| b26f4b5 | Thomas B. Mooney | 26 April 2016, 18:46:08 UTC | Merge pull request #1377 from tmooney/eliminate_staged_processing_profiles Remove support for old "Staged" processing profiles. | 26 April 2016, 18:46:08 UTC |
| 6a9c572 | APipe Tester | 26 April 2016, 12:17:15 UTC | Updated `gmt` tab completion. | 26 April 2016, 12:17:15 UTC |
| 14d5acd | APipe Tester | 26 April 2016, 12:16:32 UTC | Updated `genome` tab completion. | 26 April 2016, 12:16:32 UTC |
| f49da51 | APipe Tester | 26 April 2016, 12:14:57 UTC | Updated class browser cache. | 26 April 2016, 12:14:57 UTC |
| f7266c7 | Thomas B. Mooney | 25 April 2016, 22:30:40 UTC | Merge pull request #1336 from tmooney/remove_old_somatic_pipeline Remove "Somatic" model type. | 25 April 2016, 22:30:40 UTC |
| 4531069 | Thomas Mooney | 30 March 2016, 20:49:22 UTC | Remove "Somatic" model type. | 25 April 2016, 20:03:28 UTC |
| f974274 | Thomas B. Mooney | 25 April 2016, 20:01:05 UTC | Merge pull request #1335 from tmooney/remove_old_somaticcapture_pipeline Remove "SomaticCapture" model type. | 25 April 2016, 20:01:05 UTC |
| 2ffa52b | Thomas Mooney | 25 April 2016, 15:02:01 UTC | Remove support for old "Staged" processing profiles. | 25 April 2016, 15:02:01 UTC |
| d442a38 | Thomas B. Mooney | 25 April 2016, 14:43:40 UTC | Merge pull request #1291 from tmooney/farewell_amplicon_assembly Remove "AmpliconAseembly" model type. | 25 April 2016, 14:43:40 UTC |
| ba8d575 | sleongmgi | 25 April 2016, 14:24:23 UTC | Merge pull request #1376 from sleongmgi/check-host-max-memory add the java max memory used flag. | 25 April 2016, 14:24:23 UTC |
| e33479b | Shin Leong | 25 April 2016, 13:29:48 UTC | change it to be on the java_command_line to set the tmp_dir if it not set. | 25 April 2016, 13:29:48 UTC |
| 181db09 | Shin Leong | 25 April 2016, 13:21:49 UTC | set the default tmp directory. | 25 April 2016, 13:21:49 UTC |
| 5bf928f | Thomas B. Mooney | 25 April 2016, 13:05:52 UTC | Merge pull request #1375 from tmooney/remove_old_rnaseq_events Remove old RnaSeq events. | 25 April 2016, 13:05:52 UTC |
| 624e3c3 | Thomas B. Mooney | 25 April 2016, 13:05:37 UTC | Merge pull request #1366 from tmooney/smallrna_uses_workflowbuilder SmallRna uses WorkflowBuilder | 25 April 2016, 13:05:37 UTC |
| 494a798 | APipe Tester | 23 April 2016, 12:17:39 UTC | Updated `gmt` tab completion. | 23 April 2016, 12:17:39 UTC |
| 53c12df | APipe Tester | 23 April 2016, 12:16:55 UTC | Updated `genome` tab completion. | 23 April 2016, 12:16:55 UTC |
| 6e6a529 | APipe Tester | 23 April 2016, 12:15:20 UTC | Updated class browser cache. | 23 April 2016, 12:15:20 UTC |
| 6320ff5 | Jason Walker | 22 April 2016, 15:32:26 UTC | Merge pull request #1373 from jasonwalker80/manta_tool New GMT : Manta structural variant caller | 22 April 2016, 15:32:26 UTC |
| c996087 | Jason Walker | 22 April 2016, 14:53:54 UTC | Merge pull request #1374 from jasonwalker80/speedseq_sv DV2 : Speedseq Sv | 22 April 2016, 14:53:54 UTC |
| f2bd63c | Shin Leong | 22 April 2016, 14:39:10 UTC | add the java max memory used flag. | 22 April 2016, 14:39:10 UTC |
| 1fd25a3 | APipe Tester | 22 April 2016, 12:16:37 UTC | Updated `genome` tab completion. | 22 April 2016, 12:16:37 UTC |
| 8705fa3 | APipe Tester | 22 April 2016, 12:15:03 UTC | Updated class browser cache. | 22 April 2016, 12:15:03 UTC |
| 63a861e | Thomas Mooney | 21 April 2016, 21:34:08 UTC | Remove old RnaSeq events. These haven't been used in a long time and aren't referenced anywhere in the code anymore. Loading any past events will yield an object of class Genome::Model::Event::Generic. | 21 April 2016, 21:34:08 UTC |
| a49aba4 | Jason Walker | 21 April 2016, 20:20:53 UTC | Add a symlink with the expected file name for SVs. | 21 April 2016, 20:20:53 UTC |
| 50a2c28 | Thomas B. Mooney | 21 April 2016, 19:54:21 UTC | Merge pull request #1176 from ebelter/metagenomic-composition-shotgun Remove metagenomic composition shotgun model type | 21 April 2016, 19:54:21 UTC |
| f756122 | Jason Walker | 21 April 2016, 17:20:09 UTC | Update the tests to only build the command array ref. Use the list form of shellcmd. | 21 April 2016, 17:20:09 UTC |
| 46a3ee3 | Jason Walker | 21 April 2016, 16:47:42 UTC | Update a comment since jobs is now part of the class description. | 21 April 2016, 16:47:42 UTC |
| 399ae56 | Jason Walker | 21 April 2016, 16:46:38 UTC | Add a jobs arg to control the number of processes used during the internal manta orkflow. | 21 April 2016, 16:46:38 UTC |
| f121576 | Jason Walker | 21 April 2016, 15:49:23 UTC | Add LSF resource to increase RAM (12gb) and define tmp space(10gb). | 21 April 2016, 15:49:23 UTC |
| b52e211 | Thomas B. Mooney | 21 April 2016, 13:36:55 UTC | Merge pull request #1175 from ebelter/metagenomic-shotgun Remove metagenomic shotgun model type | 21 April 2016, 13:36:55 UTC |
| 691cc9b | APipe Tester | 21 April 2016, 12:17:43 UTC | Updated `gmt` tab completion. | 21 April 2016, 12:17:43 UTC |
| 705a667 | APipe Tester | 21 April 2016, 12:17:01 UTC | Updated `genome` tab completion. | 21 April 2016, 12:17:01 UTC |
| 47ad062 | APipe Tester | 21 April 2016, 12:15:27 UTC | Updated class browser cache. | 21 April 2016, 12:15:27 UTC |
| 7ffbb8e | Jason Walker | 20 April 2016, 21:10:30 UTC | A few changes to allow the SpeedseqSv DV2 module to run within a build. | 20 April 2016, 21:10:30 UTC |
| d136f32 | Thomas B. Mooney | 20 April 2016, 20:49:46 UTC | Merge pull request #1164 from tmooney/farewell_convergence_models Remove "Convergence" model type. | 20 April 2016, 20:49:46 UTC |
| 19bde0c | Jason Walker | 20 April 2016, 19:14:27 UTC | whitespace. | 20 April 2016, 19:14:27 UTC |
| 47d64ec | Jason Walker | 20 April 2016, 19:13:40 UTC | remove unnecessary exits from tests, *.t | 20 April 2016, 19:13:40 UTC |
| ec5b990 | Jason Walker | 20 April 2016, 19:11:45 UTC | update the syntax in the comments above _tool_param_args and _tool_input_args. | 20 April 2016, 19:11:45 UTC |
| 18ed39e | Jason Walker | 20 April 2016, 18:54:41 UTC | rely on the valid_values meta property of version rather than available_versions subroutine. | 20 April 2016, 18:54:41 UTC |
| 64f8689 | Jason Walker | 20 April 2016, 18:44:25 UTC | Add 1; and newlines as needed. | 20 April 2016, 18:44:25 UTC |
| c63546f | Thomas B. Mooney | 20 April 2016, 17:43:13 UTC | Merge pull request #1371 from tmooney/use_genome_in_path_test Use Genome so test-tracker succeeds. | 20 April 2016, 17:43:13 UTC |
| 2cf30d5 | sleongmgi | 20 April 2016, 16:05:21 UTC | Merge pull request #1372 from sleongmgi/sleong-deal-with-warning-message deal with warning message | 20 April 2016, 16:05:21 UTC |
| af982e6 | Jason Walker | 20 April 2016, 16:04:19 UTC | Initial revision of new tool tree and commands to run the Manta SV caller. | 20 April 2016, 16:04:19 UTC |
| d7d0af5 | Avi Ramu | 20 April 2016, 16:02:25 UTC | Merge pull request #1367 from gatoravi/clinseq_workflow_fix Add wgs/exome only if input builds exist | 20 April 2016, 16:02:25 UTC |
| 44c88e9 | Thomas B. Mooney | 20 April 2016, 15:38:03 UTC | Merge pull request #1369 from tmooney/refalign_summary_test_doesnt_lock RefAlign Summary Test Doesn't Lock | 20 April 2016, 15:38:03 UTC |
| b0b1890 | sleongmgi | 20 April 2016, 12:32:40 UTC | Merge pull request #1370 from sleongmgi/sleong-files-do-not-exist-cause-wait-forever fix the test that wait forever for input if the files do not exist. | 20 April 2016, 12:32:40 UTC |
| 631c689 | APipe Tester | 20 April 2016, 12:16:35 UTC | Updated `genome` tab completion. | 20 April 2016, 12:16:35 UTC |
| 27eff02 | Shin Leong | 19 April 2016, 17:43:38 UTC | default the $unfiltered_snp_calls to $filtered_snp_calls. Move the lq_snp_calls in the block. | 19 April 2016, 17:43:38 UTC |
| dd4385f | Shin Leong | 19 April 2016, 17:20:34 UTC | deal with the warning logger message and turn print to diag. | 19 April 2016, 17:31:46 UTC |
| 663535f | Thomas Mooney | 19 April 2016, 17:13:08 UTC | Use Genome so test-tracker succeeds. | 19 April 2016, 17:13:08 UTC |
| cd51c9e | Jason Walker | 19 April 2016, 17:00:16 UTC | Merge pull request #1350 from jasonwalker80/sv_annotation_build38 Add build38 options for downloading SV annotation files. | 19 April 2016, 17:00:16 UTC |
| f819d91 | Shin Leong | 19 April 2016, 16:06:11 UTC | fix the test that wait forever for input if the files do not exist. | 19 April 2016, 16:06:11 UTC |
| 610cb37 | sleongmgi | 19 April 2016, 16:01:54 UTC | Merge pull request #1368 from sleongmgi/sleong-update-config-file-not-to-use-sata420 update the config file that uses sata420. | 19 April 2016, 16:01:54 UTC |
| 6a0a3a1 | Thomas Mooney | 19 April 2016, 15:40:29 UTC | Use an actual tempdir instead of hard-coding /tmp. | 19 April 2016, 15:40:29 UTC |
| 0d708a2 | Jason Walker | 19 April 2016, 15:25:26 UTC | Add hg38 table name. | 19 April 2016, 15:25:26 UTC |
| 1db82a4 | Thomas Mooney | 19 April 2016, 15:19:11 UTC | Set NO_COMMIT to make doubly sure we're not really doing work! | 19 April 2016, 15:19:11 UTC |
| 2f1d5d7 | Thomas Mooney | 19 April 2016, 15:17:39 UTC | Set a custom lock directory for testing. We aren't really setting metrics, so don't need to lock. | 19 April 2016, 15:17:39 UTC |
| e326e1c | Avinash Ramu | 18 April 2016, 20:21:57 UTC | Move mutation spectrum into the if-block | 18 April 2016, 20:21:57 UTC |
| d169774 | Avinash Ramu | 18 April 2016, 20:16:25 UTC | Revert "Add wgs/exome only if input builds exist" This reverts commit 00711c6188d9707487ed6229908cdbea6d858308. | 18 April 2016, 20:16:25 UTC |
| 9d9e62a | Shin Leong | 18 April 2016, 19:57:12 UTC | update the config file that uses sata420. | 18 April 2016, 19:57:12 UTC |
| 00711c6 | Avinash Ramu | 18 April 2016, 19:56:21 UTC | Add wgs/exome only if input builds exist Currently if a clin-seq build only has a exome_model as an input, the wgs version of create-mutation-spectrum is still added as a step in the workflow. This pull-request hopes to fix that. | 18 April 2016, 19:56:21 UTC |
| 6cb00bf | Jason Walker | 18 April 2016, 17:47:59 UTC | Merge pull request #1365 from jasonwalker80/mouse_84_38_annotation Annotator updates for Ensembl 84 | 18 April 2016, 17:47:59 UTC |
| 7fbe17b | Feiyu Du | 14 April 2016, 21:32:53 UTC | Merge pull request #1357 from dufeiyu/cle_test_update Update CLE Test | 14 April 2016, 21:32:53 UTC |
| aed9331 | Thomas Mooney | 14 April 2016, 19:42:26 UTC | Convert to WorkflowBuilder. | 14 April 2016, 19:42:26 UTC |
| 9d713f7 | Thomas Mooney | 14 April 2016, 19:39:55 UTC | Whitespace. | 14 April 2016, 19:39:55 UTC |
| eeef94a | Thomas Mooney | 14 April 2016, 19:37:03 UTC | Convert to WorkflowBuilder. | 14 April 2016, 19:38:08 UTC |
| e8008ca | Thomas Mooney | 14 April 2016, 19:33:52 UTC | Whitespace. | 14 April 2016, 19:33:52 UTC |
| 5edc4f3 | Thomas Mooney | 14 April 2016, 19:29:23 UTC | Whitespace. | 14 April 2016, 19:29:23 UTC |
| c8c6a08 | Thomas Mooney | 14 April 2016, 19:24:27 UTC | Use WorkflowBuilder to make main workfow. | 14 April 2016, 19:24:27 UTC |
| 3284c0b | Jason Walker | 14 April 2016, 16:42:13 UTC | Add IG_pseudogene as a coding pseudogene biotype. Also move biotype_class as a class method useful for debugging and troubleshooting missing biotypes. | 14 April 2016, 16:42:13 UTC |
| 3b2460c | Jason Walker | 14 April 2016, 16:00:31 UTC | Add scRNA to the list of ncrna, non-coding RNA. | 14 April 2016, 16:00:31 UTC |
| 2ae575b | Thomas B. Mooney | 14 April 2016, 14:08:41 UTC | Merge pull request #1362 from tmooney/somvar_reports_lsf_resource_config Make LSF resource for SomaticVariation report step configurable. | 14 April 2016, 14:08:41 UTC |
| 3a07f7b | Thomas B. Mooney | 14 April 2016, 13:27:03 UTC | Merge pull request #1361 from tmooney/dont_mail_prodbuilder_reports Don't send out build reports for any production users. | 14 April 2016, 13:27:03 UTC |
| c01fdfb | APipe Tester | 14 April 2016, 12:18:34 UTC | Updated `genome` tab completion. | 14 April 2016, 12:18:34 UTC |
| 132ff5a | Avi Ramu | 13 April 2016, 21:20:09 UTC | Merge pull request #1346 from gatoravi/clinseq_junctions_fix Use Genome::Utility | 13 April 2016, 21:20:09 UTC |
| 2ec552c | Jason Walker | 13 April 2016, 19:17:38 UTC | Add bidirectional_promoter_lncRNA as a ncrna to biotype hash. | 13 April 2016, 19:17:38 UTC |
| b3eb025 | Thomas B. Mooney | 13 April 2016, 18:13:06 UTC | Merge pull request #1355 from tmooney/apipebuilder_in_build_commands Allow apipe-builder to use AbandonAndQueue. | 13 April 2016, 18:13:06 UTC |
| 2227bde | Avinash Ramu | 13 April 2016, 16:10:20 UTC | use Genome::Utility::Text first | 13 April 2016, 16:10:20 UTC |
| 9cb1bfb | Thomas Mooney | 13 April 2016, 14:35:01 UTC | Improve comment accuracy. | 13 April 2016, 14:35:01 UTC |
| f700129 | Thomas Mooney | 13 April 2016, 13:44:24 UTC | Make LSF resource for SomaticVariation report step configurable. | 13 April 2016, 13:44:24 UTC |
| 4f0c46d | Thomas B. Mooney | 13 April 2016, 13:25:57 UTC | Merge pull request #1354 from tmooney/queue_specification_for_instrumentdata_merge_command MergeAlignments: Specify an LSF queue configuration. | 13 April 2016, 13:25:57 UTC |
| dfc191c | Thomas B. Mooney | 13 April 2016, 13:25:36 UTC | Merge pull request #1339 from tmooney/ensembl_commands_use_inline_workflow Use inline workflow backend instead of NO_LSF environment variable. | 13 April 2016, 13:25:36 UTC |
| 8ce157d | Thomas Mooney | 13 April 2016, 13:23:12 UTC | Don't send out reports for any production users. | 13 April 2016, 13:23:12 UTC |
| ef048f1 | sleongmgi | 13 April 2016, 12:30:58 UTC | Merge pull request #1356 from sleongmgi/sleong-run-blast-path-fix fix the path. | 13 April 2016, 12:30:58 UTC |
| bd2b00b | APipe Tester | 13 April 2016, 12:18:28 UTC | Updated `genome` tab completion. | 13 April 2016, 12:18:28 UTC |
| af26352 | APipe Tester | 13 April 2016, 12:16:44 UTC | Updated class browser cache. | 13 April 2016, 12:16:44 UTC |
| 82edf40 | Avinash Ramu | 12 April 2016, 21:15:49 UTC | Add use File::Spec; | 12 April 2016, 21:15:49 UTC |
| 20940ef | Avinash Ramu | 12 April 2016, 21:08:43 UTC | Make fetching backwards compatible | 12 April 2016, 21:08:43 UTC |
| ba8a0e0 | Feiyu Du | 12 April 2016, 19:28:24 UTC | Update blessed process for CLE test | 12 April 2016, 19:28:24 UTC |
| a21cdb4 | Shin Leong | 12 April 2016, 18:59:39 UTC | fix the path. | 12 April 2016, 18:59:39 UTC |
| 3b9c5d8 | Thomas B. Mooney | 12 April 2016, 18:54:03 UTC | Merge pull request #1351 from tmooney/stop_testing_on_old_perl Remove some old Perl 5.8 tests. | 12 April 2016, 18:54:03 UTC |
| 1d0118f | sleongmgi | 12 April 2016, 18:44:28 UTC | Merge pull request #1343 from tmooney/correct_fasta_access_in_bsmap_tests Use correct accessor to get FASTA for bsmap tests. | 12 April 2016, 18:44:28 UTC |
| b3cb13d | Eddie Belter | 12 April 2016, 17:41:56 UTC | Merge pull request #1349 from ebelter/qc-config-cmds View and Diff Commands for QC Config | 12 April 2016, 17:41:56 UTC |
| 1667c86 | sleongmgi | 12 April 2016, 17:17:06 UTC | Merge pull request #1347 from sleongmgi/change-bsub-wait-for-completion Change bsub wait for completion | 12 April 2016, 17:17:06 UTC |
| e099796 | Thomas Mooney | 12 April 2016, 15:01:10 UTC | This list now matches the inheritance, so remove the check. | 12 April 2016, 15:01:10 UTC |
| 36cf282 | Thomas Mooney | 12 April 2016, 14:43:48 UTC | Remove "Start" from list--it doesn't even inherit from this! | 12 April 2016, 14:43:48 UTC |
| afc05f4 | Thomas Mooney | 12 April 2016, 14:43:21 UTC | Remove reference to non-existent "Remove" command. | 12 April 2016, 14:43:21 UTC |
| 69ab9eb | Thomas Mooney | 12 April 2016, 14:42:55 UTC | Add AbandonAndQueue to apipe-builderable commands. | 12 April 2016, 14:42:55 UTC |
| 36b9573 | Thomas Mooney | 12 April 2016, 14:41:40 UTC | Remove old SVN noise. | 12 April 2016, 14:41:40 UTC |
| 2b57382 | Thomas Mooney | 12 April 2016, 13:47:16 UTC | MergeAlignments: Specify an LSF queue configuration. | 12 April 2016, 13:47:16 UTC |
