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23 March 2024, 19:04:16 UTC
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Revision Author Date Message Commit Date
a9a1595 Feiyu Du 19 November 2015, 23:03:36 UTC Merge pull request #1117 from dufeiyu/tcga Several improvements for TCGA submission 19 November 2015, 23:03:36 UTC
c72b2ca Feiyu Du 19 November 2015, 22:00:54 UTC remove unnecessary check 19 November 2015, 22:00:54 UTC
b84478a David Morton 19 November 2015, 18:12:55 UTC Merge pull request #1123 from davidlmorton/remove_unused_input Remove clean_bam from workflow inputs 19 November 2015, 18:12:55 UTC
d1dc4b3 Thomas B. Mooney 18 November 2015, 22:37:07 UTC Merge pull request #1121 from tmooney/hc_bucket_iterator_specifies_lsf_queue Specify an LSF queue for the bucket iterator. 18 November 2015, 22:37:07 UTC
5da3de4 dmorton 18 November 2015, 22:21:07 UTC Remove clean_bam from workflow inputs It is not used in the workflow and WorkflowBuilder, when launching a PTero workflow disallows unused inputs. 18 November 2015, 22:21:07 UTC
e8e2a46 Thomas Mooney 18 November 2015, 20:10:22 UTC Specify an LSF queue for the bucket iterator. 18 November 2015, 20:11:07 UTC
35eb46a mkiwala 18 November 2015, 15:38:44 UTC Merge pull request #1118 from mkiwala/ptero-submit-after-process-committed Ptero submit after process committed 18 November 2015, 15:38:44 UTC
c7f8e23 Thomas B. Mooney 17 November 2015, 23:15:11 UTC Merge pull request #1119 from tmooney/gatk_34_handles_gvcf_gz Add extra parameters when gzipped GVCF requested in version 3.4 of HaplotypeCaller. 17 November 2015, 23:15:11 UTC
7582f15 Thomas Mooney 17 November 2015, 21:56:44 UTC Add in deprecated parameters when g.vcf.gz requested in 3.4. 17 November 2015, 21:56:44 UTC
be47da4 Feiyu Du 17 November 2015, 21:52:53 UTC check 17 November 2015, 21:52:53 UTC
20b9dba Michael J. Kiwala 17 November 2015, 17:08:25 UTC Wait to submit to PTero until after the Genome::Process has been committed 17 November 2015, 17:19:29 UTC
95c960a Michael J. Kiwala 17 November 2015, 17:03:47 UTC Use update_with_commit parameter to avoid committing too early Calling Genome::Process::Command::Run->create() without update_with_commit set to False, will cause a commit to happen before create() returns. In the case of the _submit_process function, which is used to submit a process's workflow to PTero, committing during Genome::Process::Command::Run->create() triggered an exception. Other functions in Genome::Process which also call Genome::Process::Command::Run->create() probably should set update_with_commit to False as well, but they are not currently having problems the way the are written. Those other calls should be investigated separately. 17 November 2015, 17:19:29 UTC
da9a77d APipe Tester 17 November 2015, 13:16:45 UTC Updated `genome` tab completion. 17 November 2015, 13:16:45 UTC
4398589 APipe Tester 17 November 2015, 13:15:12 UTC Updated class browser cache. 17 November 2015, 13:15:12 UTC
c6a6e6e Feiyu Du 16 November 2015, 20:23:20 UTC add alternative way to decide whether sample is tumor or not from sample type code of tcga id 16 November 2015, 20:23:20 UTC
fcb301a Jim Eldred 16 November 2015, 20:11:14 UTC Merge pull request #1116 from tmooney/set_all_outputs_when_skipping_VLI_CACR Set all outputs regardless of why we're skipping. 16 November 2015, 20:11:14 UTC
769e8a0 Thomas Mooney 16 November 2015, 19:48:32 UTC Set all outputs regardless of why we're skipping. 16 November 2015, 19:48:32 UTC
71a0886 Jason Walker 16 November 2015, 17:08:02 UTC Merge pull request #1090 from jasonwalker80/copy_allocation Export/Copy Allocations to 'ad hoc' disk 16 November 2015, 17:08:02 UTC
a56aa30 Thomas B. Mooney 16 November 2015, 16:36:46 UTC Merge pull request #1102 from tmooney/send_alignment_dispatcher_to_long Use primary queue to submit SomVal AlignReads job. 16 November 2015, 16:36:46 UTC
3273a3e Thomas B. Mooney 16 November 2015, 16:35:29 UTC Merge pull request #1104 from tmooney/shortcut_final_somval_steps Shortcut Several Skipped SomVal Steps 16 November 2015, 16:35:29 UTC
d2a8cf6 Jim Eldred 16 November 2015, 16:32:52 UTC Merge pull request #1115 from tmooney/haplotype_caller_vcf_naming Updates to HaplotypeCaller file naming in SSG 16 November 2015, 16:32:52 UTC
9791777 Thomas Mooney 16 November 2015, 16:07:26 UTC Add tests that VCF is created as expected. 16 November 2015, 16:07:26 UTC
c5ea958 Thomas Mooney 16 November 2015, 16:00:40 UTC Use ".gz" extension so GATK produces a compressed VCF. 16 November 2015, 16:00:40 UTC
bc0ec4f Thomas Mooney 16 November 2015, 15:59:55 UTC Add an accessor for the VCF file. This way a lister can be used to obtain all the VCF results for a build with haplotype_caller_result.vcf_file 16 November 2015, 15:59:55 UTC
82dbf77 Thomas Mooney 16 November 2015, 15:59:12 UTC Name the VCF result for the interval if there's only one. 16 November 2015, 15:59:44 UTC
ea58c81 David Morton 14 November 2015, 03:48:23 UTC Merge pull request #1113 from davidlmorton/dont_fail_ptero_builds Dont fail ptero builds 14 November 2015, 03:48:23 UTC
af2f6b4 Feiyu Du 13 November 2015, 23:07:49 UTC exclude the samples whose tcga_names are available via extraction_label or external_name 13 November 2015, 23:07:49 UTC
0bf3087 Feiyu Du 13 November 2015, 22:50:23 UTC test new methods in unit test 13 November 2015, 22:50:23 UTC
cd5d7e0 dmorton 13 November 2015, 22:16:28 UTC Fix 'build scan' to ignore PTero run builds 13 November 2015, 22:16:28 UTC
7f4e6ad dmorton 13 November 2015, 22:15:08 UTC Make and use Genome::Ptero::Utils This centeralizes url construction among other things. 13 November 2015, 22:15:08 UTC
b2f7a87 dmorton 13 November 2015, 22:09:29 UTC All reverse_as properties must be is_many even if in practice this will always return a single entity 13 November 2015, 22:09:29 UTC
123f9fa Feiyu Du 13 November 2015, 17:55:17 UTC add more potential tcga naming candidates 13 November 2015, 17:55:17 UTC
6b4d878 Feiyu Du 13 November 2015, 17:29:30 UTC Add alternative way to find sample tcga names 13 November 2015, 17:29:30 UTC
ae7f129 mkiwala 13 November 2015, 01:45:33 UTC Merge pull request #1111 from mkiwala/ptero-lsf-resources Get the lsf resource from the dag if they exist 13 November 2015, 01:45:33 UTC
e98a302 Feiyu Du 12 November 2015, 23:00:07 UTC bug fix 12 November 2015, 23:00:07 UTC
c762a83 Feiyu Du 12 November 2015, 22:48:12 UTC sort and align the list 12 November 2015, 22:48:12 UTC
46f6c33 Feiyu Du 12 November 2015, 22:15:56 UTC Add TCGASpecialSampleNamingConversion.pm to hold special sample naming conversion 12 November 2015, 22:15:56 UTC
286538f Thomas B. Mooney 12 November 2015, 22:13:18 UTC Merge pull request #1107 from tmooney/add_adders_to_ssg Add adders to SingleSampleGenotype Model. 12 November 2015, 22:13:18 UTC
e62f2c6 Michael J. Kiwala 12 November 2015, 22:08:23 UTC Get the lsf resource from the dag if they exist 12 November 2015, 22:09:10 UTC
1fa5e5e Feiyu Du 12 November 2015, 21:21:49 UTC add alternative way to get tcga patient id 12 November 2015, 21:21:49 UTC
35e3540 Thomas B. Mooney 12 November 2015, 20:00:03 UTC Merge pull request #1110 from tmooney/ssg_haplotype_caller_gets_correct_intervals Fix list evaluation in scalar context. 12 November 2015, 20:00:03 UTC
df3dc46 Thomas B. Mooney 12 November 2015, 19:59:51 UTC Merge pull request #1109 from tmooney/ssg_qc_requests_resource Add LSF queue and resource request to the SSG QC command. 12 November 2015, 19:59:51 UTC
f86ce81 Susanna Kiwala 12 November 2015, 19:30:12 UTC Merge pull request #1106 from susannasiebert/epitope_prediction_shortcut_fix Epitope prediction bugfixes 12 November 2015, 19:30:12 UTC
65b071e mkiwala 12 November 2015, 17:17:49 UTC Merge pull request #1105 from mkiwala/alignment-dispatcher-logs Set logs recursively in alignment dispatcher 12 November 2015, 17:17:49 UTC
d242b28 Thomas Mooney 12 November 2015, 15:46:10 UTC Fix list evaluation in scalar context. 12 November 2015, 15:46:10 UTC
7bbdae5 Thomas Mooney 12 November 2015, 15:30:18 UTC Add LSF queue and resource request to the SSG QC command. 12 November 2015, 15:30:18 UTC
b3f11aa APipe Tester 12 November 2015, 13:16:41 UTC Updated `genome` tab completion. 12 November 2015, 13:16:41 UTC
3841dea APipe Tester 12 November 2015, 13:15:08 UTC Updated class browser cache. 12 November 2015, 13:15:08 UTC
e6470be Eddie Belter 11 November 2015, 23:11:53 UTC Merge pull request #1101 from ebelter/instdata-cmd CHANGELOG: Removed Instrument Data Redundant Commands ignored Use auto-generated command: 'genome instrument-data update ignored --h' est-library-complexity This command works on instdata that have fastqs, which is no longer true. This makes this command unusable. Use the picard command directly with the instrument data 'bam_path' : 'gmt picard estimate-library-complexity --h' 11 November 2015, 23:11:53 UTC
5e35c5b Thomas Mooney 11 November 2015, 22:41:25 UTC Add adders to SSG--CQID needs these to work with input objects. 11 November 2015, 22:42:49 UTC
bd7265a Eddie Belter 11 November 2015, 20:14:30 UTC Merge pull request #1100 from ebelter/instdata-import3 InstData Import: Avoid shell errors associated with odd charcters 11 November 2015, 20:14:30 UTC
2d9194a Susanna Kiwala 11 November 2015, 20:09:34 UTC Delete objects that we aren't planning on executing 11 November 2015, 20:09:34 UTC
f06e254 Susanna Kiwala 11 November 2015, 20:09:06 UTC Save dag so it doesn't get created twice 11 November 2015, 20:09:06 UTC
0773c70 Jason Walker 11 November 2015, 16:20:50 UTC update output_dir to include allocation ID. updated status message. 11 November 2015, 16:20:50 UTC
67b3132 Thomas B. Mooney 11 November 2015, 16:12:55 UTC Merge pull request #1103 from ebelter/sync-users-msgs Sync Users: use status_message 11 November 2015, 16:12:55 UTC
fc31f84 Michael J. Kiwala 10 November 2015, 22:19:07 UTC Set logs recursively in alignment dispatcher 10 November 2015, 22:19:07 UTC
7f04a4d Thomas Mooney 10 November 2015, 21:17:00 UTC Shortcut DV2 if there are no detection strategies. 10 November 2015, 21:17:00 UTC
04d97d5 Thomas Mooney 10 November 2015, 20:18:49 UTC Consolidate all skip logic into skip_validation so shortcut can benefit. 10 November 2015, 20:23:12 UTC
90998d2 Thomas Mooney 10 November 2015, 20:18:10 UTC Check if we're skipping in shortcut to save scheduling a job. 10 November 2015, 20:18:10 UTC
6dc2c06 APipe Tester 10 November 2015, 19:02:24 UTC updated graphite submodule to d3b83f1 10 November 2015, 19:02:24 UTC
2d5e878 Eddie Belter 09 November 2015, 22:02:20 UTC Sync Users: use status_message Use status_message instead of custom STDOUT redirect status to allow printing of messages during cron runs. 09 November 2015, 22:03:27 UTC
7ece5e4 Eddie Belter 09 November 2015, 20:47:02 UTC InstData Import: PR 1100 suggestions 09 November 2015, 20:47:02 UTC
00be5c1 Thomas Mooney 09 November 2015, 15:29:19 UTC Use primary queue to submit AlignReads job. Some jobs scheduled by the dispatcher will end up in the "alt" queue, so this job needs to be in the lower-priority queue. 09 November 2015, 15:29:19 UTC
05fc536 Thomas B. Mooney 09 November 2015, 14:53:47 UTC Merge pull request #1092 from tmooney/remove_temporary_collect_call_info_picard Remove _collect_call_info from GMT Picard. 09 November 2015, 14:53:47 UTC
133c3de Eddie Belter 06 November 2015, 23:47:41 UTC InstData: remove est library complexity command This command works on instdata that have fastqs. It dumps the fastqs, then cnverts them to a bam, and the run gmt picard est library complexity. Since instdata sequence files are now bams, this command is unneccessary. 06 November 2015, 23:47:41 UTC
a239ff7 Eddie Belter 06 November 2015, 23:46:56 UTC InstData: remove instrument data property from command tree 06 November 2015, 23:46:56 UTC
8cda0ce Eddie Belter 06 November 2015, 23:37:55 UTC InstData: remove redundant ignore command 06 November 2015, 23:38:02 UTC
3d6979e Eddie Belter 06 November 2015, 20:06:33 UTC InstData Import: Avoid shell errors associated with odd charcters use arrayref shellcmd sanitize sample name before using it in afile name problems 06 November 2015, 23:04:43 UTC
f4eb1e5 APipe Tester 06 November 2015, 21:53:04 UTC updated jenkins submodule to 22d728f 06 November 2015, 21:53:04 UTC
88f375b APipe Tester 06 November 2015, 21:52:56 UTC updated ur submodule to d05667f 06 November 2015, 21:52:56 UTC
c3c7fc1 Feiyu Du 06 November 2015, 17:14:53 UTC Merge pull request #1094 from dufeiyu/chimerascan_config Use config to get lsf_resource for chimerascan 06 November 2015, 17:14:53 UTC
7381f9c APipe Tester 06 November 2015, 13:16:53 UTC Updated `genome` tab completion. 06 November 2015, 13:16:53 UTC
04ae129 APipe Tester 06 November 2015, 13:15:13 UTC Updated class browser cache. 06 November 2015, 13:15:13 UTC
10e2cdc David Morton 06 November 2015, 02:51:50 UTC Merge pull request #1095 from davidlmorton/run_model_test Added 'genome test run-model-test' command 06 November 2015, 02:51:50 UTC
1f34aec Feiyu Du 05 November 2015, 21:50:17 UTC config spec name change 05 November 2015, 21:50:17 UTC
bdf12c6 Feiyu Du 05 November 2015, 21:47:45 UTC name cahnge 05 November 2015, 21:47:45 UTC
00aa298 Feiyu Du 05 November 2015, 21:45:16 UTC Rename to lsf_resource_rnaseq_chimerascan 05 November 2015, 21:45:16 UTC
b0ce480 dmorton 05 November 2015, 20:29:17 UTC Added 'genome test run-model-test' command This command runs a model test but does not: - alter your environment in (i.e. setting a software result test name) - determine what version of perl to run - email anybody 05 November 2015, 20:41:24 UTC
88c6db0 Jason Walker 05 November 2015, 20:38:23 UTC Fix typo in directory. 05 November 2015, 20:38:23 UTC
5b499ec Jason Walker 05 November 2015, 20:36:46 UTC Use array ref to pass cmd. Assign sig handler with variable in scope to kill LSF job. Pass allocation objects to _do_unarchive_cmd. 05 November 2015, 20:36:46 UTC
d3fc245 Dave Larson 05 November 2015, 20:05:40 UTC Merge pull request #1088 from ernfrid/master missed some defines 05 November 2015, 20:05:40 UTC
ca6e6dd Jim Eldred 05 November 2015, 19:12:38 UTC Merge pull request #1093 from jasonwalker80/star_rna_aligner Add software result users for STAR aligner. 05 November 2015, 19:12:38 UTC
e273ae6 Feiyu Du 05 November 2015, 17:02:18 UTC use config spec to get lsf resource 05 November 2015, 17:02:18 UTC
872a252 Feiyu Du 05 November 2015, 16:57:18 UTC Add config spec for chimerascan 05 November 2015, 16:57:18 UTC
a42136b Thomas B. Mooney 04 November 2015, 23:29:32 UTC Merge pull request #1087 from tmooney/trsn_for_merged_results_in_calculatehsmetrics CalculateHsMetrics Supports Merged Results. 04 November 2015, 23:29:32 UTC
c71f9c6 Jason Walker 04 November 2015, 21:58:04 UTC Die if output_dir for export is existing allocation and absolute paths match. 04 November 2015, 21:58:04 UTC
a5d67ff Jason Walker 04 November 2015, 21:52:23 UTC cleanup the sig_handlers. 04 November 2015, 21:52:23 UTC
bab9cef Jason Walker 04 November 2015, 21:36:37 UTC Add software result users for STAR aligner. 04 November 2015, 21:36:37 UTC
9e6e088 Jason Walker 04 November 2015, 21:07:05 UTC typo. Pass allocation id to _do_unarchive_cmd 04 November 2015, 21:07:05 UTC
0c453dd Thomas B. Mooney 04 November 2015, 21:02:15 UTC Merge pull request #1089 from tmooney/run_each_haplotypecaller_bucket_serially Run the HaplotypeCaller serially on each contig in a bucket. 04 November 2015, 21:02:15 UTC
d5e4441 Jason Walker 04 November 2015, 21:00:19 UTC Use scope guard for unlocking. move common unarchiving logic to unarchiver. 04 November 2015, 21:00:19 UTC
ac783e9 Dave Larson 04 November 2015, 20:23:54 UTC allow stop coordinates of value 0 and check start <= stop 04 November 2015, 20:23:54 UTC
35ae189 mkiwala 04 November 2015, 18:04:24 UTC Merge pull request #1085 from mkiwala/lsf_cputime Lsf cputime 04 November 2015, 18:04:24 UTC
258fff8 Michael J. Kiwala 04 November 2015, 15:57:10 UTC Use `git add -p` to commit a subset of the regenerated test data 04 November 2015, 15:57:10 UTC
d07eafb Michael J. Kiwala 04 November 2015, 15:38:22 UTC Revert "Regenerate test data due to change to NullCommand" This reverts commit 67c75f30384aa2cccb6009f6fa7dd6f6b579671d. 04 November 2015, 15:38:22 UTC
f268f18 Thomas Mooney 04 November 2015, 14:39:50 UTC Remove _collect_call_info. This temporary data collection was added in PR #573. 04 November 2015, 14:39:50 UTC
9d79d2f Dave Larson 04 November 2015, 02:13:04 UTC correct lift_over typo 04 November 2015, 02:13:04 UTC
b963d7e Jason Walker 03 November 2015, 23:14:03 UTC Refactor the eval{} and Try::Tiny blocks. Removed some unnecessary complexity. 03 November 2015, 23:14:03 UTC
382d520 Dave Larson 03 November 2015, 22:33:13 UTC update tests 03 November 2015, 22:33:13 UTC
951edcf Dave Larson 03 November 2015, 22:31:36 UTC make tests be more specific 03 November 2015, 22:31:36 UTC
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