2003
Commits on Jul 8, 2003
  1. VERSION to 1.2.2

    svn path=/bioperl-run/trunk/; revision=13476
    heikkil committed Jul 8, 2003
  2. release number 1.2.2; reformatting

    svn path=/bioperl-run/trunk/; revision=13475
    heikkil committed Jul 8, 2003
Commits on Jul 7, 2003
  1. 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. Mark Wagner's enhancements bug #1399

    svn path=/bioperl-run/trunk/; revision=13470
    hyphaltip committed Jun 28, 2003