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23 March 2024, 19:04:16 UTC
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Revision Author Date Message Commit Date
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
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