beeaab2 | Thomas B. Mooney | 20 July 2016, 19:51:15 UTC | Don't warn when there's no LSB_SUB_ADDITIONAL variable defined. | 20 July 2016, 19:51:15 UTC |
9f3365d | Thomas B. Mooney | 20 July 2016, 19:47:13 UTC | Stop warning about undefined environment variables. Users don't really care about the limitations of the environment compared to Perl hashes. | 20 July 2016, 19:47:13 UTC |
591ccce | Thomas B. Mooney | 19 July 2016, 13:45:13 UTC | Merge pull request #1480 from tmooney/somvar_uses_workflowbuilder SomVar uses WorkflowBuilder | 19 July 2016, 13:45:13 UTC |
ebcc5d1 | Thomas B. Mooney | 19 July 2016, 13:44:47 UTC | Merge pull request #1481 from tmooney/mc16s_uses_workflowbuilder Convert MC16s workflow generation to WorkflowBuilder. | 19 July 2016, 13:44:47 UTC |
6a6dcbd | APipe Tester | 19 July 2016, 12:19:21 UTC | Updated `gmt` tab completion. | 19 July 2016, 12:19:21 UTC |
93199bf | APipe Tester | 19 July 2016, 12:18:37 UTC | Updated `genome` tab completion. | 19 July 2016, 12:18:37 UTC |
640bc03 | Thomas B. Mooney | 18 July 2016, 19:34:28 UTC | Merge pull request #1499 from tmooney/add_error_to_instantation_failure_message Add error to instantiation failure message. | 18 July 2016, 19:34:28 UTC |
3462b8e | Jason Walker | 18 July 2016, 18:07:38 UTC | Merge pull request #1500 from jasonwalker80/remove_sata132_jwalker Remove references to sata132/jwalker file paths. | 18 July 2016, 18:07:38 UTC |
09212f6 | Feiyu Du | 18 July 2016, 16:30:12 UTC | Merge pull request #1504 from dufeiyu/empty_bed_merge Make trio wrapper merge work if one of input reports is empty | 18 July 2016, 16:30:12 UTC |
7c7af8e | Malachi Griffith | 18 July 2016, 16:16:56 UTC | Merge pull request #1505 from malachig/master clean up all references to gscmnt paths | 18 July 2016, 16:16:56 UTC |
2204b1f | Jason Walker | 18 July 2016, 14:58:08 UTC | correct syntax for example_values | 18 July 2016, 14:58:08 UTC |
c52ff64 | Malachi Griffith | 15 July 2016, 21:28:56 UTC | update test to use cancer gene list instead of aml rmg list | 15 July 2016, 21:28:56 UTC |
1ee96eb | Malachi Griffith | 15 July 2016, 20:08:38 UTC | clean up references to specific gscmnt paths | 15 July 2016, 20:08:38 UTC |
1c3e45a | Malachi Griffith | 15 July 2016, 19:25:22 UTC | remove old readme | 15 July 2016, 19:25:22 UTC |
c481ed2 | Feiyu Du | 14 July 2016, 21:25:36 UTC | add test case to unit test | 14 July 2016, 21:25:36 UTC |
e816435 | Feiyu Du | 14 July 2016, 15:52:06 UTC | Make merge work if base or supplemental report is empty | 14 July 2016, 15:52:06 UTC |
c1aa03c | Thomas B. Mooney | 14 July 2016, 15:03:41 UTC | Merge pull request #1496 from tmooney/remove_lsf_queue_alignment_prod Remove "lsf_queue_alignment_prod" config. | 14 July 2016, 15:03:41 UTC |
fb18469 | Thomas B. Mooney | 13 July 2016, 16:57:40 UTC | Merge pull request #1449 from tmooney/keep_logs_around_when_ptero_postexec_fails Keep logs around when Ptero's post-exec fails. | 13 July 2016, 16:57:40 UTC |
15092b9 | Thomas B. Mooney | 13 July 2016, 16:57:34 UTC | Merge pull request #1501 from tmooney/remember_the_annotate_snvs_vcf_op Only create one annotate_snvs_vcf_op per type. | 13 July 2016, 16:57:34 UTC |
2be846e | Thomas B. Mooney | 13 July 2016, 15:25:18 UTC | Use the passed-in log directory. | 13 July 2016, 15:25:18 UTC |
37fa620 | APipe Tester | 13 July 2016, 12:18:35 UTC | Updated `gmt` tab completion. | 13 July 2016, 12:18:35 UTC |
85b9378 | APipe Tester | 13 July 2016, 12:17:53 UTC | Updated `genome` tab completion. | 13 July 2016, 12:17:53 UTC |
5c102db | APipe Tester | 13 July 2016, 12:16:25 UTC | Updated class browser cache. | 13 July 2016, 12:16:25 UTC |
95dc9f7 | Thomas B. Mooney | 12 July 2016, 20:53:21 UTC | Merge pull request #1479 from tmooney/remove_parallel_commands Remove GMTs that relied on Workflow integration. | 12 July 2016, 20:53:21 UTC |
f12d105 | Thomas B. Mooney | 12 July 2016, 20:21:16 UTC | Merge pull request #1484 from tmooney/remove_old_individual_cpudisksummary_command Remove `genome individual cpu-disk-summary`. | 12 July 2016, 20:21:16 UTC |
71a6825 | Thomas B. Mooney | 12 July 2016, 19:25:52 UTC | Merge pull request #1452 from tmooney/ptero_prepostexec_uses_docker Fix ptero-lsf-{pre,post}-exec within docker | 12 July 2016, 19:25:52 UTC |
97ac184 | Thomas B. Mooney | 12 July 2016, 19:02:14 UTC | Merge pull request #1497 from tmooney/ptero_null_command_uses_queue_config Use config to decide the LSF queue (Ptero NullCommand) | 12 July 2016, 19:02:14 UTC |
ebd0033 | Thomas B. Mooney | 12 July 2016, 19:01:25 UTC | Merge pull request #1478 from tmooney/parameterize_files_in_germline_filtering Replace hard-coded NHLBI and 1000 Genomes files with parameters. | 12 July 2016, 19:01:25 UTC |
3fb2e19 | Thomas B. Mooney | 09 June 2016, 22:06:11 UTC | Update expected pre and post-exec strings in JSON. | 12 July 2016, 19:00:05 UTC |
b88c75c | Thomas B. Mooney | 12 July 2016, 18:48:13 UTC | Only create one annotate_snvs_vcf_op per type. | 12 July 2016, 18:48:13 UTC |
9ed95be | Thomas B. Mooney | 12 July 2016, 18:33:12 UTC | Merge pull request #1476 from tmooney/remove_pindel_modelgroup_command Remove old `gmt pindel run-pindel-model-group` command. | 12 July 2016, 18:33:12 UTC |
69e442f | Thomas B. Mooney | 09 June 2016, 18:04:00 UTC | Use full path to pre and post-exec commands. | 12 July 2016, 18:24:00 UTC |
0dae693 | Thomas B. Mooney | 08 June 2016, 21:15:13 UTC | Make sure pre- and post-exec run within the docker container, too. | 12 July 2016, 18:24:00 UTC |
a6068ba | Thomas B. Mooney | 12 July 2016, 18:23:01 UTC | Merge pull request #1453 from tmooney/remove_old_assembly_tools_that_use_workflow Remove old Assembly tools that use Workflow. | 12 July 2016, 18:23:01 UTC |
d0e9910 | Thomas B. Mooney | 12 July 2016, 18:17:49 UTC | Merge pull request #1493 from tmooney/workflow_builder_default_queue Use Config to Select a Default LSF Queue if None Specified | 12 July 2016, 18:17:49 UTC |
332e187 | Thomas B. Mooney | 12 July 2016, 18:15:34 UTC | Merge pull request #1454 from tmooney/remove_old_polymuttpipeline Remove old "PolymuttPipeline" workflow tool. | 12 July 2016, 18:15:34 UTC |
597a6dc | Thomas B. Mooney | 12 July 2016, 18:15:20 UTC | Merge pull request #1487 from tmooney/validate_svs_steps_specify_lsf_queues Specify a default queue in several SomVal steps. | 12 July 2016, 18:15:20 UTC |
f0a0496 | APipe Tester | 12 July 2016, 12:15:38 UTC | Updated `genome` tab completion. | 12 July 2016, 12:15:38 UTC |
e3cd4c3 | APipe Tester | 12 July 2016, 12:14:05 UTC | Updated class browser cache. | 12 July 2016, 12:14:05 UTC |
1729336 | Thomas B. Mooney | 11 July 2016, 13:09:42 UTC | Merge pull request #1498 from tmooney/disk_usage_summary_command_for_software_results Command to summarize disk usage of SoftwareResults by Sponsor. | 11 July 2016, 13:09:42 UTC |
056cd1b | Jason Walker | 08 July 2016, 16:06:22 UTC | Remove references to sata132/jwalker file paths. | 08 July 2016, 16:06:22 UTC |
ce6f1b3 | APipe Tester | 08 July 2016, 12:16:59 UTC | Updated `gmt` tab completion. | 08 July 2016, 12:16:59 UTC |
d142b06 | APipe Tester | 08 July 2016, 12:16:20 UTC | Updated `genome` tab completion. | 08 July 2016, 12:16:20 UTC |
6eff3bf | Thomas B. Mooney | 07 July 2016, 21:30:46 UTC | Replace "die(error_message())" with "fatal_message()" | 07 July 2016, 21:30:46 UTC |
7d3cc59 | Thomas B. Mooney | 07 July 2016, 21:29:26 UTC | Report the error in loading the class. | 07 July 2016, 21:29:26 UTC |
5185ebc | Thomas B. Mooney | 07 July 2016, 19:56:16 UTC | Command to summarize disk usage of SoftwareResults by Sponsor. This is a slightly polished-up version of a script from past meetings. | 07 July 2016, 19:57:47 UTC |
164b644 | Thomas B. Mooney | 07 July 2016, 12:42:37 UTC | Merge pull request #1492 from tmooney/specify_queue_in_plot_segments Specify a default LSF queue in CopyNumber PlotSegments | 07 July 2016, 12:42:37 UTC |
3e84bc5 | Thomas B. Mooney | 06 July 2016, 21:56:29 UTC | Use config to decide the LSF queue. | 06 July 2016, 21:56:29 UTC |
8b310da | Thomas B. Mooney | 06 July 2016, 20:20:37 UTC | Remove lsf_queue_alignment_prod config. We haven't used this for anything in awhile. | 06 July 2016, 20:20:37 UTC |
e9d7ce6 | Thomas B. Mooney | 05 July 2016, 15:51:08 UTC | Specify a default LSF queue if the command doesn't have one. | 06 July 2016, 14:09:34 UTC |
69dc2f7 | APipe Tester | 06 July 2016, 12:18:29 UTC | Updated `gmt` tab completion. | 06 July 2016, 12:18:29 UTC |
75243d7 | APipe Tester | 06 July 2016, 12:17:44 UTC | Updated `genome` tab completion. | 06 July 2016, 12:17:44 UTC |
33f82f3 | APipe Tester | 06 July 2016, 12:16:18 UTC | Updated class browser cache. | 06 July 2016, 12:16:18 UTC |
08e9509 | Thomas B. Mooney | 05 July 2016, 18:24:57 UTC | Ignore any LSF queue specifications. | 05 July 2016, 18:27:00 UTC |
eade6d2 | Thomas B. Mooney | 05 July 2016, 18:23:30 UTC | Spelling: mathes => matches | 05 July 2016, 18:27:00 UTC |
b02fcff | Thomas B. Mooney | 05 July 2016, 15:51:46 UTC | Ignore LSF queue and resource specification when diffing XML. | 05 July 2016, 15:52:21 UTC |
dd59a10 | Thomas B. Mooney | 05 July 2016, 13:46:15 UTC | Specify a default LSF queue. | 05 July 2016, 13:46:15 UTC |
3f9657b | Thomas B. Mooney | 05 July 2016, 13:16:36 UTC | Merge pull request #1491 from tmooney/cache_username_result Cache the username in Genome::Sys->username. | 05 July 2016, 13:16:36 UTC |
31adf3a | Thomas B. Mooney | 05 July 2016, 13:15:45 UTC | Merge pull request #1486 from tmooney/remove_unused_use_workflow_includes Remove `gmt bwa align-reads` and unused "use Workflow;" includes. | 05 July 2016, 13:15:45 UTC |
c1d68ed | Thomas B. Mooney | 30 June 2016, 21:51:56 UTC | Cache the username. Since getpwuid is being unreliable, save the answer if we do succeed to save us from further travails. | 30 June 2016, 21:51:56 UTC |
c4912e0 | Thomas B. Mooney | 30 June 2016, 20:35:32 UTC | Merge pull request #1490 from tmooney/if_at_first_you_dont_succeed_getting_a_username If we don't get a username back from `getpwuid`, try again! | 30 June 2016, 20:35:32 UTC |
bbdaf40 | Thomas B. Mooney | 30 June 2016, 19:14:36 UTC | Add a comment explaining why we're sleeping. | 30 June 2016, 19:14:36 UTC |
59ea7f7 | Thomas B. Mooney | 30 June 2016, 19:10:38 UTC | Pull the ENV check out of the loop. | 30 June 2016, 19:10:38 UTC |
d1f8802 | Thomas B. Mooney | 30 June 2016, 16:27:43 UTC | Merge pull request #1483 from tmooney/instrument_data_import_helper_doesnt_use_workflow Remove unused Workflow helpers in InstrumentData Import. | 30 June 2016, 16:27:43 UTC |
5fd16f5 | Thomas B. Mooney | 30 June 2016, 16:26:45 UTC | Merge pull request #1485 from tmooney/clinseq_tells_no_lies_about_workflow ClinSeq: Remove false comment. | 30 June 2016, 16:26:45 UTC |
3fe5407 | Thomas B. Mooney | 30 June 2016, 16:26:23 UTC | Merge pull request #1477 from tmooney/remove_batchrun_eptiopepred_script Remove EpitopePrediction batchrun script. | 30 June 2016, 16:26:23 UTC |
21378b7 | Thomas B. Mooney | 30 June 2016, 16:14:59 UTC | Make it fatal to not find the username. | 30 June 2016, 16:14:59 UTC |
2532750 | Thomas B. Mooney | 30 June 2016, 13:54:20 UTC | If we don't get a username back from `getpwuid`, try again! It seems our systems are sometimes unreliable at returning a value here, causing some build failures. In my testing, it will fail to return a value on the first attempt, but the second attempt will succeed. Trying this five times is thus probably overkill(!), but hopefully is sufficient to make `Genome::Sys->username` reliable. If things really go poorly, the user_id is often "good enough" as a unique per-user value... just one less friendly to the viewer. However, it's insufficient to locate a `Genome::Sys::User` object, so anything depending on real user objects would still fail. | 30 June 2016, 13:54:20 UTC |
719cc3e | Thomas B. Mooney | 29 June 2016, 19:57:20 UTC | Add default LSF queues to small indels workflow steps. | 29 June 2016, 19:57:20 UTC |
891cad4 | Thomas B. Mooney | 29 June 2016, 19:40:31 UTC | Specify default LSF queue for various SomVal tasks. | 29 June 2016, 19:40:31 UTC |
01e9aee | Thomas B. Mooney | 29 June 2016, 18:21:40 UTC | Remove unused "use Workflow" in ViromeEvent GMTs. Do these tools even need to stick around? | 29 June 2016, 18:21:40 UTC |
baa5bf2 | Thomas B. Mooney | 29 June 2016, 18:17:19 UTC | Remove unused "use Workflow" in GenePrediction commands. Some of these were already commented-out, anyway! | 29 June 2016, 18:17:19 UTC |
8775626 | Thomas B. Mooney | 29 June 2016, 18:14:15 UTC | Remove unused "use Workflow;" from build failure report. | 29 June 2016, 18:14:15 UTC |
328b8f1 | Thomas B. Mooney | 29 June 2016, 18:12:46 UTC | Remove unused "use Workflow" includes in `gmt pindel` tools. | 29 June 2016, 18:12:46 UTC |
1ffd092 | Thomas B. Mooney | 29 June 2016, 18:10:43 UTC | Remove unused "use Workflow;" in Somatic GMTs. | 29 June 2016, 18:10:43 UTC |
2fa9639 | Thomas B. Mooney | 29 June 2016, 18:07:50 UTC | Remove unused "use Workflow;" in DV2 detectors. | 29 June 2016, 18:07:50 UTC |
fa3ae93 | Thomas B. Mooney | 29 June 2016, 18:06:15 UTC | Remove unused `gmt bwa align-reads` that has spurious `use Workflow;`. | 29 June 2016, 18:06:15 UTC |
6d401d8 | Thomas B. Mooney | 29 June 2016, 18:02:25 UTC | Remove unused "use Workflow" in Pindel indel conversion. | 29 June 2016, 18:02:25 UTC |
a35f74c | Thomas B. Mooney | 29 June 2016, 17:59:57 UTC | Remove "use Workflow;" since these don't. | 29 June 2016, 17:59:57 UTC |
37ab2f9 | Thomas B. Mooney | 29 June 2016, 17:52:32 UTC | Remove false comment. This was converted to WorkflowBuilder in #1326. | 29 June 2016, 17:52:32 UTC |
8a2b766 | Thomas B. Mooney | 29 June 2016, 17:48:16 UTC | Remove `genome individual cpu-disk-summary`. This command is coupled to Workflow builds and so it does not work in our new more Ptero-iffic world. The usage log reports no uses, so remove it rather than fixing it up. | 29 June 2016, 17:48:16 UTC |
c0d44e9 | Thomas B. Mooney | 29 June 2016, 17:26:38 UTC | Remove unused Workflow helpers. | 29 June 2016, 17:28:45 UTC |
52d7ccb | APipe Tester | 29 June 2016, 12:18:44 UTC | Updated `gmt` tab completion. | 29 June 2016, 12:18:44 UTC |
f8fce48 | APipe Tester | 29 June 2016, 12:17:59 UTC | Updated `genome` tab completion. | 29 June 2016, 12:17:59 UTC |
cd8b800 | APipe Tester | 29 June 2016, 12:16:29 UTC | Updated class browser cache. | 29 June 2016, 12:16:29 UTC |
034be20 | Thomas B. Mooney | 28 June 2016, 22:28:49 UTC | Convert MC16s workflow generation to WorkflowBuilder. | 28 June 2016, 22:28:49 UTC |
9739aab | Thomas B. Mooney | 28 June 2016, 21:26:42 UTC | Resolve a WorkflowBuilder object instead of a Workflow Operation. | 28 June 2016, 21:26:42 UTC |
d675a0c | Thomas B. Mooney | 28 June 2016, 21:23:26 UTC | Remove unfinished thought. | 28 June 2016, 21:23:26 UTC |
d02ddd5 | Thomas B. Mooney | 28 June 2016, 21:01:52 UTC | Remove GMTs that relied on Workflow integration. These used a Workflow-specific way of parallel_by that effectively made them workflows unto themselves. The underlying commands are still around for use if needed for now. | 28 June 2016, 21:02:42 UTC |
e0c9b63 | Thomas B. Mooney | 28 June 2016, 20:36:23 UTC | Replace hard-coded NHLBI and 1000 Genomes files with parameters. The hard-coded versions are on volumes slated for removal, and hardcoded paths are bad, anyway! CHANGELOG: `gmt germline filtering` now requires that the 1000 Genomes and NHLBI files be specified as parameters. This change is to faciliate the removal of old volumes where these files have historically been located. | 28 June 2016, 20:39:05 UTC |
9f1f1e0 | Thomas B. Mooney | 28 June 2016, 20:25:45 UTC | Remove EpitopePrediction batchrun script. This references volumes that are being eliminated. | 28 June 2016, 20:25:45 UTC |
e27c8bf | Thomas B. Mooney | 28 June 2016, 20:05:59 UTC | Remove old `gmt pindel run-pindel-model-group` command. | 28 June 2016, 20:05:59 UTC |
e360b94 | Thomas B. Mooney | 28 June 2016, 19:23:49 UTC | Merge pull request #1459 from tmooney/ber_uses_workflowbuilder BER/Prediction Workflow uses WorkflowBuilder | 28 June 2016, 19:23:49 UTC |
db2584e | Thomas B. Mooney | 28 June 2016, 19:19:47 UTC | Merge pull request #1460 from tmooney/remove_gene_prediction_workflow_model_uses Remove uses of Workflow::Model in GenePrediction. | 28 June 2016, 19:19:47 UTC |
f92660d | Thomas B. Mooney | 28 June 2016, 19:17:30 UTC | Merge pull request #1464 from tmooney/remove_references_to_deprecated_volumes Remove References to Volumes Being Retired | 28 June 2016, 19:17:30 UTC |
7e7be6d | Thomas B. Mooney | 28 June 2016, 19:16:37 UTC | Merge pull request #1467 from tmooney/remove_plotsv_script Remove old plotSV.pl script. | 28 June 2016, 19:16:37 UTC |
f2c994a | Thomas B. Mooney | 28 June 2016, 19:16:17 UTC | Merge pull request #1466 from tmooney/remove_capture_processmodels Remove old `gmt capture process-models`. | 28 June 2016, 19:16:17 UTC |
94bc7a8 | Thomas B. Mooney | 28 June 2016, 18:58:39 UTC | Merge pull request #1462 from tmooney/specify_queues_in_mutect_and_verifybam Specify queues in Mutect and SomVal's VerifyBam. | 28 June 2016, 18:58:39 UTC |
ccd9576 | Jason Walker | 28 June 2016, 18:31:14 UTC | Merge pull request #1469 from jasonwalker80/skip_sort_speedseq_sv Speedseq SV remove sort and symlink VCF. | 28 June 2016, 18:31:14 UTC |
bf89f4d | Thomas B. Mooney | 28 June 2016, 13:26:58 UTC | Merge pull request #1473 from tmooney/sys_lsf_bsub_works_with_docker Add Genome::Sys::LSF::bsub Docker Support | 28 June 2016, 13:26:58 UTC |