| 026e6e0 | APipe Tester | 11 February 2014, 13:18:13 UTC | Updated `genome` tab completion. | 11 February 2014, 13:18:13 UTC |
| aa9b409 | APipe Tester | 11 February 2014, 13:16:27 UTC | Updated class browser cache. | 11 February 2014, 13:16:27 UTC |
| 174c523 | Nathaniel Nutter | 11 February 2014, 00:51:58 UTC | Revert "switch to Module::Runtime" This reverts commit a163bf85a690bbd917e240c6e822818b1bfb601e because it breaks /gsc/bin/perl. | 11 February 2014, 00:51:58 UTC |
| 4915d5c | Nathaniel Nutter | 11 February 2014, 00:01:28 UTC | package does not use Genome | 11 February 2014, 00:01:28 UTC |
| a163bf8 | Nathaniel Nutter | 10 February 2014, 22:24:55 UTC | switch to Module::Runtime | 10 February 2014, 23:52:15 UTC |
| b6443bb | Jim Weible | 10 February 2014, 20:14:57 UTC | add lister for analysis menu items | 10 February 2014, 20:14:57 UTC |
| 230c787 | Jason Walker | 10 February 2014, 18:54:12 UTC | Add a method to resolve allocations to consider part of the builds disk usage | 10 February 2014, 18:54:12 UTC |
| 93d6138 | Jason Walker | 10 February 2014, 18:48:57 UTC | Resolve the superset of headers from all inputs. | 10 February 2014, 18:48:57 UTC |
| a35afd5 | apregier | 10 February 2014, 16:39:48 UTC | Merge branch 'updated' into gb_master | 10 February 2014, 16:39:48 UTC |
| e3569df | apregier | 10 February 2014, 16:38:24 UTC | Find the imported annotation model correctly. | 10 February 2014, 16:38:24 UTC |
| 68f11ba | Thomas Mooney | 10 February 2014, 15:56:34 UTC | Close the DB connection by default before running a shell command. | 10 February 2014, 15:56:34 UTC |
| a72321a | Jim Weible | 10 February 2014, 15:23:00 UTC | Stop auto generating convergence models | 10 February 2014, 15:23:00 UTC |
| cf70137 | APipe Tester | 08 February 2014, 13:18:21 UTC | Updated `gmt` tab completion. | 08 February 2014, 13:18:21 UTC |
| 894896c | APipe Tester | 08 February 2014, 13:17:35 UTC | Updated `genome` tab completion. | 08 February 2014, 13:17:35 UTC |
| d057794 | Chris Miller | 07 February 2014, 18:21:23 UTC | adding option to override reference-transcript build | 07 February 2014, 18:23:18 UTC |
| 388ff62 | apregier | 07 February 2014, 18:05:21 UTC | Merge branch 'updated' into gb_master | 07 February 2014, 18:05:21 UTC |
| 157e376 | apregier | 07 February 2014, 18:03:17 UTC | Check that reference sequence matches before re-using a model | 07 February 2014, 18:04:13 UTC |
| 1f3d1c6 | Avinash Ramu | 07 February 2014, 17:56:06 UTC | shell has 2 l s | 07 February 2014, 17:56:06 UTC |
| 7245dea | Nathaniel Nutter | 06 February 2014, 21:51:53 UTC | refactor _launch | 07 February 2014, 16:14:17 UTC |
| 6c85e8a | Nathaniel Nutter | 06 February 2014, 21:51:36 UTC | remove TODOs | 07 February 2014, 16:14:14 UTC |
| bfce2c2 | Nathaniel Nutter | 06 February 2014, 21:46:56 UTC | pass model instead of build into function | 07 February 2014, 16:14:12 UTC |
| dfee689 | Nathaniel Nutter | 03 February 2014, 23:52:43 UTC | extract _job_dispatch | 07 February 2014, 16:14:11 UTC |
| 21b7e19 | Nathaniel Nutter | 03 February 2014, 23:50:55 UTC | extract _server_dispatch | 07 February 2014, 16:14:09 UTC |
| 46e6617 | Nathaniel Nutter | 01 February 2014, 01:09:43 UTC | refactor _job_group_spec for conciseness | 07 February 2014, 16:14:07 UTC |
| 47d6619 | Nathaniel Nutter | 01 February 2014, 01:04:24 UTC | refactor test to use _default_job_group instead of duplicating | 07 February 2014, 16:14:05 UTC |
| fc81306 | Nathaniel Nutter | 01 February 2014, 00:55:06 UTC | extract _default_job_group | 07 February 2014, 16:14:04 UTC |
| c127de4 | Nathaniel Nutter | 01 February 2014, 00:52:59 UTC | extract _job_group_spec | 07 February 2014, 16:14:01 UTC |
| 612aa1e | Susanna Siebert | 07 February 2014, 15:20:03 UTC | test to ensure that the initialization doesn't read in the first line | 07 February 2014, 15:47:46 UTC |
| 4c53df7 | Susanna Siebert | 07 February 2014, 15:18:34 UTC | remove the lsf_resource param after the refactor this module works with the default LSF memory requirements | 07 February 2014, 15:47:45 UTC |
| 2419d71 | Susanna Siebert | 07 February 2014, 15:15:55 UTC | remove the old way of processing the input variants file | 07 February 2014, 15:47:45 UTC |
| ef75183 | Susanna Siebert | 06 February 2014, 21:29:35 UTC | Throw an error if there is an empty line in the file to process | 07 February 2014, 15:47:44 UTC |
| 7285eb4 | Susanna Siebert | 06 February 2014, 21:28:49 UTC | don't parse the first line on initialization | 07 February 2014, 15:47:43 UTC |
| 5efaed7 | Susanna Siebert | 05 February 2014, 20:56:49 UTC | edit test messages for clarity | 07 February 2014, 15:47:43 UTC |
| d6b0a2d | Susanna Siebert | 05 February 2014, 20:56:02 UTC | use OrderedPosition for the variant file | 07 February 2014, 15:47:42 UTC |
| b8d504f | Susanna Siebert | 05 February 2014, 20:54:00 UTC | support string chromosome values | 07 February 2014, 15:47:42 UTC |
| 16bb827 | Susanna Siebert | 05 February 2014, 19:52:35 UTC | minor code cleanup | 07 February 2014, 15:47:41 UTC |
| 7d72af2 | Susanna Siebert | 05 February 2014, 19:50:11 UTC | improved the way the header is retrieved | 07 February 2014, 15:47:40 UTC |
| 1655dbb | Susanna Siebert | 05 February 2014, 16:41:06 UTC | remove templating comments | 07 February 2014, 15:47:40 UTC |
| b63e221 | Susanna Siebert | 05 February 2014, 16:40:02 UTC | use Genome::File::OrderedPosition | 07 February 2014, 15:47:39 UTC |
| b138031 | Susanna Siebert | 05 February 2014, 16:36:53 UTC | new file format for files sorted by chromosome and start position allow retrieval of whole line based on those keys retrieval has to happen in sort order | 07 February 2014, 15:47:38 UTC |
| 6d7bfd0 | Susanna Siebert | 03 February 2014, 18:54:52 UTC | use Genome::Sys->create_directories instead of mkdir | 07 February 2014, 15:47:38 UTC |
| 9afb623 | APipe Tester | 07 February 2014, 13:17:35 UTC | Updated `genome` tab completion. | 07 February 2014, 13:17:35 UTC |
| 72c2343 | Anthony Brummett | 06 February 2014, 19:58:53 UTC | error message now includes to class get_with_lock was called on | 06 February 2014, 19:58:53 UTC |
| e08b0c6 | Feiyu Du | 06 February 2014, 16:33:49 UTC | Fix DV2 filter unit tests to prevent DV2 filter parameter bug in the future | 06 February 2014, 16:36:33 UTC |
| 5d0f466 | Malachi Griffith | 06 February 2014, 15:45:09 UTC | clin-seq add ignore rule for result file containing a build id | 06 February 2014, 15:45:09 UTC |
| 7bae385 | Nathaniel Nutter | 06 February 2014, 15:40:26 UTC | remove build's restart option | 06 February 2014, 15:40:26 UTC |
| 4e240d4 | Nathaniel Nutter | 04 February 2014, 01:01:48 UTC | remove restart | 06 February 2014, 15:38:30 UTC |
| b664dfc | Nathaniel Nutter | 05 February 2014, 20:55:03 UTC | remove restart option | 06 February 2014, 15:38:29 UTC |
| cc285d3 | Nathaniel Nutter | 05 February 2014, 20:54:36 UTC | use build's workflow_name instead of duplicating code | 06 February 2014, 15:38:27 UTC |
| 9c91ed8 | APipe Tester | 06 February 2014, 13:17:13 UTC | Updated `genome` tab completion. | 06 February 2014, 13:17:13 UTC |
| 44759d9 | APipe Tester | 06 February 2014, 13:15:30 UTC | Updated class browser cache. | 06 February 2014, 13:15:30 UTC |
| 7b08bf1 | Malachi Griffith | 06 February 2014, 05:51:26 UTC | clin-seq add snv-indel-report to clinseq workflow | 06 February 2014, 05:51:26 UTC |
| dde1f5f | Malachi Griffith | 06 February 2014, 03:53:02 UTC | fix documentation and other minor details related to installation of file based dbs from github | 06 February 2014, 03:53:02 UTC |
| 7c2a5ad | Chris Miller | 06 February 2014, 02:52:10 UTC | added code to prevent negative numbers for minimum insert size | 06 February 2014, 02:52:31 UTC |
| 8685bdd | Malachi Griffith | 06 February 2014, 01:52:16 UTC | add modules so that cancer-gene-list can be accessed via Genome::Db | 06 February 2014, 01:52:16 UTC |
| 59c1385 | Eddie Belter | 06 February 2014, 00:29:33 UTC | Alignment Result: add class for aligners having intermediate results | 06 February 2014, 00:30:10 UTC |
| 8c66ca6 | Eddie Belter | 05 February 2014, 20:35:52 UTC | AR: store iar id to test removal | 06 February 2014, 00:30:09 UTC |
| 6b56ceb | Eddie Belter | 05 February 2014, 20:35:21 UTC | AR: rm dumper statement | 06 February 2014, 00:30:09 UTC |
| 2c09aac | Eddie Belter | 05 February 2014, 20:34:34 UTC | BWA IAR: rm redundant command | 06 February 2014, 00:30:08 UTC |
| fa7ef99 | Eddie Belter | 05 February 2014, 19:50:07 UTC | BWA AR: use intermediate class directly instead of command class | 06 February 2014, 00:30:07 UTC |
| 5aa9d34 | Eddie Belter | 05 February 2014, 19:41:46 UTC | BWA AR: update messages | 06 February 2014, 00:30:07 UTC |
| b64992d | Eddie Belter | 05 February 2014, 19:30:34 UTC | BWA AR: move intermediate params outside of each pass | 06 February 2014, 00:30:06 UTC |
| 0ab0281 | Eddie Belter | 05 February 2014, 19:26:04 UTC | BWA AR: add user to intermedaite result right after creating | 06 February 2014, 00:30:05 UTC |
| 0d3901e | Eddie Belter | 05 February 2014, 19:24:37 UTC | BWA AR: check that intermediate results are removed | 06 February 2014, 00:30:05 UTC |
| 229ebd5 | Eddie Belter | 05 February 2014, 19:23:36 UTC | Alignment Result: removes underlying intermediate results | 06 February 2014, 00:30:04 UTC |
| 8fef958 | Ben Ainscough | 05 February 2014, 23:15:12 UTC | changed hardcoded cancer_annotation_db | 05 February 2014, 23:15:12 UTC |
| 9d5ce45 | Jim Weible | 05 February 2014, 20:48:37 UTC | Remove useless temp files Remove the last output temp files these tests were creating. Inability to remove them because of file permissions was breaking tests. | 05 February 2014, 20:48:37 UTC |
| 38613de | Jim Weible | 04 February 2014, 14:28:28 UTC | change warning to debug message for AUE-19 | 05 February 2014, 15:35:11 UTC |
| b786f94 | Jim Weible | 29 January 2014, 16:27:00 UTC | change noisy status messages to debug_messages | 05 February 2014, 15:35:11 UTC |
| 30b1058 | Thomas Mooney | 05 February 2014, 15:18:11 UTC | Test whether the boolean is true, not whether self is true! | 05 February 2014, 15:18:11 UTC |
| 80bc696 | Eddie Belter | 04 February 2014, 23:49:49 UTC | BWA AR: modernize and simplify test | 04 February 2014, 23:49:49 UTC |
| 37005b6 | Eddie Belter | 04 February 2014, 21:30:26 UTC | BWA AR: get or create aligner index | 04 February 2014, 21:30:26 UTC |
| ddc8509 | Eddie Belter | 04 February 2014, 21:28:24 UTC | Revert "BWA AR: remove indexing ref in test" This reverts commit 26f6cda8d7e07fea66423888fa6c08201484126c. | 04 February 2014, 21:28:24 UTC |
| 26f6cda | Eddie Belter | 04 February 2014, 21:19:40 UTC | BWA AR: remove indexing ref in test | 04 February 2014, 21:19:40 UTC |
| 583f745 | Malachi Griffith | 04 February 2014, 16:39:42 UTC | clin-seq - snv-indel-report - add gene labeling and variant tracking over time to plots | 04 February 2014, 16:39:42 UTC |
| dc7cac2 | Thomas Mooney | 04 February 2014, 15:04:47 UTC | Still run the child query when testing allocations. | 04 February 2014, 15:04:47 UTC |
| 06352ad | APipe Tester | 04 February 2014, 13:17:30 UTC | Updated `genome` tab completion. | 04 February 2014, 13:17:30 UTC |
| 8cd6b87 | APipe Tester | 04 February 2014, 13:15:49 UTC | Updated class browser cache. | 04 February 2014, 13:15:49 UTC |
| 3151ea1 | APipe Tester | 03 February 2014, 22:35:34 UTC | updated graphite submodule to 00ac7bb | 03 February 2014, 22:35:34 UTC |
| 252b7ed | Anthony Brummett | 03 February 2014, 22:28:38 UTC | Update blessed build for rnaseq test model Jason Walker changed some metadata for its instrument data which lead to different tophat args related to inner insert size | 03 February 2014, 22:32:37 UTC |
| 4f924c0 | Mark Burnett | 03 February 2014, 22:06:29 UTC | don't check for child allocations during testing | 03 February 2014, 22:06:29 UTC |
| d5a007b | Malachi Griffith | 03 February 2014, 20:52:45 UTC | clin-seq: further tweaks to snv-indel report graphics | 03 February 2014, 20:52:45 UTC |
| b9ba593 | Jim Weible | 03 February 2014, 19:44:47 UTC | remove all the database stuff from these, since it no longer matters | 03 February 2014, 19:47:51 UTC |
| 75adf64 | Jim Weible | 03 February 2014, 19:31:03 UTC | remove unused cruft | 03 February 2014, 19:47:49 UTC |
| abe5dd8 | APipe Tester | 03 February 2014, 19:40:07 UTC | updated jenkins submodule to ad9380d | 03 February 2014, 19:40:07 UTC |
| 646ed11 | apregier | 03 February 2014, 18:51:54 UTC | Merge branch 'updated' into gb_master | 03 February 2014, 18:51:54 UTC |
| e71ecca | apregier | 03 February 2014, 18:50:41 UTC | Add error message for duplicate annotations | 03 February 2014, 18:50:59 UTC |
| ee8b272 | apregier | 03 February 2014, 18:32:54 UTC | rsids are optional and don't cause warnings if not there | 03 February 2014, 18:50:58 UTC |
| 68ffca0 | Jim Weible | 29 January 2014, 15:10:12 UTC | move fastq files to temp_staging_directory to avoid filling up temp. also, cleanup afterwards | 03 February 2014, 18:48:29 UTC |
| 17f0da0 | Jim Weible | 27 January 2014, 16:44:36 UTC | clean up our temp space after we use it so we do not run out | 03 February 2014, 18:48:28 UTC |
| 93840be | APipe Tester | 01 February 2014, 13:18:05 UTC | Updated `gmt` tab completion. | 01 February 2014, 13:18:05 UTC |
| 589693d | APipe Tester | 01 February 2014, 13:17:19 UTC | Updated `genome` tab completion. | 01 February 2014, 13:17:19 UTC |
| 1bb350e | APipe Tester | 01 February 2014, 13:15:42 UTC | Updated class browser cache. | 01 February 2014, 13:15:42 UTC |
| 01d1708 | Gabriel Sanderson | 31 January 2014, 22:24:15 UTC | Fixed |= -> ||= , we were doing a bitwise or when we did not mean to be | 31 January 2014, 22:24:47 UTC |
| 77e03be | Dave Larson | 31 January 2014, 22:07:28 UTC | partially finished script for adding menu items to existing projects | 31 January 2014, 22:07:44 UTC |
| 17661ff | Malachi Griffith | 31 January 2014, 21:04:23 UTC | various fixes to snv-indel-report to cover edge cases encountered with small test variant lists | 31 January 2014, 21:04:23 UTC |
| 7d66cb2 | apregier | 31 January 2014, 18:52:43 UTC | Merge branch 'updated' into gb_master | 31 January 2014, 18:52:43 UTC |
| 2c714eb | apregier | 31 January 2014, 18:51:26 UTC | Update status messages so they reflect what is happening. | 31 January 2014, 18:51:26 UTC |
| 1bf6c7f | Avinash Ramu | 31 January 2014, 16:42:28 UTC | new somatic variation build used in clinseq couple of things - new somatic variation build has different variants, changes to bam read counts by chris miller and changes to the DV2 filter might be causing the diffs with the previous blessed build. | 31 January 2014, 16:42:28 UTC |
| cb3cbac | APipe Tester | 31 January 2014, 13:19:30 UTC | Updated `genome` tab completion. | 31 January 2014, 13:19:30 UTC |
