| 2010-11-05 |
Chris Fields | remove cruft, gunge, and implement searchio()
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commit | commitdiff | tree |
| 2010-11-05 |
Chris Fields | allow other SearchIO formats and parameters (though...
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commit | commitdiff | tree |
| 2010-11-05 |
Chris Fields | tests for regions, require a .2bit database so only...
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commit | commitdiff | tree |
| 2010-11-05 |
Chris Fields | add an uppercase alias for db, tests pass
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commit | commitdiff | tree |
| 2010-11-05 |
Chris Fields | initial checkin of revamped Blat wrapper
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commit | commitdiff | tree |
| 2010-08-05 |
Chris Fields | [bug 2987] remove warning (patch courtesy Adam Witney
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commit | commitdiff | tree |
| 2010-07-23 |
Chris Fields | Revert "add dots param"
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commit | commitdiff | tree |
| 2010-07-23 |
Chris Fields | add dots param
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commit | commitdiff | tree |
| 2010-07-23 |
Chris Fields | [RT 58464] patching to allow file names with spaces
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commit | commitdiff | tree |
| 2010-07-05 |
Chris Fields | small fixes, but the previous code does work when setting...
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commit | commitdiff | tree |
| 2010-07-04 |
Chris Fields | spelling
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commit | commitdiff | tree |
| 2010-07-01 |
Chris Fields | move tests over to tempfile use (tmpdir not being cleaned up)
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commit | commitdiff | tree |
| 2010-07-01 |
Chris Fields | move to tempfiles for cleanup
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commit | commitdiff | tree |
| 2010-07-01 |
Chris Fields | algorithm can be SSEARCH as well; use test_output_file...
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commit | commitdiff | tree |
| 2010-07-01 |
Chris Fields | contigs off with Ubuntu packaged MAQ
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | no_sequences -> num_sequences
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | some tweaks to get rid of warnings
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | more robust call to ulimit
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | is(), not ok()
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | skip if version greater than 1.2 (old primer3 code)
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | add version() (backport from primer3redux)
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | align left
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | fix odd verbosity-dependent bug with EMBOSS tests
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | add minimal gitignore
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | add ulimit -n check, as these tests fail from too many...
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | add email
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | correct skipped number of tests
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | skip test count off, fixed
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commit | commitdiff | tree |
| 2010-06-30 |
Chris Fields | Merge branch 'master' of github.com:bioperl/bioperl-run
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commit | commitdiff | tree |
| 2010-06-06 |
Chris Fields | add default manifest
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commit | commitdiff | tree |
| 2010-03-04 |
cjfields | [bug 3002] add a bit o' code for email address prompting...
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commit | commitdiff | tree |
| 2010-03-04 |
cjfields | use safe_parse (deafferret++); tests now run, but fail...
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commit | commitdiff | tree |
| 2010-03-04 |
cjfields | throw error if XML::Twig borks on a parse
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commit | commitdiff | tree |
| 2010-03-03 |
cjfields | skipping wrong number of tests
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commit | commitdiff | tree |
| 2009-11-02 |
cjfields | add infernal data file
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commit | commitdiff | tree |
| 2009-10-30 |
cjfields | update Changes
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commit | commitdiff | tree |
| 2009-10-27 |
cjfields | remove debugging; tests pass w/ Clustalw 1.82 and clustalw...
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commit | commitdiff | tree |
| 2009-10-26 |
cjfields | [bug 2728]
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commit | commitdiff | tree |
| 2009-10-22 |
cjfields | [RT 50363]
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commit | commitdiff | tree |
| 2009-10-22 |
cjfields | skip only tests that fail, not all of them (these fail...
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commit | commitdiff | tree |
| 2009-09-30 |
cjfields | update changes
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commit | commitdiff | tree |
| 2009-09-30 |
cjfields | skip tests if executable isn't installed
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commit | commitdiff | tree |
| 2009-09-30 |
cjfields | add test data for cmalign
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commit | commitdiff | tree |
| 2009-09-30 |
cjfields | skip tests if infernal isn't installed
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commit | commitdiff | tree |
| 2009-09-30 |
cjfields | * pod fixes
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commit | commitdiff | tree |
| 2009-07-04 |
cjfields | doc fixes; cmscore may need some tweaking at some point...
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commit | commitdiff | tree |
| 2009-07-04 |
cjfields | for cmcalibrate tests
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commit | commitdiff | tree |
| 2009-07-04 |
cjfields | more commits and tests; cmcalibrate works but commenting...
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commit | commitdiff | tree |
| 2009-07-03 |
cjfields | add some infernal data
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commit | commitdiff | tree |
| 2009-07-03 |
cjfields | add some infernal tests (data to follow)
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commit | commitdiff | tree |
| 2009-07-03 |
cjfields | [bug 2713]
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commit | commitdiff | tree |
| 2009-03-23 |
cjfields | [bug 2798]
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commit | commitdiff | tree |
| 2009-02-25 |
cjfields | fix test numbering
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commit | commitdiff | tree |
| 2009-02-14 |
cjfields | get Vista.t passing
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commit | commitdiff | tree |
| 2009-02-14 |
cjfields | fix for neg. scores (courtesy of Bruno Vecchi)
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commit | commitdiff | tree |
| 2009-02-12 |
cjfields | allow either primer3 or primer3_core
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commit | commitdiff | tree |
| 2009-02-10 |
cjfields | skip ConfigData for now
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commit | commitdiff | tree |
| 2009-02-09 |
cjfields | requires network connection to work
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commit | commitdiff | tree |
| 2009-02-05 |
cjfields | TODO now passes (thanks to Mahmut Uludag and Martin...
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commit | commitdiff | tree |
| 2009-02-03 |
cjfields | Fix Bio::DB::EUtilities (API changed considerably from...
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commit | commitdiff | tree |
| 2009-02-02 |
cjfields | version to 1.6.9 (pre-1.7)
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commit | commitdiff | tree |
| 2009-01-31 |
cjfields | switch to simple die
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commit | commitdiff | tree |
| 2009-01-31 |
cjfields | use eval to check for Bio::Root::Build, die gracefully
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commit | commitdiff | tree |
| 2009-01-31 |
cjfields | TCoffee now passes
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commit | commitdiff | tree |
| 2009-01-30 |
cjfields | remove debugging line
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commit | commitdiff | tree |
| 2009-01-30 |
cjfields | partial fix for TCoffee version above v5 (still breaking...
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commit | commitdiff | tree |
| 2009-01-30 |
cjfields | comma causing tests to fail on some systems if Java...
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commit | commitdiff | tree |
| 2009-01-29 |
cjfields | add some flexibility for older model names
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commit | commitdiff | tree |
| 2009-01-28 |
cjfields | small tweaks to primer3 (should try getting this to...
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commit | commitdiff | tree |
| 2009-01-27 |
cjfields | tweak error message
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commit | commitdiff | tree |
| 2009-01-27 |
cjfields | * newer versions of t_coffee failing this test, may...
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commit | commitdiff | tree |
| 2009-01-27 |
cjfields | * TODO failing AnalysisFactory_soap.t test (appears...
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commit | commitdiff | tree |
| 2009-01-27 |
cjfields | catch version if it contains alphanumeric
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commit | commitdiff | tree |
| 2009-01-13 |
cjfields | * small updates
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commit | commitdiff | tree |
| 2009-01-13 |
cjfields | Remove Pise-related stuff, update with other dependencies
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commit | commitdiff | tree |
| 2009-01-13 |
cjfields | Add DEPENDENCIES file.
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commit | commitdiff | tree |
| 2009-01-13 |
cjfields | Remove Pise-related examples (moved into bioperl-pise)
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commit | commitdiff | tree |
| 2009-01-13 |
cjfields | Remove Pise-related module (moved into bioperl-pise)
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commit | commitdiff | tree |
| 2009-01-13 |
cjfields | Remove Pise modules and tests (moved into bioperl-pise)
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commit | commitdiff | tree |
| 2009-01-13 |
cjfields | Remove Pise modules and tests (moved into bioperl-pise)
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commit | commitdiff | tree |
| 2009-01-10 |
cjfields | Don't TODO the test, actually attempt to run it and...
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commit | commitdiff | tree |
| 2009-01-10 |
cjfields | Actually make tests complete (not skipped if there...
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commit | commitdiff | tree |
| 2009-01-10 |
cjfields | TODO failing test (problem with SOAP protocol)
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commit | commitdiff | tree |
| 2009-01-10 |
cjfields | * finish up bioperl-run conversion
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commit | commitdiff | tree |
| 2009-01-08 |
cjfields | requires not required
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commit | commitdiff | tree |
| 2009-01-08 |
cjfields | * convert over to Bio::Root::Test and update some to...
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commit | commitdiff | tree |
| 2009-01-08 |
cjfields | * convert to Bio::Root::Test
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commit | commitdiff | tree |
| 2009-01-08 |
cjfields | * convert to Bio::Root::Test
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commit | commitdiff | tree |
| 2009-01-07 |
cjfields | Getting a failed test using latest EnsEMBL perl API...
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commit | commitdiff | tree |
| 2009-01-07 |
cjfields | Catch version, skip tests if version isn't supported...
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commit | commitdiff | tree |
| 2008-11-14 |
cjfields | [bug 2644]
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commit | commitdiff | tree |
| 2008-08-22 |
cjfields | * add_sequences option (adds sequences to an alignment...
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commit | commitdiff | tree |
| 2008-07-30 |
cjfields | patching the correct Primer3.pm (not Bio::Tools::Primer3.pm)
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commit | commitdiff | tree |
| 2008-06-19 |
cjfields | bug 2523
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commit | commitdiff | tree |
| 2008-04-15 |
cjfields | Update to 0.81 params. Need to set up tests for this...
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commit | commitdiff | tree |
| 2008-02-27 |
cjfields | bug 2460
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commit | commitdiff | tree |
| 2008-01-15 |
cjfields | test
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commit | commitdiff | tree |
| 2007-07-16 |
cjfields | bug 2202
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commit | commitdiff | tree |
| 2007-07-16 |
cjfields | bug 2299
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commit | commitdiff | tree |
| 2007-07-01 |
cjfields | bug 2299
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commit | commitdiff | tree |
