| 2011-05-19 |
Chris Fields | don't call executable()
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commit | commitdiff | tree |
| 2011-04-21 |
Chris Fields | skip # off
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commit | commitdiff | tree |
| 2011-04-21 |
Chris Fields | hack in a workaround for version(), which conflicts...
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commit | commitdiff | tree |
| 2011-04-21 |
Chris Fields | passthrough Makefile is deprecated; add BEDTools dependency
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commit | commitdiff | tree |
| 2011-04-21 |
Chris Fields | a few last additions
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commit | commitdiff | tree |
| 2011-04-20 |
Chris Fields | some more Changes
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commit | commitdiff | tree |
| 2011-04-20 |
Chris Fields | some initial Changes stuff, getting ready for a run...
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commit | commitdiff | tree |
| 2011-04-20 |
Chris Fields | add comment on the required BLAST+ version, refs #3213
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commit | commitdiff | tree |
| 2011-04-20 |
Chris Fields | get SABlast tests passing with v 2.2.24+ and up
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commit | commitdiff | tree |
| 2011-04-20 |
Chris Fields | fix hit count to go with database change, tests pass...
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commit | commitdiff | tree |
| 2011-04-20 |
Chris Fields | get BLAST+ tests to actually finish w/o a crash using...
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commit | commitdiff | tree |
| 2011-04-20 |
Chris Fields | BLAST+ tests passing so far, refs #3213
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commit | commitdiff | tree |
| 2011-04-20 |
Chris Fields | changes to deal with indexing of FASTA with dup ID...
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commit | commitdiff | tree |
| 2011-04-14 |
Chris Fields | get MAFFT working
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commit | commitdiff | tree |
| 2011-04-14 |
Chris Fields | latest samtools needs a sorted BAM for indexing
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commit | commitdiff | tree |
| 2011-04-14 |
Chris Fields | update for EMBOSS 6.2.0
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commit | commitdiff | tree |
| 2011-04-04 |
Chris Fields | Revert "test hook from run (issue might be CGI params)"
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commit | commitdiff | tree |
| 2011-04-04 |
Chris Fields | test hook from run (issue might be CGI params)
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commit | commitdiff | tree |
| 2010-11-05 |
Chris Fields | simplify some bits, pass on query/target types to the...
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commit | commitdiff | tree |
| 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 |
