| be14ea7 | Thomas B. Mooney | 13 July 2015, 14:24:05 UTC | Merge pull request #847 from tmooney/cleanup_per_lane_tophat Minor Cleanup of PerLaneTophat module | 13 July 2015, 14:24:05 UTC |
| 8fe968d | Thomas B. Mooney | 13 July 2015, 14:23:38 UTC | Merge pull request #854 from tmooney/fix_process_pindel_reads_error_message List the path we checked in error message. | 13 July 2015, 14:23:38 UTC |
| d7e5e4b | David Morton | 13 July 2015, 00:24:01 UTC | Merge pull request #818 from davidlmorton/ptero_wrapper_logging Ensure reason for error is written to the log file | 13 July 2015, 00:24:01 UTC |
| 5a34f0b | dmorton | 11 July 2015, 07:15:46 UTC | Save $_ to named variable | 11 July 2015, 07:15:46 UTC |
| 9f706f5 | Eddie Belter | 10 July 2015, 17:43:19 UTC | Merge pull request #860 from ebelter/dv2-alloc-error DV2: correct error message and use built in sprintf | 10 July 2015, 17:43:19 UTC |
| 9ea66a8 | APipe Tester | 09 July 2015, 20:47:31 UTC | updated ur submodule to ac1d211 | 09 July 2015, 20:47:31 UTC |
| 51d4454 | Susanna Siebert | 09 July 2015, 15:54:29 UTC | Merge pull request #857 from susannasiebert/qc_framework_verify_bam_id_merged Allow QC framework to work on merged alignment results | 09 July 2015, 15:54:29 UTC |
| 8d4cb66 | Susanna Siebert | 09 July 2015, 14:57:20 UTC | Even better error message | 09 July 2015, 14:57:20 UTC |
| 9f22972 | APipe Tester | 09 July 2015, 12:19:23 UTC | Updated `genome` tab completion. | 09 July 2015, 12:19:23 UTC |
| aa9c079 | APipe Tester | 09 July 2015, 12:17:43 UTC | Updated class browser cache. | 09 July 2015, 12:17:43 UTC |
| e3c12f3 | Thomas B. Mooney | 08 July 2015, 22:40:25 UTC | Merge pull request #856 from tmooney/gp_eukaryotic_split_fasta_is_many GP Eukaryotic: Make fasta_files is_many in SplitFasta | 08 July 2015, 22:40:25 UTC |
| 4cb8b00 | Thomas B. Mooney | 08 July 2015, 22:40:14 UTC | Merge pull request #855 from tmooney/add_block_operation_to_workflowbuilder WorkflowBuilder class for Block operations. | 08 July 2015, 22:40:14 UTC |
| c57fa8a | Thomas Mooney | 08 July 2015, 20:51:33 UTC | Require the module we're about to use. | 08 July 2015, 20:51:33 UTC |
| dfbf8b4 | Eddie Belter | 08 July 2015, 19:51:22 UTC | DV2 Alloc Error: class instead of self | 08 July 2015, 19:51:22 UTC |
| f5bf38d | Eddie Belter | 08 July 2015, 19:49:34 UTC | DV2: call error_message instead of using variable | 08 July 2015, 19:49:34 UTC |
| b44e8cf | dmorton | 16 June 2015, 18:53:54 UTC | Allow for Block type operations in WorkflowBuilder Conflicts: lib/perl/Genome/WorkflowBuilder/Block.pm | 08 July 2015, 17:56:46 UTC |
| 74d0a30 | Susanna Siebert | 30 June 2015, 18:20:24 UTC | Add test for running qc on merged alignment result | 08 July 2015, 14:15:53 UTC |
| 51e305f | Susanna Siebert | 30 June 2015, 18:20:04 UTC | Make is_capture subroutine work for merged alignment results | 08 July 2015, 13:34:18 UTC |
| 7c9d2d2 | Susanna Siebert | 30 June 2015, 18:19:38 UTC | Better error message | 08 July 2015, 13:34:17 UTC |
| 2b2a306 | APipe Tester | 08 July 2015, 12:23:42 UTC | Updated `gmt` tab completion. | 08 July 2015, 12:23:42 UTC |
| 8ae155d | APipe Tester | 08 July 2015, 12:22:43 UTC | Updated `genome` tab completion. | 08 July 2015, 12:22:43 UTC |
| 49b709a | Thomas Mooney | 07 July 2015, 21:34:39 UTC | Make fasta_files is_many. WorkflowBuilder cares about the difference between an ARRAY and an is_many property as the input to a parallelBy workflow. The name must be changed to split_fasta_files, because otherwise UR creates a singular "fasta_file" accessor that overwrites the input property. | 07 July 2015, 23:00:03 UTC |
| ffd5d0d | Thomas Mooney | 07 July 2015, 20:39:39 UTC | WorkflowBuilder class for Block operations. | 07 July 2015, 22:01:42 UTC |
| 1a2e07d | Thomas B. Mooney | 07 July 2015, 21:43:19 UTC | Merge pull request #850 from tmooney/configurable_dv2_dispatcher_lsf_resource Extract DV2 dispatcher resource requirements to a configuration variable. | 07 July 2015, 21:43:19 UTC |
| 9abe84e | Thomas B. Mooney | 07 July 2015, 21:43:07 UTC | Merge pull request #852 from tmooney/design_set_reference_doesnt_matter Don't worry about design_set reference in SomaticValidation | 07 July 2015, 21:43:07 UTC |
| faaf36c | Thomas Mooney | 07 July 2015, 19:42:32 UTC | Consistently use "default" instead of "default_value". | 07 July 2015, 19:42:32 UTC |
| dcee00b | Thomas B. Mooney | 07 July 2015, 19:40:39 UTC | Merge pull request #848 from tmooney/ligers_and_tigons_and_bears_oh_my Typofix: aliger => aligner | 07 July 2015, 19:40:39 UTC |
| 328fc8f | Eddie Belter | 07 July 2015, 19:03:39 UTC | DV2: correct error message and use built in sprintf | 07 July 2015, 19:03:39 UTC |
| 1ed3e51 | Thomas Mooney | 07 July 2015, 14:37:55 UTC | Whitespace. | 07 July 2015, 14:37:55 UTC |
| 42adcb0 | Thomas Mooney | 07 July 2015, 14:37:12 UTC | Print the path we actually tried to find! | 07 July 2015, 14:37:12 UTC |
| 679e196 | Thomas Mooney | 06 July 2015, 20:55:27 UTC | Don't worry about design set reference. | 06 July 2015, 20:55:27 UTC |
| 79970db | Eddie Belter | 06 July 2015, 19:05:25 UTC | Merge pull request #835 from ebelter/rt-auth-config RT Auth: use config for RT login/password | 06 July 2015, 19:05:25 UTC |
| 82f4dde | Thomas Mooney | 06 July 2015, 18:05:31 UTC | Extract DV2 dispatcher resource requirements to a configuration variable. | 06 July 2015, 18:05:31 UTC |
| bacc066 | APipe Tester | 06 July 2015, 14:56:19 UTC | updated ur submodule to eb315e1 | 06 July 2015, 14:56:19 UTC |
| 9430b6f | Thomas B. Mooney | 06 July 2015, 13:08:16 UTC | Merge pull request #843 from tmooney/cqid_forces_instrument_data_assignment CQID: Trust the configuration to know what instrument data to assign. | 06 July 2015, 13:08:16 UTC |
| 82c9b18 | APipe Tester | 03 July 2015, 12:20:10 UTC | Updated `genome` tab completion. | 03 July 2015, 12:20:10 UTC |
| 7cbad24 | Thomas Mooney | 02 July 2015, 22:32:54 UTC | aliger => aligner | 02 July 2015, 22:32:54 UTC |
| ae7a365 | Thomas Mooney | 02 July 2015, 22:01:52 UTC | Fix typo; replace "has" with a plural verb | 02 July 2015, 22:05:53 UTC |
| ef3042d | Thomas Mooney | 02 July 2015, 22:00:48 UTC | Whitespace. | 02 July 2015, 22:00:48 UTC |
| 1e9ffca | Thomas Mooney | 02 July 2015, 22:00:04 UTC | Remove old TODOs | 02 July 2015, 22:00:04 UTC |
| 32ecd74 | Feiyu Du | 02 July 2015, 21:58:49 UTC | Merge pull request #844 from dufeiyu/bug_fix Making annotation index process optional | 02 July 2015, 21:58:49 UTC |
| 255122a | Ben Ainscough | 02 July 2015, 18:22:00 UTC | Merge pull request #821 from kkrysiak/clinseq_validation_data Add options to clinseq update-analysis to use validation data as exome data | 02 July 2015, 18:22:00 UTC |
| 2345794 | Susanna Siebert | 02 July 2015, 16:54:14 UTC | Merge pull request #841 from susannasiebert/speedseq_version New speedseq freeze version using Samblaster 0.1.22 | 02 July 2015, 16:54:14 UTC |
| e2635af | Kilannin Krysiak | 02 July 2015, 16:31:29 UTC | Fixed commented text | 02 July 2015, 16:31:29 UTC |
| ac71c9b | Allison Penner Regier | 02 July 2015, 15:52:31 UTC | Merge pull request #840 from apregier/vaf-filter Add exclusive flag to vaf-filter | 02 July 2015, 15:52:31 UTC |
| 8887314 | Thomas Mooney | 02 July 2015, 15:47:39 UTC | Trust the configuration to know what instrument data to assign. | 02 July 2015, 15:47:39 UTC |
| 0b24371 | Kilannin Krysiak | 02 July 2015, 14:44:20 UTC | Merged my_trsn and validation_as_exome into 1 parameter | 02 July 2015, 14:44:20 UTC |
| 79e7d00 | APipe Tester | 02 July 2015, 12:17:48 UTC | Updated `genome` tab completion. | 02 July 2015, 12:17:48 UTC |
| b1868a2 | APipe Tester | 02 July 2015, 12:16:14 UTC | Updated class browser cache. | 02 July 2015, 12:16:14 UTC |
| f0c2b15 | Eddie Belter | 01 July 2015, 22:07:00 UTC | RT Credentials: remove default values | 01 July 2015, 22:07:00 UTC |
| ce006ba | Eddie Belter | 01 July 2015, 21:04:45 UTC | RT Auth Config: move RT URL to config | 01 July 2015, 21:04:45 UTC |
| 6edb541 | Eddie Belter | 01 July 2015, 21:02:48 UTC | RT Auth Config add default values until the puppet changes can be implemented (the new ENVs break CLE validation) | 01 July 2015, 21:02:48 UTC |
| 0e7a157 | Eddie Belter | 01 July 2015, 20:40:54 UTC | RT Auth Config: update comments | 01 July 2015, 20:40:54 UTC |
| 7bd1b9d | Eddie Belter | 01 July 2015, 20:40:02 UTC | Config: fix POD | 01 July 2015, 20:40:06 UTC |
| a84c379 | Feiyu Du | 01 July 2015, 20:18:58 UTC | Annotation index is not required since annotation_build is optional | 01 July 2015, 20:18:58 UTC |
| db39322 | Eddie Belter | 01 July 2015, 20:05:44 UTC | Merge pull request #837 from ebelter/gm GenotypeMicroarray: remove unused import_format param | 01 July 2015, 20:05:44 UTC |
| fa11dcf | Susanna Siebert | 01 July 2015, 19:59:58 UTC | Merge pull request #822 from susannasiebert/qc_framework_verify_bam_id QC tool wrappers to run verify bam id | 01 July 2015, 19:59:58 UTC |
| e6d9eb2 | Susanna Siebert | 29 June 2015, 20:00:53 UTC | Use new speedseq freeze version | 30 June 2015, 21:50:11 UTC |
| 7af0f9a | apregier | 30 June 2015, 18:20:13 UTC | Add exclusive flag to vaf-filter | 30 June 2015, 18:20:13 UTC |
| 1a7f7b2 | mkiwala | 29 June 2015, 16:49:07 UTC | Merge pull request #838 from mkiwala/genome-ptero-integration-config Set workflow_builder_backend outside of BEGIN | 29 June 2015, 16:49:07 UTC |
| 8a0d0cb | Michael J. Kiwala | 26 June 2015, 18:05:30 UTC | Set workflow_builder_backend outside of begin Setting 'workflow_builder_backend' inside the BEGIN block prevents the new setting from taking effect outside of the BEGIN block. Before this change, the 'workflow_builder_backend' reverted back to 'workflow', which is clearly wrong for these Ptero integration tests. This bug remained uncaught for nearly two months because of another bug. The configuration of the Genome Ptero Integration had a typo which caused the tests to only run against a particular commit of the genome repository, a commit which was from April 2015. | 26 June 2015, 18:18:01 UTC |
| e76d49e | APipe Tester | 26 June 2015, 12:18:32 UTC | Updated `genome` tab completion. | 26 June 2015, 12:18:32 UTC |
| ee0d334 | Eddie Belter | 25 June 2015, 22:38:03 UTC | GenotypeMicroarray: remove unused import_format param | 25 June 2015, 22:38:03 UTC |
| e0116f0 | Eddie Belter | 25 June 2015, 19:57:25 UTC | Merge pull request #832 from ebelter/ref-align RefAlign | 25 June 2015, 19:57:25 UTC |
| 34a3d5f | Eddie Belter | 25 June 2015, 19:43:46 UTC | Merge pull request #834 from ebelter/refseq-converter RefSeq Converter: add and use valid algorithms | 25 June 2015, 19:43:46 UTC |
| 60f27b6 | Eddie Belter | 25 June 2015, 19:25:23 UTC | Merge pull request #836 from ebelter/clin-seq CHANGELOG: bump clin-seq blessed build | 25 June 2015, 19:25:23 UTC |
| db74f0c | Eddie Belter | 24 June 2015, 19:59:23 UTC | CHANGELOG: bump clin-seq blessed build | 24 June 2015, 19:59:23 UTC |
| 348750b | Allison Penner Regier | 24 June 2015, 18:33:54 UTC | Merge pull request #829 from apregier/bedpe More tweaks to compare-bedpes | 24 June 2015, 18:33:54 UTC |
| 4fbb286 | Jason Walker | 24 June 2015, 16:46:41 UTC | Merge pull request #720 from jasonwalker80/clinseq_time_point ClinSeq caTissue Timepoint | 24 June 2015, 16:46:41 UTC |
| cdd96cc | Jason Walker | 24 June 2015, 15:51:11 UTC | Merged genome/genome master with PR720 | 24 June 2015, 15:51:11 UTC |
| 5e4c84d | apregier | 24 June 2015, 15:43:28 UTC | Error if we would overwrite a given metadata column | 24 June 2015, 15:43:28 UTC |
| 4021797 | apregier | 24 June 2015, 15:43:13 UTC | Fix doc punctuation | 24 June 2015, 15:43:13 UTC |
| 2512176 | Susanna Siebert | 24 June 2015, 13:24:38 UTC | WithVariationListVcf needs to be abstract | 24 June 2015, 13:24:38 UTC |
| 30e34c5 | APipe Tester | 24 June 2015, 12:20:45 UTC | Updated `genome` tab completion. | 24 June 2015, 12:20:45 UTC |
| ed5a3c0 | APipe Tester | 24 June 2015, 12:18:49 UTC | Updated class browser cache. | 24 June 2015, 12:18:49 UTC |
| 07ae57b | Eddie Belter | 24 June 2015, 00:17:27 UTC | RT Auth: failed model tickets command uses config for rt auth | 24 June 2015, 00:17:27 UTC |
| e6e8660 | Eddie Belter | 23 June 2015, 23:54:20 UTC | RT Login: add config for RT login and auth | 23 June 2015, 23:54:20 UTC |
| c613e74 | Eddie Belter | 23 June 2015, 23:21:38 UTC | RefSeq Converter: remove uneeded use statement | 23 June 2015, 23:21:38 UTC |
| 09dff7b | Eddie Belter | 23 June 2015, 22:39:59 UTC | RefSeq Converter: use valid values from property instead of variable | 23 June 2015, 22:39:59 UTC |
| a171e36 | Eddie Belter | 23 June 2015, 22:10:24 UTC | RefSeq Converter: add and use valid algoritms variable | 23 June 2015, 22:10:24 UTC |
| 0ee62dc | Jason Walker | 23 June 2015, 20:43:39 UTC | Updated blessed build for apipe-test-clinseq-wer | 23 June 2015, 20:43:39 UTC |
| c163e7a | Eddie Belter | 23 June 2015, 19:41:37 UTC | Merge pull request #827 from ebelter/cqid Minor CQID updates | 23 June 2015, 19:41:37 UTC |
| 6739b6b | Eddie Belter | 23 June 2015, 19:38:06 UTC | RefAlign add die when getting default model name for lane qc adn no instdata is assigned add tests | 23 June 2015, 19:38:17 UTC |
| d86057e | Eddie Belter | 23 June 2015, 19:33:21 UTC | RefAlign: update accumulated alignments directory test | 23 June 2015, 19:33:21 UTC |
| 473f3eb | Susanna Siebert | 23 June 2015, 18:19:48 UTC | Change inheritance hierarchy of G::Qc::Tool::WithVariationListVcf | 23 June 2015, 18:19:48 UTC |
| a0159b8 | Eddie Belter | 23 June 2015, 18:07:23 UTC | CQID: update skipped status message | 23 June 2015, 18:07:23 UTC |
| 9dd5a47 | Adam Coffman | 23 June 2015, 15:58:35 UTC | Merge pull request #826 from acoffman/dynamic_resource_requirements_for_align_and_merge Dynamic resource requirements for AlignAndMerge (Speedseq) | 23 June 2015, 15:58:35 UTC |
| 7d7c583 | Susanna Siebert | 23 June 2015, 15:36:09 UTC | Make variation_list_build an id_by property | 23 June 2015, 15:36:09 UTC |
| baa88c9 | Adam Coffman | 23 June 2015, 15:25:04 UTC | remove confusing reuse of "class" | 23 June 2015, 15:25:04 UTC |
| 5bf8129 | Adam Coffman | 23 June 2015, 15:22:45 UTC | define abstract subroutine with appropriate error | 23 June 2015, 15:22:45 UTC |
| e4bcd7c | Susanna Siebert | 23 June 2015, 13:53:27 UTC | Remove comment | 23 June 2015, 13:53:27 UTC |
| 27275fb | Thomas B. Mooney | 23 June 2015, 13:32:01 UTC | Merge pull request #816 from tmooney/failed_model_ticket_status New command: failed-model-ticket-status | 23 June 2015, 13:32:01 UTC |
| 5135c9b | Eddie Belter | 22 June 2015, 22:03:06 UTC | Merge pull request #830 from ebelter/gmt-validation GMT Validation: status_message | 22 June 2015, 22:03:06 UTC |
| be959f8 | Eddie Belter | 22 June 2015, 21:33:23 UTC | GMT Validation: status_message | 22 June 2015, 21:33:23 UTC |
| 4b00282 | apregier | 18 June 2015, 20:07:15 UTC | Add count of unique gold calls | 22 June 2015, 20:41:10 UTC |
| 4905e17 | apregier | 18 June 2015, 16:36:15 UTC | Flatten stats hash into the general hash | 22 June 2015, 20:41:09 UTC |
| 6356f30 | apregier | 12 June 2015, 19:42:44 UTC | Make script more flexible to pass through arbitrary metadata | 22 June 2015, 20:41:08 UTC |
| 93c23bd | Eddie Belter | 19 June 2015, 22:03:52 UTC | Merge pull request #814 from ebelter/gm-dep-cron-ref-align Genotype Microarray Dependent Cron RefAlign | 19 June 2015, 22:03:52 UTC |
| 8f259d8 | Eddie Belter | 19 June 2015, 22:01:32 UTC | Merge pull request #820 from ebelter/rm-unused-solr-scripts Remove unsed solr scripts | 19 June 2015, 22:01:32 UTC |
| baace95 | Eddie Belter | 19 June 2015, 22:01:13 UTC | Merge pull request #825 from ebelter/instdata-command-update InstData Update Command | 19 June 2015, 22:01:13 UTC |
