| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 082497d | David Morton | 03 November 2015, 05:13:08 UTC | Merge pull request #1072 from davidlmorton/submit_url Use submit_url option when submitting PTero workflows | 03 November 2015, 05:13:08 UTC |
| 9af3cb5 | Thomas Mooney | 02 November 2015, 21:30:58 UTC | Exclude index results from CLE verification. | 02 November 2015, 21:30:58 UTC |
| 24f7788 | Thomas Mooney | 02 November 2015, 20:38:26 UTC | Include the error when we couldn't open the groups file. | 02 November 2015, 20:38:26 UTC |
| 0095262 | Thomas Mooney | 02 November 2015, 20:37:56 UTC | Wording change: "proceeding" instead of "preceding". | 02 November 2015, 20:37:56 UTC |
| da03797 | Thomas Mooney | 02 November 2015, 18:55:47 UTC | Add new model define doc testcase for the SingleSampleGenotype pipeline. | 02 November 2015, 18:55:47 UTC |
| 67ac1d4 | Chris Miller | 02 November 2015, 18:38:16 UTC | Merge pull request #1081 from chrisamiller/modelgroup removing comma that makes text harder to select | 02 November 2015, 18:38:16 UTC |
| 07b280a | Chris Miller | 02 November 2015, 18:03:30 UTC | removing comma that makes text harder to select | 02 November 2015, 18:03:30 UTC |
| 5247629 | Thomas B. Mooney | 02 November 2015, 17:51:55 UTC | Merge pull request #1070 from tmooney/reference_variation_fast New Very Specific Pipeline for Alignment + HaplotypeCaller | 02 November 2015, 17:51:55 UTC |
| a3fe467 | APipe Tester | 31 October 2015, 12:21:29 UTC | Updated `gmt` tab completion. | 31 October 2015, 12:21:29 UTC |
| d1e910f | APipe Tester | 31 October 2015, 12:20:33 UTC | Updated `genome` tab completion. | 31 October 2015, 12:20:33 UTC |
| 0043343 | APipe Tester | 31 October 2015, 12:18:45 UTC | Updated class browser cache. | 31 October 2015, 12:18:45 UTC |
| 00d4331 | Susanna Kiwala | 30 October 2015, 15:03:32 UTC | Merge pull request #1074 from susannasiebert/epitope_prediction_wrappers Add wrappers to run the epitope prediction pipeline with the variant reporting components | 30 October 2015, 15:03:32 UTC |
| 38591b6 | Feiyu Du | 29 October 2015, 19:05:25 UTC | Merge pull request #1078 from dufeiyu/sdrf Add adjacent normal to the case of is_not_tumor | 29 October 2015, 19:05:25 UTC |
| bcbd46c | APipe Tester | 29 October 2015, 16:16:58 UTC | updated ur submodule to 7c77471 | 29 October 2015, 17:37:13 UTC |
| 430b404 | Feiyu Du | 29 October 2015, 17:36:28 UTC | adjacent normal is not tumor | 29 October 2015, 17:36:28 UTC |
| c541b70 | Thomas Mooney | 29 October 2015, 16:53:48 UTC | The committee is very insistent about its naming selection! | 29 October 2015, 16:53:48 UTC |
| ae4f175 | Allison Penner Regier | 29 October 2015, 16:51:40 UTC | Merge pull request #1022 from apregier/evaluate_vcf Allow evaluation to be re-parsed | 29 October 2015, 16:51:40 UTC |
| 46f6b87 | Thomas B. Mooney | 29 October 2015, 16:05:44 UTC | Merge pull request #1073 from tmooney/lock_before_setting_build_metrics Lock before setting build metrics. | 29 October 2015, 16:05:44 UTC |
| 499583d | Thomas B. Mooney | 29 October 2015, 16:04:43 UTC | Merge pull request #873 from tmooney/add_status_to_menu_items Add status to AnalysisMenu Items | 29 October 2015, 16:04:43 UTC |
| 03afc8e | Thomas B. Mooney | 29 October 2015, 15:18:15 UTC | Merge pull request #1077 from tmooney/determine_error_finds_fatal_messages Look for output from new UR fatal_message(). | 29 October 2015, 15:18:15 UTC |
| 6650764 | Thomas B. Mooney | 29 October 2015, 13:51:09 UTC | Merge pull request #1076 from tmooney/dont_run_refalign_summary_report_twice Don't Generate RefAlign Summary Report Data Twice | 29 October 2015, 13:51:09 UTC |
| 97f2158 | APipe Tester | 29 October 2015, 12:18:09 UTC | Updated `genome` tab completion. | 29 October 2015, 12:18:09 UTC |
| 0a1d5b2 | APipe Tester | 29 October 2015, 12:16:23 UTC | Updated class browser cache. | 29 October 2015, 12:16:23 UTC |
| bca6e4c | APipe Tester | 28 October 2015, 19:51:32 UTC | updated sqitch/genome submodule to 734c786 | 28 October 2015, 22:48:16 UTC |
| e2a2492 | Thomas B. Mooney | 28 October 2015, 21:30:52 UTC | Merge pull request #1069 from tmooney/remove_obsolete_define_command Remove old "Msi" and "ReferenceVariationSanger" definers (and build class) | 28 October 2015, 21:30:52 UTC |
| d5f47a3 | Adam Coffman | 28 October 2015, 19:46:07 UTC | Merge pull request #1041 from acoffman/qc_table_test_db_snapshot New test-db snapshot | 28 October 2015, 19:46:07 UTC |
| cb0d317 | Susanna Kiwala | 28 October 2015, 18:30:21 UTC | Use create_directory instead of make_path | 28 October 2015, 18:30:21 UTC |
| 345045c | Susanna Kiwala | 28 October 2015, 18:25:39 UTC | Add documentation | 28 October 2015, 18:25:39 UTC |
| 250083f | Susanna Kiwala | 28 October 2015, 18:22:24 UTC | Removed unused packages | 28 October 2015, 18:22:24 UTC |
| 6c5426e | Susanna Kiwala | 28 October 2015, 17:39:12 UTC | Remove code redundancy | 28 October 2015, 17:39:12 UTC |
| 3197ee6 | Susanna Kiwala | 28 October 2015, 14:40:06 UTC | Remove unused subroutine | 28 October 2015, 17:37:42 UTC |
| 06634d5 | Susanna Kiwala | 28 October 2015, 14:39:50 UTC | Simplify accessor string | 28 October 2015, 17:37:41 UTC |
| 0a67780 | Susanna Kiwala | 28 October 2015, 14:34:54 UTC | Use reference_sequence_build subroutine on som var build instead of going through tumor build | 28 October 2015, 17:37:41 UTC |
| 37b0ff2 | Susanna Kiwala | 28 October 2015, 14:32:30 UTC | Use build as an input instead of its model | 28 October 2015, 17:37:41 UTC |
| b160818 | Jason Walker | 28 October 2015, 15:32:48 UTC | Merge pull request #1061 from jasonwalker80/operations_coverage_qc Operations QC WGS Coverage | 28 October 2015, 15:32:48 UTC |
| 4671633 | Thomas Mooney | 28 October 2015, 14:53:18 UTC | Look for output from new UR fatal_message(). | 28 October 2015, 14:53:18 UTC |
| 9ef9782 | Susanna Kiwala | 28 October 2015, 14:26:31 UTC | Fix typo | 28 October 2015, 14:26:31 UTC |
| 3a52606 | Susanna Kiwala | 28 October 2015, 14:24:02 UTC | Replace `die $self->error_message` with `$self->fatal_message` | 28 October 2015, 14:24:02 UTC |
| dbf973b | Susanna Kiwala | 28 October 2015, 14:21:03 UTC | Remove unneeded error handling | 28 October 2015, 14:21:46 UTC |
| 649548b | Thomas Mooney | 28 October 2015, 13:18:45 UTC | Save the generated vars instead for use in subsequent templates. | 28 October 2015, 13:59:11 UTC |
| 00e7c67 | Thomas Mooney | 28 October 2015, 13:14:18 UTC | Extract subroutine to generate the summary report data. | 28 October 2015, 13:59:04 UTC |
| 39f0930 | Thomas Mooney | 28 October 2015, 13:52:47 UTC | Remove unused data structure. | 28 October 2015, 13:54:59 UTC |
| 672fd68 | David Morton | 28 October 2015, 03:42:06 UTC | Merge pull request #1071 from davidlmorton/formatters Add formatters to ResourceParser | 28 October 2015, 03:42:06 UTC |
| 65a55a2 | dmorton | 28 October 2015, 03:25:03 UTC | Update test data after ResourceParser formatters were added | 28 October 2015, 03:25:03 UTC |
| c6dc5c6 | dmorton | 28 October 2015, 03:22:32 UTC | Make null_formatter a string_formatter | 28 October 2015, 03:22:32 UTC |
| a99b4cf | Feiyu Du | 27 October 2015, 21:56:17 UTC | Merge pull request #1075 from dufeiyu/sdrf Add reagent info of new target_region_set_name to TCGA Sdrf.pm | 27 October 2015, 21:56:17 UTC |
| 0597880 | Feiyu Du | 27 October 2015, 20:50:43 UTC | add info for new reagent | 27 October 2015, 20:50:43 UTC |
| c653d1c | APipe Tester | 27 October 2015, 18:33:33 UTC | updated jenkins submodule to c4d38e7 | 27 October 2015, 20:10:16 UTC |
| 03ef329 | Eddie Belter | 27 October 2015, 20:09:50 UTC | Merge pull request #1068 from ebelter/site-command Add Genome Site Command | 27 October 2015, 20:09:50 UTC |
| 7694243 | Susanna Kiwala | 27 October 2015, 19:33:42 UTC | Add test for new epitope prediction pipeline | 27 October 2015, 19:42:06 UTC |
| 84b353c | Susanna Kiwala | 26 October 2015, 15:51:11 UTC | Point to the NetMHC version that contains the bugfix for too many filehandles | 27 October 2015, 19:41:58 UTC |
| 2cc5ac6 | Thomas Mooney | 27 October 2015, 18:55:54 UTC | Limit length of lock name. | 27 October 2015, 19:00:01 UTC |
| 470e40c | Thomas Mooney | 27 October 2015, 18:44:07 UTC | Lock before attempting to set a metric. | 27 October 2015, 18:44:07 UTC |
| 751dfcf | dmorton | 26 October 2015, 19:48:02 UTC | Use submit_url option when submitting PTero workflows Instead of setting the PTERO_WORKFLOW_SUBMIT_URL env variable | 27 October 2015, 05:21:37 UTC |
| 3ee65c1 | dmorton | 27 October 2015, 04:52:35 UTC | Add formatters to ResourceParser | 27 October 2015, 05:19:02 UTC |
| 669522d | APipe Tester | 26 October 2015, 22:30:48 UTC | updated sqitch/genome submodule to 6ea7fdc | 26 October 2015, 22:30:48 UTC |
| 98abcb8 | APipe Tester | 26 October 2015, 18:30:45 UTC | updated jenkins submodule to 34e51e1 | 26 October 2015, 18:30:45 UTC |
| 51730a4 | Eddie Belter | 26 October 2015, 18:27:44 UTC | Site Cmd: add verb sync to lims and genome | 26 October 2015, 18:27:44 UTC |
| 540a5ae | Eddie Belter | 26 October 2015, 18:26:26 UTC | Site Cmd: remove unused sync capture sets | 26 October 2015, 18:26:26 UTC |
| 5f3a96b | Thomas Mooney | 26 October 2015, 18:24:31 UTC | Remove build class corresponding to previously removed model class. | 26 October 2015, 18:24:31 UTC |
| fed0988 | Thomas Mooney | 26 October 2015, 18:08:00 UTC | Remove define command for non-existent model types. These model types were removed in 8e1fbc694dc4d39a525ca2d0271188adad3c1290. | 26 October 2015, 18:09:41 UTC |
| 1d74802 | Susanna Kiwala | 26 October 2015, 15:46:27 UTC | New process to run the full epitope prediction pipeline with fasta creation via VRS | 26 October 2015, 17:02:18 UTC |
| 5b76ebe | Susanna Kiwala | 26 October 2015, 15:40:23 UTC | Make report_path an output on GenerateReport | 26 October 2015, 17:02:17 UTC |
| f532f02 | Susanna Kiwala | 14 October 2015, 13:51:55 UTC | Command to run the remaining epitope prediction steps after creating the fasta file with the VRS | 26 October 2015, 15:49:24 UTC |
| 336422f | Susanna Kiwala | 14 October 2015, 13:51:18 UTC | Wrapper to run the VRS eptiope prediction report | 26 October 2015, 15:49:24 UTC |
| 72f7e69 | Thomas Mooney | 26 October 2015, 14:57:30 UTC | The committee has decided to call this "SingleSampleGenotype". | 26 October 2015, 14:57:30 UTC |
| 1d65185 | Thomas Mooney | 08 October 2015, 19:37:39 UTC | Defer adding result label so it only applies to final result. | 26 October 2015, 14:42:00 UTC |
| c7afa70 | Thomas Mooney | 08 October 2015, 19:19:17 UTC | Error message if buckets haven't been generated. | 26 October 2015, 14:42:00 UTC |
| ee01088 | Thomas Mooney | 26 October 2015, 14:36:32 UTC | Test for QualityControl command. | 26 October 2015, 14:42:00 UTC |
| b730592 | Thomas Mooney | 26 October 2015, 14:35:31 UTC | Test for HaplotypeCaller command. | 26 October 2015, 14:42:00 UTC |
| ef62595 | Thomas Mooney | 26 October 2015, 14:35:06 UTC | Make intervals optional in HaplotypeCaller command. | 26 October 2015, 14:42:00 UTC |
| 1a3048d | Thomas Mooney | 07 October 2015, 20:45:37 UTC | Get aligner params from the model; add test. | 26 October 2015, 14:41:59 UTC |
| 5b715f7 | Thomas Mooney | 07 October 2015, 20:35:32 UTC | Basic test for reference-variation model and build classes. | 26 October 2015, 14:41:59 UTC |
| 6f8bcd0 | Thomas Mooney | 07 October 2015, 15:52:08 UTC | Add output connections from both branches to make a valid workflow. | 26 October 2015, 14:41:42 UTC |
| c11c772 | Thomas Mooney | 07 October 2015, 14:32:19 UTC | Command to prepare the buckets for a ReferenceVariation build. | 26 October 2015, 14:39:07 UTC |
| 340c07f | Thomas Mooney | 06 October 2015, 21:42:00 UTC | Add a user command to generate the required aligner index. | 26 October 2015, 14:39:07 UTC |
| 53e0304 | Thomas Mooney | 07 October 2015, 18:42:47 UTC | Test factory for reference-variation processing-profile and model. | 26 October 2015, 14:39:07 UTC |
| f255cbf | Thomas Mooney | 07 October 2015, 14:31:23 UTC | Parallelize haplotype caller by bucket. | 26 October 2015, 14:39:07 UTC |
| c042972 | Thomas Mooney | 06 October 2015, 22:29:30 UTC | Add HaplotypeCaller step to the ReferenceVariation pipeline. A future step will break the reference into regions and call the new tool multiple times. | 26 October 2015, 14:39:07 UTC |
