ec50914 | Thomas B. Mooney | 03 August 2016, 17:25:19 UTC | Merge pull request #1517 from tmooney/use_simpler_translation_variable_in_lsf_paths Use %J (LSF's standard) instead of %%JOB_ID%%. | 03 August 2016, 17:25:19 UTC |
3e016d2 | Thomas B. Mooney | 02 August 2016, 20:39:07 UTC | Use %J (LSF's standard) instead of %%JOB_ID%%. LSF will translate this for us to be the LSF Job ID. | 02 August 2016, 20:39:07 UTC |
f716fad | Thomas B. Mooney | 02 August 2016, 19:56:16 UTC | Merge pull request #1509 from tmooney/ptero_builder_doesnt_determine_final_logdir Defer to new Ptero feature to decide the log paths. | 02 August 2016, 19:56:16 UTC |
67fa0b6 | Feiyu Du | 29 July 2016, 19:54:00 UTC | Merge pull request #1516 from dufeiyu/update_process Update blessed process for Jenkins genome-process-test | 29 July 2016, 19:54:00 UTC |
edf290e | Feiyu Du | 29 July 2016, 18:30:42 UTC | Update blessed process | 29 July 2016, 18:30:42 UTC |
6c545be | Feiyu Du | 28 July 2016, 21:27:04 UTC | Merge pull request #1515 from dufeiyu/vcf_description Update vcf description with more info | 28 July 2016, 21:27:04 UTC |
58f4521 | Feiyu Du | 28 July 2016, 20:48:28 UTC | Give better vcf description | 28 July 2016, 20:48:28 UTC |
0eefeb3 | Thomas B. Mooney | 28 July 2016, 15:39:56 UTC | Merge pull request #1512 from tmooney/sort_before_running_bedtools_merge bedtools merge requires the file to be sorted. | 28 July 2016, 15:39:56 UTC |
2e27636 | Thomas B. Mooney | 27 July 2016, 18:59:24 UTC | Merge pull request #1489 from tmooney/more_correct_somatic_filter_workflow_test SomaticFilterWorkflow test: Quote parameters to `diff`. | 27 July 2016, 18:59:24 UTC |
a7ede01 | Thomas B. Mooney | 27 July 2016, 18:59:05 UTC | Merge pull request #1494 from tmooney/refalign_bamqc_server_uses_lower_queue Use lower queue for BamQc "server" process. | 27 July 2016, 18:59:05 UTC |
9688ecb | Thomas B. Mooney | 27 July 2016, 18:58:46 UTC | Merge pull request #1488 from tmooney/find_fewer_irrelevant_results AlignmentResult: Check the reference and annotation builds when seeking our Merged result(s) | 27 July 2016, 18:58:46 UTC |
3279ff3 | Thomas B. Mooney | 27 July 2016, 15:45:59 UTC | Merge pull request #1510 from tmooney/make_logging_revision_failures_nonfatal Don't die just because we can't revert the logging. | 27 July 2016, 15:45:59 UTC |
83196e6 | Thomas B. Mooney | 27 July 2016, 15:00:50 UTC | Merge pull request #1511 from tmooney/disable_tcga_queries_for_old_systems Require a newer SSL implementation to perform the web queries. | 27 July 2016, 15:00:50 UTC |
1bfb161 | APipe Tester | 27 July 2016, 12:16:18 UTC | Updated `gmt` tab completion. | 27 July 2016, 12:16:18 UTC |
3645600 | APipe Tester | 27 July 2016, 12:15:31 UTC | Updated `genome` tab completion. | 27 July 2016, 12:15:31 UTC |
2a7e7b0 | Thomas B. Mooney | 26 July 2016, 22:00:21 UTC | bedtools merge requires the file to be sorted. Although imported feature-lists often are sorted, we don't guarantee that, so better sort here. | 26 July 2016, 22:02:33 UTC |
dfcdaf3 | Eddie Belter | 26 July 2016, 19:26:15 UTC | Merge pull request #1503 from ebelter/sx-trim-by-pos-with-ns Trim by positions can handle scaffold/supercontigs | 26 July 2016, 19:26:15 UTC |
1933bba | Thomas B. Mooney | 25 July 2016, 18:26:17 UTC | Require a newer SSL implementation to perform the web queries. The GDC portal now requires newer SSL to perform the handshake, so disable the TCGA support for older systems. (Running with an outdated OpenSSL is scary, and one probably shouldn't do it, anyway!) | 25 July 2016, 18:26:17 UTC |
fbda4f7 | Feiyu Du | 21 July 2016, 20:30:09 UTC | Merge pull request #1506 from dufeiyu/plan_file Update CLE plan files with new filters | 21 July 2016, 20:30:09 UTC |
65f6cfc | Thomas B. Mooney | 21 July 2016, 18:59:47 UTC | Don't die just because we can't revert the logging. Letting a few messages leak into the task's log files is far better than throwing out all of our work when there's an issue reopening the original log file! | 21 July 2016, 18:59:47 UTC |
4c0127d | Thomas B. Mooney | 20 July 2016, 19:37:07 UTC | Defer to new Ptero feature to decide the log paths. This uses genome/ptero-lsf#124 and genome/ptero-perl-sdk#117 to ensure a unique filename is chosen for each job, even during a parallel-by. As a bonus that filename's UUID will now be the Job ID making it easier to match to the job to which it belongs. | 20 July 2016, 19:37:07 UTC |
dd261bd | Thomas B. Mooney | 20 July 2016, 19:35:23 UTC | Stop redirecting output of post-exec. This was supposedly for debugging, but we never looked at it, and until recently it was written to /tmp/ where it vanished anyway. | 20 July 2016, 19:36:54 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 |
c2c4522 | Feiyu Du | 14 July 2016, 17:41:51 UTC | Add vaf-cutoff filter to cle snv plan files | 14 July 2016, 17:41:51 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 |
e961086 | Eddie Belter | 13 July 2016, 21:46:19 UTC | Trim by positions can handle scaffold/supercontigs | 13 July 2016, 21:47:40 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 |
2303017 | Thomas B. Mooney | 05 July 2016, 18:33:55 UTC | Use lower queue for BamQc "server" process. This shouldn't use the same queue as its workers, lest they potentially deadlock. | 05 July 2016, 18:33:55 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 |
8e4f3c6 | Feiyu Du | 01 July 2016, 20:30:41 UTC | add new filters to cle trio plan files | 01 July 2016, 20:30:41 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 |
2b5a586 | Thomas B. Mooney | 30 June 2016, 14:25:36 UTC | Quote the patterns so they get through to `diff`. If files in the current directory matched the patterns, the shell would expand them. If not, then the shell passed them along to `diff`. This test would thus pass or fail depending on the place from which it was launched. | 30 June 2016, 14:25:36 UTC |
4dbac88 | Thomas B. Mooney | 30 June 2016, 14:24:34 UTC | Remove breakpoint. | 30 June 2016, 14:24:34 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 |
609dd1d | Thomas B. Mooney | 30 June 2016, 13:15:44 UTC | Also check the reference and annotation builds for matches. This reduces the number of false-positives when the same data has been aligned to many references, saving us from collecting all their individual alignments when we know they won't match. | 30 June 2016, 13:15:44 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 |