| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 63d2508 | Jason Walker | 03 November 2015, 21:46:08 UTC | Initial revision of copy/export commands for allocations. | 03 November 2015, 21:46:08 UTC |
| 013e077 | Thomas B. Mooney | 03 November 2015, 21:04:06 UTC | Merge pull request #1084 from tmooney/exclude_index_results_in_cle_verification Exclude index results from CLE verification. | 03 November 2015, 21:04:06 UTC |
| b176529 | Thomas B. Mooney | 03 November 2015, 20:57:39 UTC | Merge pull request #1083 from tmooney/alignment_print_error_opening_groups_file Alignment print error opening groups file | 03 November 2015, 20:57:39 UTC |
| 67c75f3 | Michael J. Kiwala | 03 November 2015, 20:46:45 UTC | Regenerate test data due to change to NullCommand The lsf_resource string hardcoded in Genome/Ptero/TestCommand/NullCommand.pm has changed, so we need to regernate test data. GENERATE_TEST_DATA=1 /usr/bin/perl -Ilib/perl lib/perl/Genome/Ptero/ToJSON.t GENERATE_TEST_DATA=1 /usr/bin/perl -Ilib/perl lib/perl/Genome/Ptero/ToJSONForProcess.t | 03 November 2015, 20:46:45 UTC |
| 1f46d0e | Thomas Mooney | 03 November 2015, 20:30:12 UTC | Run the HaplotypeCaller serially on each contig in a bucket. It has been decided that it is preferable to produce per-chromosome GVCFs rather than have collections of chromosomes bundled together. In order to still have consistently-sized jobs (and avoid splitting hundreds of ways, which will pound the source BAM file), run the HaplotypeCaller on each entry in the bucket in turn. | 03 November 2015, 20:30:12 UTC |
| ad9b194 | Michael J. Kiwala | 03 November 2015, 20:21:03 UTC | BUGFIX: Convert value supplied with -c from minutes to seconds On the command line, the -c option value is in minutes. In the lsb_submit data structure, this value is in seconds. | 03 November 2015, 20:22:20 UTC |
| f76f6bf | Michael J. Kiwala | 03 November 2015, 20:08:32 UTC | Remove the construct_lsf_param_string functionality This function worked as long as no values in the param structure needed to be translated to construct the lsf param string. The units of the value associated with the -c option should be minutes in the lsf param string and seconds in the lsf param structure, which means a translation of the value would be required to construct the lsf param string. Instead of implementing this translation for the -c option, I'm removing the construct_lsf_param_string function, since nobody uses it anyway. | 03 November 2015, 20:08:32 UTC |
| 40d15a5 | Thomas B. Mooney | 03 November 2015, 19:43:50 UTC | Merge pull request #1082 from tmooney/define_docs_data_for_ssg Add model define doc testcase for the new SingleSampleGenotype pipeline. | 03 November 2015, 19:43:50 UTC |
| 4a65d82 | Dave Larson | 03 November 2015, 17:57:02 UTC | missed some defines | 03 November 2015, 17:57:02 UTC |
| a33cf25 | Dave Larson | 03 November 2015, 16:55:01 UTC | Merge pull request #1086 from ernfrid/master fix ancient bug testing convertability | 03 November 2015, 16:55:01 UTC |
| 502435b | Thomas Mooney | 03 November 2015, 16:34:03 UTC | Extract subroutine for alignment-result => feature-list mapping. | 03 November 2015, 16:34:03 UTC |
| 2f57448 | Dave Larson | 03 November 2015, 16:08:37 UTC | fix ancient bug testing convertability | 03 November 2015, 16:08:37 UTC |
| 30c91e3 | Thomas Mooney | 03 November 2015, 15:55:11 UTC | Handle merged results in CalculateHsMetrics | 03 November 2015, 15:55:11 UTC |
| de83afb | Michael J. Kiwala | 03 November 2015, 14:44:22 UTC | Remove '-c 10' from lsf_resource string We shouldn't depend on the -c option until https://jira.gsc.wustl.edu/browse/INFOSYS-17692 has been resolved. | 03 November 2015, 14:44:22 UTC |
| 2452717 | APipe Tester | 03 November 2015, 13:18:23 UTC | Updated `genome` tab completion. | 03 November 2015, 13:18:23 UTC |
| 6109b55 | APipe Tester | 03 November 2015, 13:16:33 UTC | Updated class browser cache. | 03 November 2015, 13:16:33 UTC |
