| 8a7edd8 | Thomas B. Mooney | 21 October 2015, 13:14:20 UTC | Merge pull request #1060 from tmooney/stop_testing_58 Stop testing that Genome classes work under older Perl. | 21 October 2015, 13:14:20 UTC |
| 4a18780 | APipe Tester | 20 October 2015, 19:36:45 UTC | updated ur submodule to 45bb80e | 20 October 2015, 20:56:27 UTC |
| c65add8 | Thomas B. Mooney | 20 October 2015, 20:11:24 UTC | Merge pull request #1057 from tmooney/java7_in_gatk Make Java 1.7 the default for running GATK tools. | 20 October 2015, 20:11:24 UTC |
| 58c4230 | Thomas B. Mooney | 20 October 2015, 19:12:49 UTC | Merge pull request #1055 from tmooney/remove_db_skip_postgres Remove old db_skip_postgres configuration variable. | 20 October 2015, 19:12:49 UTC |
| 0b13da1 | Thomas Mooney | 19 October 2015, 20:56:36 UTC | Stop testing that Genome classes work under older Perl. | 19 October 2015, 20:56:36 UTC |
| 2f15f25 | Thomas Mooney | 19 October 2015, 19:34:49 UTC | Make Java 1.7 the default for GATK. | 19 October 2015, 19:39:51 UTC |
| 6c94eb7 | Thomas B. Mooney | 19 October 2015, 14:03:13 UTC | Merge pull request #1054 from tmooney/use_array_form_in_import_helper_shellcmd Use array form of shellcmd. | 19 October 2015, 14:03:13 UTC |
| 9942417 | APipe Tester | 15 October 2015, 20:45:11 UTC | updated workflow submodule to c0f1230 | 15 October 2015, 20:45:11 UTC |
| dfe51e3 | Thomas Mooney | 15 October 2015, 20:24:32 UTC | Remove old db_skip_postgres configuration variable. | 15 October 2015, 20:24:32 UTC |
| 13e2f3d | Thomas Mooney | 15 October 2015, 19:15:31 UTC | Use array form of shellcmd. | 15 October 2015, 19:15:31 UTC |
| f4e03af | Thomas B. Mooney | 15 October 2015, 16:49:11 UTC | Merge pull request #1053 from tmooney/add_run_as_to_mc16s_test_factory_model Add run_as to test factory model. | 15 October 2015, 16:49:11 UTC |
| c10972d | Dan Koboldt | 15 October 2015, 16:34:36 UTC | Added LSF log output files | 15 October 2015, 16:34:36 UTC |
| 520b980 | Thomas B. Mooney | 15 October 2015, 16:21:25 UTC | Merge pull request #1051 from tmooney/alignandmerge_lsf_resource_determination_to_command Move AlignAndMerge LSF Resource generation to the command. | 15 October 2015, 16:21:25 UTC |
| 3404f3e | Thomas Mooney | 15 October 2015, 14:03:46 UTC | Add run_as to test factory model. That way G:SR:User->user_hash_for_build() can find a sponsor. | 15 October 2015, 14:03:46 UTC |
| 3e1c832 | Thomas B. Mooney | 14 October 2015, 20:10:04 UTC | Merge pull request #1043 from tmooney/disable_indexing_in_mutect Disable index creation in `gmt mutect`. | 14 October 2015, 20:10:04 UTC |
| c235827 | APipe Tester | 14 October 2015, 17:52:08 UTC | updated jenkins submodule to b67763e | 14 October 2015, 19:44:48 UTC |
| e1791c8 | mkiwala | 14 October 2015, 19:38:43 UTC | Merge pull request #1027 from davidlmorton/genome-ptero-lsf-integration Genome ptero lsf integration | 14 October 2015, 19:38:43 UTC |
| 7ff2f2d | Thomas B. Mooney | 14 October 2015, 18:53:11 UTC | Merge pull request #1050 from tmooney/typos_in_instrument_data_launch Fix typos in InstrumentData Import Launcher | 14 October 2015, 18:53:11 UTC |
| be94f1a | Eddie Belter | 14 October 2015, 17:51:57 UTC | Merge pull request #1052 from gatoravi/update_clinseq_blessed Build with results from https://github.com/genome/genome/pull/1012 | 14 October 2015, 17:51:57 UTC |
| 73fdaa8 | APipe Tester | 14 October 2015, 12:18:48 UTC | Updated `gmt` tab completion. | 14 October 2015, 12:18:48 UTC |
| 409a261 | APipe Tester | 14 October 2015, 12:17:58 UTC | Updated `genome` tab completion. | 14 October 2015, 12:17:58 UTC |
| 8888d3e | Eddie Belter | 13 October 2015, 21:45:14 UTC | Merge pull request #1042 from ebelter/instdata-import-use-rgid-as-instdata-id Inst Data Import: use read group id as instdata id | 13 October 2015, 21:45:14 UTC |
| 62394e3 | Avinash Ramu | 13 October 2015, 21:19:55 UTC | Update to reflect https://github.com/genome/genome/pull/1012 \#1012 switched to separatedvaluereader from an incorrect regex. The updated blessed-build has the correct results. | 13 October 2015, 21:19:55 UTC |
| 0f8ba75 | Eddie Belter | 13 October 2015, 20:52:58 UTC | InstData Import: die when setting headers/read groups | 13 October 2015, 20:52:58 UTC |
| d648d98 | Eddie Belter | 13 October 2015, 20:47:40 UTC | InstData Import: chomp line | 13 October 2015, 20:47:40 UTC |
| 8f9afc6 | Eddie Belter | 13 October 2015, 20:46:58 UTC | InstData Import: set autogen uuid outside of helper sub | 13 October 2015, 20:46:58 UTC |
| a22ed57 | Eddie Belter | 13 October 2015, 20:45:09 UTC | InstData Import: update debug msgs | 13 October 2015, 20:45:09 UTC |
| f502619 | Eddie Belter | 13 October 2015, 20:44:09 UTC | InstData Import: die error instead of return undef | 13 October 2015, 20:44:09 UTC |
| 6122ee1 | Eddie Belter | 13 October 2015, 20:43:25 UTC | InstData Import: do not catch rv of _write_reads_based_on_read_group_and_pairedness | 13 October 2015, 20:43:25 UTC |
| 9d5d6ae | Thomas Mooney | 13 October 2015, 20:01:05 UTC | In this new location, $class already holds the class we need. | 13 October 2015, 20:01:05 UTC |
| 243cf7b | Thomas Mooney | 06 October 2015, 20:22:43 UTC | Move LSF Resource string generation to the command. | 13 October 2015, 19:58:13 UTC |
| 5ec6886 | Thomas B. Mooney | 13 October 2015, 19:28:07 UTC | Merge pull request #1048 from tmooney/intervals_for_genotype_caller Add intervals parameter for GATK HaplotypeCaller | 13 October 2015, 19:28:07 UTC |
| 677d2e9 | Thomas B. Mooney | 13 October 2015, 19:27:56 UTC | Merge pull request #1047 from tmooney/test_factory_for_speedseq_results Create a Test Factory for speedseq results. | 13 October 2015, 19:27:56 UTC |
| 6677317 | Thomas Mooney | 13 October 2015, 18:49:12 UTC | Fix another typo, add serial comma and pluralization! | 13 October 2015, 18:49:12 UTC |
| 269e4a1 | Anthony Brummett | 13 October 2015, 18:17:03 UTC | Merge pull request #1028 from brummett/volume-lister Make the volume lister work | 13 October 2015, 18:17:03 UTC |
| 83b0808 | Avi Ramu | 13 October 2015, 16:51:18 UTC | Merge pull request #1049 from gatoravi/clinseq_ignore_dgidb_diff Add a dgidb file to files ignored by diff. | 13 October 2015, 16:51:18 UTC |
| 22461f1 | Thomas Mooney | 13 October 2015, 15:37:32 UTC | Fix typos. | 13 October 2015, 15:37:32 UTC |
| 1ccd412 | Susanna Kiwala | 13 October 2015, 15:04:16 UTC | Merge pull request #1046 from susannasiebert/qc_lsf_resources Set queue to apipe-pd and request 4 slots instead of 6 for QC runs | 13 October 2015, 15:04:16 UTC |
| 2663d22 | Avinash Ramu | 13 October 2015, 14:35:13 UTC | Add a dgidb file to files ignored by diff. | 13 October 2015, 14:35:13 UTC |
| 2d0736f | APipe Tester | 13 October 2015, 12:17:46 UTC | Updated `gmt` tab completion. | 13 October 2015, 12:17:46 UTC |
| b6fadeb | APipe Tester | 13 October 2015, 12:16:58 UTC | Updated `genome` tab completion. | 13 October 2015, 12:16:58 UTC |
| b68e16a | Thomas Mooney | 12 October 2015, 20:32:55 UTC | Add read filters option as well. | 12 October 2015, 20:32:55 UTC |
| 3c9fd6d | Thomas Mooney | 06 October 2015, 21:52:17 UTC | Add intervals parameter for GATK HaplotypeCaller | 12 October 2015, 19:28:43 UTC |
| aced5a0 | Thomas Mooney | 07 October 2015, 20:02:57 UTC | Create a test factory for speedseq results. | 12 October 2015, 19:11:17 UTC |
| c41887c | Susanna Kiwala | 12 October 2015, 18:25:27 UTC | Move lsf_resource to a genome config | 12 October 2015, 18:25:27 UTC |
| 899571c | Susanna Kiwala | 12 October 2015, 18:24:05 UTC | Use lsf_queue param to specify desired queue | 12 October 2015, 18:24:05 UTC |
| 2eea781 | Chris Miller | 12 October 2015, 17:55:49 UTC | Merge pull request #1037 from chrisamiller/process adds EVS maf columns | 12 October 2015, 17:55:49 UTC |
| 1d6e7dc | Susanna Kiwala | 12 October 2015, 15:26:12 UTC | Set queue to apipe-pd and request 4 slots instead of 6 for QC runs | 12 October 2015, 17:32:15 UTC |
| d0f92bf | David Morton | 12 October 2015, 17:24:31 UTC | Merge pull request #882 from rfugina/parse_lsf_memlimit Parse MEMLIMIT with units, normalize to kb as expected | 12 October 2015, 17:24:31 UTC |
| 35a8d2e | Chris Miller | 12 October 2015, 16:14:42 UTC | deduping code | 12 October 2015, 16:14:42 UTC |
| cad559f | dmorton | 12 October 2015, 15:39:04 UTC | Move Utility/LSFResourceParser to Sys/LSF/ResourceParser | 12 October 2015, 15:42:48 UTC |
| 4e274d5 | dmorton | 12 October 2015, 15:20:37 UTC | Use Genome::Config::set_env, add missing lsf_service_url | 12 October 2015, 15:28:45 UTC |
| ca2b5ed | dmorton | 30 September 2015, 17:54:18 UTC | Change 'execute' jobs to use LSF | 12 October 2015, 15:28:45 UTC |
| 73d39fb | dmorton | 30 September 2015, 17:50:23 UTC | Add ptero_lsf_service_url config | 12 October 2015, 15:28:45 UTC |
| d209d11 | Michael J. Kiwala | 11 September 2015, 15:27:32 UTC | Add support for lsf maxNumProcessors submit field | 12 October 2015, 15:28:45 UTC |
| 330d545 | Michael J. Kiwala | 11 September 2015, 14:51:14 UTC | Fix some invalid lsf_resource specifications | 12 October 2015, 15:28:45 UTC |
| 28fe017 | Michael J. Kiwala | 10 September 2015, 20:42:16 UTC | LSF Resource Parser | 12 October 2015, 15:28:44 UTC |
| db969f1 | Chris Miller | 12 October 2015, 14:53:08 UTC | Merge pull request #1032 from chrisamiller/llr Adds sanity checks to header and required cols | 12 October 2015, 14:53:08 UTC |
| d720d5b | Thomas B. Mooney | 12 October 2015, 14:36:08 UTC | Merge pull request #1039 from tmooney/refalign_microarray_concordance_picard_metrics Bugfix for RefAlign GenotypeMicroarray metric parsing | 12 October 2015, 14:36:08 UTC |
| 776425e | Thomas B. Mooney | 12 October 2015, 13:27:08 UTC | Merge pull request #1012 from kkrysiak/correct_makecircosplot fixed broken regex to appropriately display RNA expression | 12 October 2015, 13:27:08 UTC |
| 9f7a239 | Chris Miller | 09 October 2015, 01:21:18 UTC | removes unused variable | 09 October 2015, 01:21:18 UTC |
| 6482c23 | Thomas Mooney | 08 October 2015, 21:55:48 UTC | Disable index creation in `gmt mutect`. When run in the pipeline it uses a hardcoded ROD that should already be indexed. (See also <http://gatkforums.broadinstitute.org/discussion/1252/unifiedgenotyper-gets-hung-waiting-for-file-lock> for more information.) | 08 October 2015, 21:55:48 UTC |
| fcc28c6 | Eddie Belter | 08 October 2015, 21:27:37 UTC | InstData Import: update basic tests rg_ids | 08 October 2015, 21:45:44 UTC |
| 1bf3c2c | Eddie Belter | 08 October 2015, 21:22:27 UTC | InstData Import: update basic bam multi rg | 08 October 2015, 21:45:44 UTC |
| 6b08fcc | Eddie Belter | 08 October 2015, 20:39:17 UTC | InstData Import: Split by RG generate read groups on demand from reads instead of from header | 08 October 2015, 21:45:43 UTC |
| de983c6 | Eddie Belter | 08 October 2015, 20:38:31 UTC | InstData Import: update SRA import test | 08 October 2015, 21:45:42 UTC |
| 9bbb73a | Eddie Belter | 07 October 2015, 22:31:31 UTC | InstData Import: update basic downsample bam test | 08 October 2015, 21:45:41 UTC |
| ab19329 | Eddie Belter | 07 October 2015, 21:49:17 UTC | InstData Import: more tests use consolidated data dir | 08 October 2015, 21:45:41 UTC |
| e1f2547 | Eddie Belter | 06 October 2015, 19:36:52 UTC | InstData: fastq tests use consolidated data dir | 08 October 2015, 21:45:40 UTC |
| d4aa20a | Eddie Belter | 06 October 2015, 19:32:05 UTC | InstData: fix basic archive fastq test | 08 October 2015, 21:45:39 UTC |
| b18f843 | Eddie Belter | 06 October 2015, 19:23:50 UTC | InstData: fix basic bam test | 08 October 2015, 21:45:39 UTC |
| b822ae3 | Eddie Belter | 06 October 2015, 17:21:33 UTC | InstData Import: chomp last sam token, add debug msgs | 08 October 2015, 21:45:38 UTC |
| 04f2c82 | Eddie Belter | 05 October 2015, 22:56:14 UTC | InstData Import: add uuid overload to helpers | 08 October 2015, 21:45:37 UTC |
| d90cd72 | Eddie Belter | 02 October 2015, 22:22:04 UTC | InstData Import: add new rg_id for singletons | 08 October 2015, 21:45:37 UTC |
| b059c1f | Eddie Belter | 02 October 2015, 22:21:23 UTC | InstData Import: use read group id as instdata id | 08 October 2015, 21:45:36 UTC |
| daff515 | Eddie Belter | 02 October 2015, 22:11:08 UTC | InstData Import: create instdata test use new bams with updated read groups | 08 October 2015, 21:45:35 UTC |
| 702db34 | Eddie Belter | 02 October 2015, 21:39:32 UTC | InstData Import: use File::Spec in create instdata test | 08 October 2015, 21:45:35 UTC |
| 7f14f1e | Eddie Belter | 02 October 2015, 21:26:31 UTC | InstData Import: spell check | 08 October 2015, 21:45:34 UTC |
| 5ebd2d1 | Eddie Belter | 02 October 2015, 21:09:15 UTC | InstData Import: rename write reads to process reads | 08 October 2015, 21:45:33 UTC |
| e6051d9 | Eddie Belter | 02 October 2015, 21:08:35 UTC | InstData Import: remove unused read group ids var and property | 08 October 2015, 21:45:32 UTC |
| 78d6a40 | Eddie Belter | 02 October 2015, 21:06:15 UTC | InstData Import: split out getting rg_id and updating to new rg_id | 08 October 2015, 21:45:32 UTC |
| fbbca35 | Eddie Belter | 02 October 2015, 20:59:57 UTC | InstData Import: add writing of reads to method of getting fh to write to | 08 October 2015, 21:45:31 UTC |
| a3e4c3d | Eddie Belter | 02 October 2015, 20:31:50 UTC | InstData Import: separate hash for old to new rg id mapping | 08 October 2015, 21:45:30 UTC |
| 333abe5 | Eddie Belter | 01 October 2015, 22:54:50 UTC | InstData Import: split by rg converts rg ids to instdata ids | 08 October 2015, 21:45:29 UTC |
| ff27187 | Eddie Belter | 01 October 2015, 22:19:06 UTC | InstData Import: add unknown read group during setting of read groups | 08 October 2015, 21:45:28 UTC |
| 9128756 | Eddie Belter | 01 October 2015, 22:13:41 UTC | InstData Import: split by rg uses rg tags | 08 October 2015, 21:45:28 UTC |
| ddc7b34 | Eddie Belter | 01 October 2015, 22:13:11 UTC | InstData Import: more stringent test for split by rg | 08 October 2015, 21:45:26 UTC |
| c65dd94 | Eddie Belter | 01 October 2015, 21:05:05 UTC | InstData Import: return RG tags instead of line from read_groups_and_tags_from_headers | 08 October 2015, 21:45:25 UTC |
| 68e9ab8 | Eddie Belter | 01 October 2015, 20:55:02 UTC | InstData Import: use throws_ok instead of eval | 08 October 2015, 21:45:24 UTC |
| bffa712 | Eddie Belter | 30 September 2015, 22:54:45 UTC | InstData Import: print/store split token instead of lines | 08 October 2015, 21:45:24 UTC |
| 71b4a91 | Eddie Belter | 30 September 2015, 22:29:50 UTC | InstData Import: remove unused removed_reads_cnt | 08 October 2015, 21:45:23 UTC |
| e15618a | Eddie Belter | 29 September 2015, 22:35:08 UTC | InstData Import: use autogen id for read group id in fastq to bam | 08 October 2015, 21:45:22 UTC |
| 744b6c2 | Thomas Mooney | 08 October 2015, 18:26:06 UTC | Fix for new metric parsing. | 08 October 2015, 18:26:06 UTC |
| 122c6ea | Allison Penner Regier | 08 October 2015, 15:46:31 UTC | Merge pull request #1008 from apregier/bedToVcfFix Create a valid vcf | 08 October 2015, 15:46:31 UTC |
| 20a1dbd | Thomas B. Mooney | 07 October 2015, 22:25:34 UTC | Merge pull request #1030 from tmooney/speedup_usage_log In the UsageLog, don't call getpwuid. | 07 October 2015, 22:25:34 UTC |
| 0c18b44 | Chris Miller | 07 October 2015, 21:32:48 UTC | cleaner implementation | 07 October 2015, 21:32:48 UTC |
| 21ed4d2 | APipe Tester | 07 October 2015, 17:41:38 UTC | updated ur submodule to 91eae3e | 07 October 2015, 17:41:38 UTC |
| 43101e7 | Thomas B. Mooney | 07 October 2015, 15:25:56 UTC | Merge pull request #1035 from tmooney/add_delay_in_wait_for_lsf_jobs Wait 10s before checking status of LSF jobs again. | 07 October 2015, 15:25:56 UTC |
| a5d0895 | APipe Tester | 07 October 2015, 12:18:25 UTC | Updated `genome` tab completion. | 07 October 2015, 12:18:25 UTC |
| 48d0801 | Thomas B. Mooney | 06 October 2015, 20:27:29 UTC | Merge pull request #1036 from tmooney/build_start_unit_test_doesnt_launch_builds Don't really start builds in this test. | 06 October 2015, 20:27:29 UTC |
