| 975fabc | Thomas B. Mooney | 15 August 2017, 17:49:07 UTC | Merge pull request #1742 from tmooney/more_transition_test_fixes More Test Fixes | 15 August 2017, 17:49:07 UTC |
| 1ae89ed | Thomas B. Mooney | 15 August 2017, 15:30:29 UTC | Add define-docs testcase for new CWL pipeline. | 15 August 2017, 17:28:55 UTC |
| 4f70cf2 | Thomas B. Mooney | 15 August 2017, 15:29:05 UTC | Use dummy IDs when making fake disk groups. | 15 August 2017, 15:29:05 UTC |
| 7dcadaa | Thomas B. Mooney | 15 August 2017, 15:24:15 UTC | Remove tests that depend on old GSC modules. This ends up looking at an ancient version of the GSC modules that is no longer functional. | 15 August 2017, 15:26:49 UTC |
| 5f0b9ea | Thomas B. Mooney | 15 August 2017, 15:20:36 UTC | Correct column type for edit_date in MISC_UPDATE. | 15 August 2017, 15:20:36 UTC |
| f949546 | Thomas B. Mooney | 15 August 2017, 13:34:18 UTC | Merge pull request #1741 from tmooney/move_bamcram_convert_commands Move new BAM <=> CRAM conversion commands for command-line use. | 15 August 2017, 13:34:18 UTC |
| b1d6a02 | Thomas B. Mooney | 15 August 2017, 13:34:01 UTC | Merge pull request #1740 from tmooney/use_dummy_ids_for_test_volumes Ensure create_dummy_volume uses dummy IDs. | 15 August 2017, 13:34:01 UTC |
| ec41774 | Thomas B. Mooney | 15 August 2017, 12:55:05 UTC | Use Dummy IDs in tests that themselves generated volumes. | 15 August 2017, 12:55:05 UTC |
| d932f3f | Thomas B. Mooney | 14 August 2017, 21:35:53 UTC | Ensure dummy volumes created by test factory use DummyIDs. | 15 August 2017, 12:54:55 UTC |
| 4e0033a | Thomas B. Mooney | 14 August 2017, 21:23:45 UTC | Move new BAM <=> CRAM conversion commands for command-line use. There are two similar command directories, but only one of them is included in `genome`. | 14 August 2017, 21:23:45 UTC |
| 3603e9b | Thomas B. Mooney | 14 August 2017, 20:47:33 UTC | Ensure dummy volume uses dummy IDs. Even if we're not running in Dummy ID mode, we still don't want to query a real sequence generator for these fake volumes. | 14 August 2017, 20:47:33 UTC |
| 8446144 | Thomas B. Mooney | 14 August 2017, 16:35:10 UTC | Merge pull request #1739 from tmooney/synch_pg_compat_fixes SQL updates to Synchronize classes for Postgres compatibility. | 14 August 2017, 16:35:10 UTC |
| 68abb8d | Thomas B. Mooney | 14 August 2017, 14:06:21 UTC | SQL updates for Postgres compatibility. | 14 August 2017, 14:06:21 UTC |
| 45db7a9 | APipe Tester | 11 August 2017, 12:15:48 UTC | Updated `genome` tab completion. | 11 August 2017, 12:15:48 UTC |
| 91c6ec8 | APipe Tester | 11 August 2017, 12:14:14 UTC | Updated class browser cache. | 11 August 2017, 12:14:14 UTC |
| 28ea85d | Thomas B. Mooney | 10 August 2017, 18:18:05 UTC | Merge pull request #1735 from tmooney/alignment_result_cram_commands First version of BAM <=> CRAM conversion for Merged AlignmentResults | 10 August 2017, 18:18:05 UTC |
| f0f971f | Thomas B. Mooney | 10 August 2017, 18:12:17 UTC | Merge pull request #1710 from tmooney/cwl_model_type Draft CWL Pipeline type. | 10 August 2017, 18:12:17 UTC |
| ada19fb | Thomas B. Mooney | 09 August 2017, 13:24:12 UTC | Merge pull request #1732 from tmooney/improve_subjectmapping_predict_errors Fix error messages in SomVal SubjectMapping prediction. | 09 August 2017, 13:24:12 UTC |
| 6e348aa | Thomas B. Mooney | 03 August 2017, 13:39:46 UTC | Merge pull request #1737 from tmooney/fix_feature_list_and_capture_tests Fixes for FeatureList tests and Removal of "Capture" tree. | 03 August 2017, 13:39:46 UTC |
| 14c5876 | Jason Walker | 02 August 2017, 17:58:26 UTC | Merge pull request #1733 from tmooney/correct_error_message_in_allocation_mover Disk Allocation move: Report correct new path in error message. | 02 August 2017, 17:58:26 UTC |
| 88493a1 | Thomas B. Mooney | 26 July 2017, 17:12:22 UTC | Remove classes for obsolete "capture" database tables. These tables were dropped from the LIMS, so there's nothing to see here! | 26 July 2017, 17:12:22 UTC |
| af63a4b | Thomas B. Mooney | 26 July 2017, 16:59:35 UTC | FeatureList tests: Replace symlink with sample BED file. | 26 July 2017, 17:05:44 UTC |
| 049da8a | Thomas B. Mooney | 18 July 2017, 22:48:27 UTC | Add locking to prevent concurrent conversion operations. | 18 July 2017, 22:48:27 UTC |
| 50f249a | Thomas B. Mooney | 17 July 2017, 21:57:45 UTC | Commands to convert an alignment result between BAM and CRAM. | 17 July 2017, 22:01:49 UTC |
| 7994661 | Thomas B. Mooney | 10 July 2017, 22:08:52 UTC | Remove extra error-checking--the lower-level call already checks. | 10 July 2017, 22:08:52 UTC |
| 32c7eb9 | Thomas B. Mooney | 10 July 2017, 20:52:31 UTC | A command to "restart" CwlPipeline builds. This code is based on the old Genome::Model::Build::Command::Restart and Genome::Model::Build->restart that were removed in 2011 and 2014 respectively. This should take advantage of cwltoil's "--restart" flag to continue an in-progress workflow. | 10 July 2017, 20:52:31 UTC |
| 968a7f0 | Thomas B. Mooney | 10 July 2017, 20:50:54 UTC | Test Factory for CwlPipeline models. | 10 July 2017, 20:50:54 UTC |
| 97916d7 | Thomas B. Mooney | 10 July 2017, 18:05:42 UTC | Remove the "input_data" extra filter from the bx before UR's get/create. | 10 July 2017, 18:05:42 UTC |
| 0ba6e0a | Thomas B. Mooney | 10 July 2017, 13:51:14 UTC | Merge pull request #1725 from tmooney/remove_strange_file_copy_in_processvalidation_test Remove strange file copy in process-validation test. | 10 July 2017, 13:51:14 UTC |
| 24bd0e0 | Thomas B. Mooney | 06 July 2017, 21:52:54 UTC | Fix processing-profile creator and add test. | 06 July 2017, 21:52:54 UTC |
| 058c8b8 | Thomas B. Mooney | 06 July 2017, 21:21:18 UTC | Fill in some missing documentation sections. | 06 July 2017, 21:21:18 UTC |
| 56545b4 | Thomas B. Mooney | 06 July 2017, 20:19:25 UTC | A matching special case for "get" as for "create" with input_data. | 06 July 2017, 20:19:25 UTC |
| 7e21b08 | Thomas B. Mooney | 05 July 2017, 22:33:55 UTC | Allow for input data to be specified at creation time. | 05 July 2017, 22:33:55 UTC |
| 5829eef | Thomas B. Mooney | 05 July 2017, 21:23:29 UTC | Commands for manipulating inputs of CwlPipeline models. The logic used to implement the `add` command should be able to be used to add inputs at creation time (via CQID or some other means), but it hasn't been connected to create() yet. | 05 July 2017, 22:33:39 UTC |
| d172a1b | Thomas B. Mooney | 05 July 2017, 21:07:52 UTC | Add a sub-command group. | 05 July 2017, 21:07:52 UTC |
| 50ccaac | Jason Walker | 03 July 2017, 21:27:26 UTC | Merge pull request #1729 from jasonwalker80/fix_move_help clarify docs for disk group when moving allocations. | 03 July 2017, 21:27:26 UTC |
| d2e4895 | Jason Walker | 03 July 2017, 21:24:11 UTC | correct punctuation | 03 July 2017, 21:24:11 UTC |
| 58b7918 | Thomas B. Mooney | 03 July 2017, 21:01:14 UTC | Disk Allocation move: Report correct new path in error message. | 03 July 2017, 21:01:14 UTC |
| 1ca5f69 | Thomas B. Mooney | 03 July 2017, 19:19:27 UTC | Make the sets be IDs so some operations don't stringify object refs. | 03 July 2017, 19:19:27 UTC |
| 4b3d309 | Thomas B. Mooney | 03 July 2017, 19:19:07 UTC | Refer back to the original arrays instead of reading the set membership. | 03 July 2017, 19:19:07 UTC |
| 07b4edc | Jason Walker | 27 June 2017, 14:44:12 UTC | Merge pull request #1730 from jasonwalker80/skip_454_sync Skip RegionIndex454 when syncing LIMS-GMS | 27 June 2017, 14:44:12 UTC |
| 3c0590f | Jason Walker | 27 June 2017, 14:12:37 UTC | Update the number of entity names in Dictionary test. | 27 June 2017, 14:12:37 UTC |
| 423a044 | Jason Walker | 26 June 2017, 19:10:20 UTC | Another occurence of the run_region_454 table queried by the sync. | 26 June 2017, 19:10:20 UTC |
| 91712ba | Jason Walker | 26 June 2017, 18:51:03 UTC | Skip RegionIndex454 when syncing LIMS-GMS | 26 June 2017, 18:51:03 UTC |
| 4e60639 | Jason Walker | 22 June 2017, 18:33:12 UTC | clarify docs for disk group when moving allocations. | 22 June 2017, 18:33:12 UTC |
| 2c0c17e | Jason Walker | 22 June 2017, 18:15:41 UTC | Merge pull request #1728 from jasonwalker80/increase_tophat_ram Increate PerLaneTophat LSF RAM to 64GB from 32GB | 22 June 2017, 18:15:41 UTC |
| 908e1cb | Jason Walker | 22 June 2017, 18:13:27 UTC | Merge pull request #1727 from jasonwalker80/move_active_allocations Only attempt to move allocations that are still active. | 22 June 2017, 18:13:27 UTC |
| 0b99149 | Jason Walker | 22 June 2017, 16:59:50 UTC | Only attempt to move allocations that are still active. | 22 June 2017, 16:59:50 UTC |
| 9ee928d | Jason Walker | 22 June 2017, 16:55:18 UTC | Increate PerLaneTophat LSF RAM to 64GB from 32GB | 22 June 2017, 16:55:18 UTC |
| c7bcbed | Jason Walker | 19 June 2017, 20:17:46 UTC | Merge pull request #1724 from tmooney/alignment_results_support_alternate_filetypes Support the notion of alternative filetypes for alignment files. | 19 June 2017, 20:17:46 UTC |
| 6935448 | APipe Tester | 19 June 2017, 20:02:09 UTC | Updated `gmt` tab completion. | 19 June 2017, 20:02:09 UTC |
| 5eb1a7a | APipe Tester | 19 June 2017, 19:59:34 UTC | Updated `genome` tab completion. | 19 June 2017, 19:59:34 UTC |
| 0a8a5eb | APipe Tester | 19 June 2017, 19:55:26 UTC | Updated class browser cache. | 19 June 2017, 19:55:26 UTC |
| 74d79e0 | Thomas B. Mooney | 15 June 2017, 13:02:28 UTC | Remove strange file copy in process-validation test. As best I can tell, this is copying a file and then diffing that file against its copy... Just skip doing that :) | 15 June 2017, 13:03:12 UTC |
| 887b2c5 | Thomas B. Mooney | 14 June 2017, 18:12:05 UTC | Support the notion of alternative filetypes for alignment files. Nothing uses this...yet. It creates feature-parity with the proposed filetype field for external merged results in #1719. | 14 June 2017, 18:12:05 UTC |
| c406ee5 | Thomas B. Mooney | 06 June 2017, 21:40:45 UTC | Make sure `bsub` is not quiet. | 06 June 2017, 21:52:26 UTC |
| 704bd10 | Thomas B. Mooney | 06 June 2017, 15:59:04 UTC | Escape braces for compliance with newer Perls. | 06 June 2017, 15:59:04 UTC |
| c70e451 | Thomas B. Mooney | 06 June 2017, 14:33:15 UTC | Add the "--restart" option if the jobStore already exists. | 06 June 2017, 14:33:15 UTC |
| 4fa3311 | Thomas B. Mooney | 05 June 2017, 21:51:21 UTC | Specify the queue for LSF jobs launched by toil. | 05 June 2017, 21:51:21 UTC |
| 91fa64c | Thomas B. Mooney | 05 June 2017, 21:00:16 UTC | Consistently use model object to get PP params. | 05 June 2017, 21:00:16 UTC |
| 70e19a8 | Thomas B. Mooney | 05 June 2017, 20:34:09 UTC | Allow the specification of a per-pipeline docker image. The base command will still run in using the `lsb_sub_addtional` genome configuration, but for pipelines that don't use "DockerRequirement" we'll want to specify an image for workers to use. | 05 June 2017, 20:34:09 UTC |
| 7d9e067 | Thomas B. Mooney | 01 June 2017, 22:22:24 UTC | A mechanism by which to generate the YAML from a script. | 01 June 2017, 22:22:24 UTC |
| e7d28e0 | Thomas B. Mooney | 01 June 2017, 22:18:42 UTC | Merge pull request #1723 from tmooney/methratio_uses_job_group Specify a job group to limit concurrent MethRatio processes. | 01 June 2017, 22:18:42 UTC |
| f22fc96 | Thomas B. Mooney | 01 June 2017, 20:58:30 UTC | Make clear we don't handle object inputs yet. | 01 June 2017, 21:00:05 UTC |
| 2c1726b | Thomas B. Mooney | 01 June 2017, 20:14:12 UTC | First version of a processing-profile creator for a new pipeline. | 01 June 2017, 20:14:12 UTC |
| 561bb13 | Thomas B. Mooney | 01 June 2017, 15:26:06 UTC | Specify a job group to limit concurrent MethRatio processes. | 01 June 2017, 15:26:06 UTC |
| 57f9260 | Thomas B. Mooney | 30 May 2017, 17:29:55 UTC | Merge pull request #1717 from tmooney/use_sys_abspath_in_snapshot_revision Use Genome::Sys->abs_path for DB and snapshot locations. | 30 May 2017, 17:29:55 UTC |
| 5c5d5ec | Thomas B. Mooney | 30 May 2017, 17:00:01 UTC | Merge pull request #1722 from tmooney/move_allocations_doesnt_push_undef Better handling of disk groups in `gmb move-allocations`. | 30 May 2017, 17:00:01 UTC |
| 9e55d49 | Thomas B. Mooney | 30 May 2017, 16:13:22 UTC | Complain if we can't determine a disk group to use. | 30 May 2017, 16:13:22 UTC |
| ef422e3 | Thomas B. Mooney | 30 May 2017, 16:12:42 UTC | Only include the build's allocation if it has one! | 30 May 2017, 16:12:42 UTC |
| 38f39fe | Thomas B. Mooney | 24 May 2017, 20:10:12 UTC | Merge pull request #1716 from tmooney/typo_director_plus_y Typo fix: add "y" to "directory". | 24 May 2017, 20:10:12 UTC |
| 48704b0 | Thomas B. Mooney | 23 May 2017, 15:07:36 UTC | Use Genome::Sys->abs_path for DB and snapshot locations. This is in a further effort to avoid /vol/ paths. | 23 May 2017, 15:07:36 UTC |
| ec5b8a0 | Thomas B. Mooney | 22 May 2017, 22:47:09 UTC | Merge pull request #1709 from tmooney/support_bsmap_in_movecommand Add Bsmap alignment as a possible result class for ReferenceAlignment. | 22 May 2017, 22:47:09 UTC |
| 18d711a | Thomas B. Mooney | 22 May 2017, 22:46:56 UTC | Merge pull request #1711 from tmooney/remove_keggpathway_tool Remove disused "ImportTranscriptFeature" tool tree. | 22 May 2017, 22:46:56 UTC |
| 5bf6d35 | Thomas B. Mooney | 22 May 2017, 22:46:45 UTC | Merge pull request #1712 from tmooney/remove_methylarray_tree Remove disused "MethylArray" tool tree. | 22 May 2017, 22:46:45 UTC |
| 431c0f1 | Thomas B. Mooney | 22 May 2017, 22:46:34 UTC | Merge pull request #1713 from tmooney/remove_simulation_tree Remove disused "Simulation" tool tree. | 22 May 2017, 22:46:34 UTC |
| 43ad7ed | Thomas B. Mooney | 22 May 2017, 22:46:21 UTC | Merge pull request #1714 from tmooney/remove_svsim_tree Remove disused "SvSim" tool tree. | 22 May 2017, 22:46:21 UTC |
| 0752cfc | Thomas B. Mooney | 22 May 2017, 22:46:03 UTC | Merge pull request #1715 from tmooney/only_process_each_sr_once Only process each SR once when purging an AnP. | 22 May 2017, 22:46:03 UTC |
| df49245 | Thomas B. Mooney | 22 May 2017, 21:58:49 UTC | Typo fix: add "y" to "directory". | 22 May 2017, 21:58:49 UTC |
| f0559b7 | Thomas B. Mooney | 18 May 2017, 21:34:28 UTC | Only process each SR once when purging an AnP. | 18 May 2017, 21:34:28 UTC |
| 51e91ba | Thomas B. Mooney | 18 May 2017, 14:38:51 UTC | Remove disused "SvSim" tool tree. | 18 May 2017, 14:46:32 UTC |
| a71620d | Thomas B. Mooney | 18 May 2017, 14:34:38 UTC | Remove disused "Simulation" tool tree. | 18 May 2017, 14:34:38 UTC |
| ccebf22 | Thomas B. Mooney | 18 May 2017, 14:25:43 UTC | Remove disused "MethylArray" tool tree. | 18 May 2017, 14:25:43 UTC |
| 25c7e99 | Thomas B. Mooney | 18 May 2017, 14:16:32 UTC | Remove disused "ImportTranscriptFeature" tool tree. | 18 May 2017, 14:16:32 UTC |
| 707dc3e | Thomas B. Mooney | 17 May 2017, 20:17:43 UTC | First draft of CWL Pipeline type. (Not yet functional.) | 17 May 2017, 20:17:43 UTC |
| 2dda798 | Jason Walker | 17 May 2017, 14:36:23 UTC | Merge pull request #1625 from jasonwalker80/unarchive_model_instdata Unarchive Instrument Data | 17 May 2017, 14:36:23 UTC |
| 01091e2 | Thomas B. Mooney | 17 May 2017, 14:03:58 UTC | Add Bsmap alignment as a possible result class for ReferenceAlignment. | 17 May 2017, 14:03:58 UTC |
| e922a6c | Thomas B. Mooney | 16 May 2017, 19:58:11 UTC | Merge pull request #1702 from tmooney/move_allocations_for_build Command to move "all" allocations for a build. | 16 May 2017, 19:58:11 UTC |
| 0672ec5 | Thomas B. Mooney | 16 May 2017, 19:52:46 UTC | Merge pull request #1708 from tmooney/update_speedseq_path Update speedseq path to newer disk array. | 16 May 2017, 19:52:46 UTC |
| 7b46eca | Thomas B. Mooney | 16 May 2017, 19:52:29 UTC | Merge pull request #1700 from tmooney/abs_path_doesnt_return_vol_paths Site: Avoid using `/vol/` paths as canonical. | 16 May 2017, 19:52:29 UTC |
| 574bc09 | Thomas B. Mooney | 16 May 2017, 17:43:27 UTC | Merge pull request #1707 from tmooney/remove_iprscan_predictor Remove `gmt predictor interproscan`. | 16 May 2017, 17:43:27 UTC |
| 30c306d | Thomas B. Mooney | 11 May 2017, 21:24:19 UTC | Update speedseq path to newer disk array. | 11 May 2017, 21:24:19 UTC |
| c2947d0 | Thomas B. Mooney | 10 May 2017, 21:07:30 UTC | Add clarifying parentheses around list-building. | 10 May 2017, 21:07:30 UTC |
| 3e341bc | Thomas B. Mooney | 10 May 2017, 20:24:54 UTC | Use a common list of subclasses for all RunsDV2 build types. | 10 May 2017, 20:24:54 UTC |
| 46522b4 | Thomas B. Mooney | 10 May 2017, 19:21:09 UTC | Only run move command if we have allocations that need moving. | 10 May 2017, 19:21:09 UTC |
| 8cc300a | Thomas B. Mooney | 10 May 2017, 19:17:04 UTC | Add RnaSeq support to the build move command. | 10 May 2017, 19:17:04 UTC |
| 3e85a2e | Thomas B. Mooney | 10 May 2017, 19:16:46 UTC | Need to update to the destination disk group as well! | 10 May 2017, 19:16:46 UTC |
| d0abf56 | Thomas B. Mooney | 10 May 2017, 13:46:47 UTC | Remove `gmt predictor interproscan`. | 10 May 2017, 13:46:47 UTC |
| e170167 | Thomas B. Mooney | 09 May 2017, 21:23:24 UTC | Merge pull request #1703 from tmooney/dont_use_docker_for_archives Don't use docker for archive processes! | 09 May 2017, 21:23:24 UTC |
| 383b7dc | Thomas B. Mooney | 09 May 2017, 21:23:13 UTC | Merge pull request #1697 from tmooney/stop_swallowing_errors_in_model_create Stop swallowing errors in Model create. | 09 May 2017, 21:23:13 UTC |
