| 8b8bed3 | Eddie Belter | 22 April 2013, 23:15:07 UTC | InstData Import: dump sam from copied sra file | 22 April 2013, 23:15:07 UTC |
| f21d603 | Eddie Belter | 22 April 2013, 23:06:25 UTC | Sync: institutes a sync order for update apipe classes | 22 April 2013, 23:11:27 UTC |
| 7aa29b5 | Thomas Mooney | 22 April 2013, 21:12:40 UTC | Add some more abbreviations per RT#91971. | 22 April 2013, 21:12:40 UTC |
| 6bf4189 | APipe Tester | 22 April 2013, 18:18:54 UTC | updated jenkins submodule to 186aa31 | 22 April 2013, 18:18:54 UTC |
| 8fc5987 | apregier | 22 April 2013, 17:41:42 UTC | model input remove had bug for objects with display names | 22 April 2013, 17:41:42 UTC |
| b6321fe | APipe Tester | 22 April 2013, 14:46:16 UTC | updated jenkins submodule to 8d6d12d | 22 April 2013, 14:46:16 UTC |
| 274f264 | nnutter | 22 April 2013, 14:27:11 UTC | set copyCat pointer to master, old one was broken | 22 April 2013, 14:27:11 UTC |
| afe4940 | apregier | 19 April 2013, 22:53:12 UTC | Remove cp from debugging | 19 April 2013, 22:53:12 UTC |
| a2f1d3a | apregier | 19 April 2013, 21:56:35 UTC | Remove file copy from test | 19 April 2013, 21:57:16 UTC |
| 225bc1f | nnutter | 19 April 2013, 18:26:28 UTC | auto generate bare minimum tests | 19 April 2013, 21:22:01 UTC |
| 39d1e60 | nnutter | 19 April 2013, 19:28:12 UTC | should only look for .pm files This should only look for .pm files, tests will be added soon and they should not load. | 19 April 2013, 21:21:47 UTC |
| eb82a42 | Ben Oberkfell | 19 April 2013, 20:36:03 UTC | forgot to add this env module for query pausing | 19 April 2013, 20:36:03 UTC |
| 46e484e | Ben Oberkfell | 19 April 2013, 19:37:15 UTC | Set up pause blockers to stop querying & connects to Postgres. This will allow us to safely take down the PG server for sysadmin work and minimize disruption | 19 April 2013, 19:50:10 UTC |
| 4cbe84c | APipe Tester | 19 April 2013, 19:36:39 UTC | updated ur submodule to e1700d2 | 19 April 2013, 19:36:39 UTC |
| 1063e25 | nnutter | 19 April 2013, 19:26:02 UTC | add diag to help reproduce failure on apipe-ci | 19 April 2013, 19:26:02 UTC |
| 850e345 | nnutter | 19 April 2013, 18:37:40 UTC | load Test::* after 'use above' so we our Test::* | 19 April 2013, 18:44:38 UTC |
| 1be8ec4 | Ian Ferguson | 19 April 2013, 18:35:58 UTC | Modify Bwa memory request for certain ref builds Some reference sequence builds will consistently cause Bwa to reach its LSF memory limit. The AlignReads Event now provides the reference sequence build when calling the aligner module's required_rusage method. Bwa will now double the memory requirement from 8 to 16 GB when the provided reference sequence build matches a build that we have determined requires more memory. | 19 April 2013, 18:42:54 UTC |
| a73e6d5 | Ian Ferguson | 19 April 2013, 18:19:55 UTC | Increase bwamem memory rusage | 19 April 2013, 18:20:04 UTC |
| c5530f8 | Gabriel Sanderson | 19 April 2013, 18:11:48 UTC | Merge branch 'master' into gb_master | 19 April 2013, 18:11:48 UTC |
| 125f294 | Gabriel Sanderson | 18 April 2013, 23:04:49 UTC | Allow both gzipped and non gzipped vcfs as input | 19 April 2013, 18:11:10 UTC |
| 4c50713 | nnutter | 19 April 2013, 17:42:55 UTC | Merge branch 'test_more' | 19 April 2013, 17:42:55 UTC |
| dbbd532 | nnutter | 19 April 2013, 17:38:20 UTC | remove _subtest since we can now use Test::More's subtest | 19 April 2013, 17:38:20 UTC |
| 31bfc67 | nnutter | 19 April 2013, 17:37:05 UTC | remove sub_test since we can now use Test::More's subtest | 19 April 2013, 17:37:05 UTC |
| 9532180 | nnutter | 19 April 2013, 16:14:30 UTC | update to use Test::More's subtest | 19 April 2013, 16:22:38 UTC |
| 90e2546 | nnutter | 19 April 2013, 16:22:17 UTC | apply bugfix from Test::More 1.5 that hasn't been pulled into 0.98 | 19 April 2013, 16:22:38 UTC |
| 7bbae9e | nnutter | 19 April 2013, 16:21:34 UTC | pull in Test::More master @ 74efe123 | 19 April 2013, 16:22:37 UTC |
| 04096aa | nnutter | 19 April 2013, 15:20:45 UTC | whitespace | 19 April 2013, 15:47:39 UTC |
| 207c3f9 | nnutter | 19 April 2013, 15:18:47 UTC | make test pass even if UR_COMMAND_DUMP_STATUS_MESSAGES is set Since test depends on status messages not being shown we should also set $ENV{UR_COMMAND_DUMP_STATUS_MESSAGES} to 0 in case the tester has that enabled. | 19 April 2013, 15:47:38 UTC |
| d6db9c7 | nnutter | 19 April 2013, 15:20:31 UTC | add diagnostics | 19 April 2013, 15:47:38 UTC |
| 659c1fb | nnutter | 18 April 2013, 23:21:03 UTC | also get new lock The old lock includes subdirectories and should not. In order to transition to a new lock scheme we currently have to lock both schemes. Later we can remove the old scheme. | 18 April 2013, 23:40:44 UTC |
| 408c0d0 | nnutter | 18 April 2013, 23:11:08 UTC | refactor locking code Pull locking code into separate function. Same code is used in several modules so it still isn't completely refactored. Will fix that next. Moving towards fixing the fact that locks shouldn't contain subdirectories. | 18 April 2013, 23:40:42 UTC |
| 0b71bda | Ian Ferguson | 18 April 2013, 21:55:19 UTC | Add bwa-0.7.3a | 18 April 2013, 21:55:19 UTC |
| cc4ba0f | APipe Tester | 18 April 2013, 19:51:16 UTC | Updated `gmt` tab completion. | 18 April 2013, 19:51:16 UTC |
| fc422eb | APipe Tester | 18 April 2013, 19:49:58 UTC | Updated `genome` tab completion. | 18 April 2013, 19:49:58 UTC |
| a4d00c9 | Travis Abbott | 18 April 2013, 19:32:06 UTC | rename examples_values => example_values; add test | 18 April 2013, 19:32:06 UTC |
| 1941e02 | APipe Tester | 18 April 2013, 18:37:03 UTC | updated jenkins submodule to 63461be | 18 April 2013, 18:37:03 UTC |
| eda6d1f | Thomas Mooney | 18 April 2013, 18:16:40 UTC | This parameter is required. | 18 April 2013, 18:16:40 UTC |
| 7c5bfeb | Thomas Mooney | 18 April 2013, 18:14:02 UTC | Hardcode path to the rrna_database. This minimally restores the MGAP pipeline to functionality. | 18 April 2013, 18:14:02 UTC |
| 312a299 | apregier | 18 April 2013, 04:14:21 UTC | Bug fix | 18 April 2013, 04:14:50 UTC |
| 71f56cb | Travis Abbott | 17 April 2013, 21:44:41 UTC | update clinseq test data to fix broken test | 17 April 2013, 21:44:41 UTC |
| 1d27bde | Eddie Belter | 17 April 2013, 19:26:01 UTC | ClinSeq: update output for new builds | 17 April 2013, 20:08:25 UTC |
| 43cc8c3 | Ian Ferguson | 17 April 2013, 19:27:18 UTC | Added 1; to end of some aligner modules | 17 April 2013, 19:27:18 UTC |
| 04cf5df | Ian Ferguson | 17 April 2013, 19:24:25 UTC | Initial commit for Bwamem aligner module | 17 April 2013, 19:24:25 UTC |
| 107e345 | Ian Ferguson | 17 April 2013, 19:15:00 UTC | Refactoring in GMT::Bwa Tried to refactor GMT::Bwa to better manage the many different versions and features of Bwa. Includes tests. | 17 April 2013, 19:15:00 UTC |
| 5195186 | Adam Coffman | 17 April 2013, 17:42:05 UTC | add database entities to support analysis project configuration | 17 April 2013, 17:42:05 UTC |
| 1220f64 | apregier | 17 April 2013, 14:31:46 UTC | Fix bug | 17 April 2013, 14:31:46 UTC |
| 027df79 | apregier | 16 April 2013, 22:33:24 UTC | Remove hard-coded path to sv annotation files | 16 April 2013, 22:48:27 UTC |
| d564199 | Eddie Belter | 16 April 2013, 22:45:51 UTC | Sync: fix recocile test | 16 April 2013, 22:45:51 UTC |
| fc25052 | Adam Coffman | 16 April 2013, 21:55:21 UTC | add new genome env variable to point to default analysis config location | 16 April 2013, 21:55:21 UTC |
| 3654a54 | Eddie Belter | 16 April 2013, 21:10:33 UTC | Sync: _create_librarysummary points to _create_object | 16 April 2013, 21:10:41 UTC |
| 6867b57 | Eddie Belter | 16 April 2013, 21:09:15 UTC | Sync: update apipe classes uses org sample in classes dir | 16 April 2013, 21:10:40 UTC |
| 65a9c4d | Eddie Belter | 16 April 2013, 18:19:32 UTC | Sync: fix misc update test after removing is_control | 16 April 2013, 21:10:40 UTC |
| c1a6499 | Eddie Belter | 16 April 2013, 17:58:09 UTC | Sync: remove is_control from being synced | 16 April 2013, 21:10:39 UTC |
| 89ec1b0 | Eddie Belter | 16 April 2013, 17:57:32 UTC | Sync: change smaple class used to organism sample in classes dir | 16 April 2013, 21:10:39 UTC |
| a267888 | Eddie Belter | 16 April 2013, 16:46:16 UTC | Sync: mv sample to organism sample | 16 April 2013, 21:10:39 UTC |
| 29b5f72 | apregier | 16 April 2013, 20:15:24 UTC | Merge branch 'fix' into gb_master | 16 April 2013, 20:15:24 UTC |
| 5fe91ea | apregier | 11 April 2013, 21:52:12 UTC | Add ensembl stable gene id column to transcript output Bug fix Update blessed builds | 16 April 2013, 20:13:50 UTC |
| 4cbd2a0 | apregier | 11 April 2013, 21:18:12 UTC | Add unit test | 16 April 2013, 20:13:46 UTC |
| fe7818b | apregier | 11 April 2013, 21:10:37 UTC | Add unit test for segdup | 16 April 2013, 20:13:45 UTC |
| 5c36b1a | apregier | 03 April 2013, 20:04:19 UTC | Improve sv annotation algorithm for dbsnp/dbvar/segdup Add unit tests Refactor to use interval tree -Add Set::IntervalTree package -genome-snapshot-deps Update blessed build | 16 April 2013, 20:13:44 UTC |
| 8bd427e | APipe Tester | 16 April 2013, 18:37:45 UTC | updated jenkins submodule to cf04f73 | 16 April 2013, 18:37:45 UTC |
| ce74916 | Adam Coffman | 16 April 2013, 18:01:32 UTC | add postgres mappings for new genome tables | 16 April 2013, 18:01:32 UTC |
| 95529e7 | Mark Burnett | 16 April 2013, 14:34:18 UTC | add variants/*.{err,out} to ignored files (RefAlign & SomVar) | 16 April 2013, 17:04:49 UTC |
| 97f282e | APipe Tester | 16 April 2013, 16:02:41 UTC | updated jenkins submodule to 7a9a1e4 | 16 April 2013, 16:02:41 UTC |
| 00d156a | Adam Coffman | 16 April 2013, 14:41:34 UTC | Add ObjectWithTimestamps mixin | 16 April 2013, 14:41:34 UTC |
| ec340c7 | Thomas Mooney | 16 April 2013, 14:18:19 UTC | Cleanup these temp files we're throwing around. | 16 April 2013, 14:19:06 UTC |
| 7e6e13f | Ian Ferguson | 15 April 2013, 19:12:41 UTC | Restore GMT/Predictor/FastaChunker.pm FastaChunker was removed while cleaning up default parameters. Added it back to fix failing protein annotation builds. | 15 April 2013, 19:12:41 UTC |
| 5bad97c | APipe Tester | 15 April 2013, 15:39:15 UTC | updated jenkins submodule to 19d09e5 | 15 April 2013, 15:39:15 UTC |
| 172bc59 | Thomas Mooney | 15 April 2013, 15:33:20 UTC | Only pull back results matching our test name. If a test name was added to some VCF results for our result after-the-fact, they would've been grabbed by this query even though the present build did not use them. | 15 April 2013, 15:33:20 UTC |
| d2ef5b6 | nnutter | 15 April 2013, 13:49:26 UTC | redirect stderr This was producing a *ton* of output in it's test so I opted to log stderr. If that is not an OK solution in general we'll still have to address the test. | 15 April 2013, 13:49:26 UTC |
| 5ce1ddc | nnutter | 15 April 2013, 13:49:08 UTC | specify output_directories | 15 April 2013, 13:49:08 UTC |
| 3beb52a | nnutter | 15 April 2013, 13:29:15 UTC | re-enable test Upstream builds finished building so re-enabled test. Add an additional test because it now get's the model's latest build instead of a specific build. Updated expected output which was mostly due to changes in build IDs and paths but there were also a few changes in output that looked minor. | 15 April 2013, 13:30:41 UTC |
| f823d8e | nnutter | 15 April 2013, 13:28:34 UTC | update expected output genome-model-rnaseq-list2.out has a new build. | 15 April 2013, 13:28:34 UTC |
| 507de3e | APipe Tester | 12 April 2013, 23:51:54 UTC | updated graphite submodule to 466bfdb | 12 April 2013, 23:51:54 UTC |
| 7cfe2ab | APipe Tester | 12 April 2013, 23:51:47 UTC | updated ur submodule to 334ab66 | 12 April 2013, 23:51:47 UTC |
| e1b8cb3 | Adam Coffman | 12 April 2013, 22:45:02 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 12 April 2013, 22:45:02 UTC |
| ac0fd42 | Adam Coffman | 12 April 2013, 22:44:52 UTC | create abstract parent classes for interfaces to use in configuration readers | 12 April 2013, 22:44:52 UTC |
| 66233b5 | APipe Tester | 12 April 2013, 21:46:17 UTC | updated ur submodule to fb1b003 | 12 April 2013, 21:46:17 UTC |
| c5fca6f | nnutter | 12 April 2013, 21:33:49 UTC | move _sync_database shortcut closer to source of problem This @changed_objects "shortcut" is to avoid an issue with autocommit on the Pg driver where it would cause an unwanted lock. This was previously in Command::Dispatch::Shell from UR commit 7fd973b. | 12 April 2013, 21:35:48 UTC |
| 90ba06d | Adam Coffman | 12 April 2013, 20:48:59 UTC | add MaskedConfigurationReader to use in Analysis configuration | 12 April 2013, 20:48:59 UTC |
| 2e1c63c | nnutter | 12 April 2013, 19:33:14 UTC | remove _lock_model_for_start It doesn't do anything to prevent duplicate builds but does cause intermittent failures when trying to start test models under different configurations. | 12 April 2013, 20:11:53 UTC |
| 8f9614f | Adam Coffman | 12 April 2013, 19:10:46 UTC | remove breakpoint, whoops | 12 April 2013, 19:10:46 UTC |
| 737b7ce | Adam Coffman | 12 April 2013, 19:09:41 UTC | add TreeCopy strategy for use in analysis configuration | 12 April 2013, 19:09:41 UTC |
| 51a9e6f | nnutter | 12 April 2013, 15:44:48 UTC | Merge branch 'heartbeat' | 12 April 2013, 18:17:41 UTC |
| eaa51a0 | nnutter | 12 April 2013, 15:43:11 UTC | set "RnaSeq Alignment" to allow 7 days for max_elapsed_log_time | 12 April 2013, 18:17:40 UTC |
| 740f8a4 | nnutter | 12 April 2013, 15:35:05 UTC | allow commands to specify the max_elapsed_log_time | 12 April 2013, 18:17:38 UTC |
| 20fd3b0 | nnutter | 12 April 2013, 15:34:37 UTC | get logs from workflow instead of parsing bjobs | 12 April 2013, 18:17:37 UTC |
| 061077b | Charles Lu | 12 April 2013, 17:51:48 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 12 April 2013, 17:51:48 UTC |
| 21afb2f | Charles Lu | 12 April 2013, 17:51:42 UTC | made --referene option required now | 12 April 2013, 17:51:42 UTC |
| 14651ab | Gabriel Sanderson | 12 April 2013, 17:34:19 UTC | Merge branch 'master' into gb_master | 12 April 2013, 17:34:19 UTC |
| 3145890 | Gabriel Sanderson | 12 April 2013, 17:33:46 UTC | Slightly clearer error when versions are a problem | 12 April 2013, 17:33:55 UTC |
| 76479bd | Feiyu Du | 12 April 2013, 15:45:07 UTC | 1.add condition of empty contig.fasta for som-val pipeline; 2. bug fix for samtools mpileup snv vcf converter | 12 April 2013, 15:45:07 UTC |
| 5a9ba0e | Adam Coffman | 12 April 2013, 15:37:03 UTC | add YAML parser to use in analysis project config | 12 April 2013, 15:37:03 UTC |
| fe5acf2 | APipe Tester | 12 April 2013, 15:06:19 UTC | Updated `gmt` tab completion. | 12 April 2013, 15:06:19 UTC |
| 89e07a4 | APipe Tester | 12 April 2013, 15:05:29 UTC | Updated `genome` tab completion. | 12 April 2013, 15:05:29 UTC |
| 2a89318 | APipe Tester | 12 April 2013, 14:58:40 UTC | Updated `genome` tab completion. | 12 April 2013, 14:59:48 UTC |
| 129c3e8 | Adam Coffman | 12 April 2013, 14:49:41 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 12 April 2013, 14:49:41 UTC |
| d8e33af | Adam Coffman | 11 April 2013, 22:07:39 UTC | Add tree handler class for use in analysis project config | 12 April 2013, 14:48:46 UTC |
| cb9f82a | nnutter | 11 April 2013, 19:11:51 UTC | approved new build after reviewing with Malachi There were several causes of changes: - Some files were added in: 9bb4d83 ClinSeq - generate clonality plots test now takes ~60s instead of ~1400s to run, other minor fixes - Some paths change due to rebuild of upstream models, e.g. tumor_rnaseq_build - Some floating point changes/error that correlated very strongly with previous. - Several log files were removed and are now inline. | 11 April 2013, 19:15:09 UTC |
| 8d2d644 | Malachi Griffith | 11 April 2013, 19:12:46 UTC | Ignore .R.stderr files in build diffing | 11 April 2013, 19:12:46 UTC |
