| 941a234 | APipe Tester | 25 August 2017, 13:50:07 UTC | Updated `genome` tab completion. | 25 August 2017, 13:50:07 UTC |
| 1ae98ce | APipe Tester | 25 August 2017, 13:33:37 UTC | Updated class browser cache. | 25 August 2017, 13:33:37 UTC |
| 376c6dd | Thomas B. Mooney | 24 August 2017, 16:30:42 UTC | Merge pull request #1757 from tmooney/revert_changing_column_type_for_anp_id Change columntype for AnP ID back to text. | 24 August 2017, 16:30:42 UTC |
| 884f084 | Jason Walker | 24 August 2017, 16:30:23 UTC | Merge pull request #1731 from jasonwalker80/somval_speedseq_qc_move Somval speedseq qc move | 24 August 2017, 16:30:23 UTC |
| 32f9135 | Thomas B. Mooney | 24 August 2017, 15:36:35 UTC | Change columntype for AnP ID back to text. This one really holds non-numeric data, so no need to have changed it in the first place :) | 24 August 2017, 15:36:35 UTC |
| d81d5b2 | Thomas B. Mooney | 24 August 2017, 12:49:19 UTC | Merge pull request #1751 from tmooney/refactor_anpbridge_synch_sql Synch: SQL refactor for AnP bridge class | 24 August 2017, 12:49:19 UTC |
| 270eef9 | Thomas B. Mooney | 24 August 2017, 12:48:22 UTC | Merge pull request #1752 from tmooney/remove_proteinannotation_uploadresults Remove obsolete `genome model protein-annotation upload-results` command | 24 August 2017, 12:48:22 UTC |
| ce86f95 | Thomas B. Mooney | 24 August 2017, 12:47:49 UTC | Merge pull request #1750 from tmooney/remove_obsolete_adaptor_path Stop filling in some obsolete properties for Illumina data | 24 August 2017, 12:47:49 UTC |
| acaafae | Thomas B. Mooney | 24 August 2017, 12:47:35 UTC | Merge pull request #1749 from tmooney/remove_dw_crossdb_link More Postgres fixes for Synchronization classes | 24 August 2017, 12:47:35 UTC |
| 536c273 | Thomas B. Mooney | 24 August 2017, 12:47:18 UTC | Merge pull request #1753 from tmooney/fix_bam_cram_conversion A few fixes to BAM <=> CRAM conversion | 24 August 2017, 12:47:18 UTC |
| 5a6aac2 | Thomas B. Mooney | 24 August 2017, 12:47:04 UTC | Merge pull request #1736 from tmooney/import_a_workorder Command to manually trigger the import of WO data from the LIMS. | 24 August 2017, 12:47:04 UTC |
| 22630c1 | Thomas B. Mooney | 24 August 2017, 12:46:46 UTC | Merge pull request #1748 from tmooney/dont_cast_ii_id_to_text Don't cast analysis_id to text. | 24 August 2017, 12:46:46 UTC |
| f729807 | Thomas B. Mooney | 24 August 2017, 12:46:28 UTC | Merge pull request #1747 from tmooney/sync_endures_empty_strings_in_lims_tables Treat empty strings like undef values in LIMS objects. | 24 August 2017, 12:46:28 UTC |
| 1454f08 | Thomas B. Mooney | 24 August 2017, 12:46:06 UTC | Merge pull request #1746 from tmooney/update_more_blessed_builds_after_testdata_reconstruction More test "blessed build" updates | 24 August 2017, 12:46:06 UTC |
| a32d1dc | Thomas B. Mooney | 23 August 2017, 17:16:49 UTC | Correct accessor name for alignment_result. | 23 August 2017, 17:16:49 UTC |
| ac8a399 | Thomas B. Mooney | 23 August 2017, 17:16:16 UTC | Fix Genome::Config set_env call. | 23 August 2017, 17:16:16 UTC |
| e9c9980 | Thomas B. Mooney | 23 August 2017, 15:35:33 UTC | Remove obsolete `genome model protein-annotation upload-results` command. | 23 August 2017, 15:35:33 UTC |
| b0a14a8 | Thomas B. Mooney | 23 August 2017, 14:22:48 UTC | Remove casts, and pull joins inside of union. This speeds up the query enough that it returns before I give up and Ctrl+C it :) | 23 August 2017, 14:22:48 UTC |
| 35a1720 | Thomas B. Mooney | 22 August 2017, 20:28:37 UTC | Remove old gc_bias_path and fastqc_path properties from synch. They last had values in 2011 and 2014, so assume NULL for all new data. | 22 August 2017, 20:28:37 UTC |
| d202111 | Thomas B. Mooney | 22 August 2017, 18:50:07 UTC | Remove disused "samplesheet export" command. No recorded usage is found in the usage DB (based on a search from 2015-01-01 to present). | 22 August 2017, 18:50:07 UTC |
| d011d9f | Thomas B. Mooney | 22 August 2017, 18:48:36 UTC | Stop filling in the "adaptor_path" property. This requires two big joins and the path it produces is not currently valid, regardless. | 22 August 2017, 18:48:36 UTC |
| e24ac05 | Thomas B. Mooney | 22 August 2017, 18:09:35 UTC | Be explicit that "name" is an alias. | 22 August 2017, 18:09:35 UTC |
| b7d55fa | Thomas B. Mooney | 22 August 2017, 18:03:59 UTC | These columns have a numeric type. | 22 August 2017, 18:09:27 UTC |
| b5f939b | Thomas B. Mooney | 22 August 2017, 17:59:51 UTC | Remove obsolete 'dw' cross-db link. The two databases are combined now. | 22 August 2017, 17:59:51 UTC |
| 8db15ac | Thomas B. Mooney | 17 August 2017, 22:43:29 UTC | Don't cast analysis_id to text. This plus the default sorting leads to a verrrrry slow query. | 17 August 2017, 22:43:29 UTC |
| 9b3d1db | Thomas B. Mooney | 17 August 2017, 18:11:01 UTC | Merge pull request #1745 from tmooney/create_manifest_for_ssg_tar Add a MD5 manifest file to the SSG VCF TAR file. | 17 August 2017, 18:11:01 UTC |
| 0c0206a | Thomas B. Mooney | 17 August 2017, 17:55:53 UTC | Update manifest file format and name. The new format better matches the output of `md5sum` executable. | 17 August 2017, 17:59:00 UTC |
| 06deb9f | Thomas B. Mooney | 17 August 2017, 14:28:12 UTC | Treat empty strings like undef values in LIMS objects. The LIMS system has started storing empty strings in columns sometimes when they mean NULL, so treat them the same. | 17 August 2017, 14:31:59 UTC |
| e5421d2 | Thomas B. Mooney | 17 August 2017, 14:14:45 UTC | Update ClinSeq blessed build again now that more data has been restored. | 17 August 2017, 14:14:45 UTC |
| 9bcaeef | Thomas B. Mooney | 16 August 2017, 22:16:47 UTC | Add a MD5 manifest file to the SSG VCF TAR file. | 16 August 2017, 22:16:47 UTC |
| a2b9a55 | Thomas B. Mooney | 16 August 2017, 18:48:30 UTC | Merge pull request #1743 from tmooney/converter_supports_speedseq Support "Speedseq" merged alignments in format converters. | 16 August 2017, 18:48:30 UTC |
| 3efb998 | Thomas B. Mooney | 16 August 2017, 15:01:44 UTC | Support "Speedseq" merged alignments in format converters. | 16 August 2017, 15:01:44 UTC |
| f139a2e | Thomas B. Mooney | 16 August 2017, 13:55:45 UTC | Updated RnaSeq blessed build after test-data reconstruction. | 16 August 2017, 13:55:45 UTC |
| 92830f0 | APipe Tester | 16 August 2017, 12:15:27 UTC | Updated `genome` tab completion. | 16 August 2017, 12:15:27 UTC |
| 3c98298 | APipe Tester | 16 August 2017, 12:14:04 UTC | Updated class browser cache. | 16 August 2017, 12:14:04 UTC |
| d6384de | Thomas B. Mooney | 15 August 2017, 17:49:14 UTC | Merge pull request #1738 from tmooney/update_blessed_builds_after_testdata_reset Update blessed builds to new builds after reconstructing test data. | 15 August 2017, 17:49:14 UTC |
| 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 |
| 1eb3945 | Thomas B. Mooney | 09 August 2017, 21:56:01 UTC | Update blessed builds to new builds after reconstructing test data. | 15 August 2017, 15:12:43 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 |
| dd7faeb | Thomas B. Mooney | 19 July 2017, 22:31:09 UTC | Command to manually trigger the import of WO data from the LIMS. | 19 July 2017, 22:31:09 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 |
| 2ec80c8 | Jason Walker | 27 June 2017, 19:50:13 UTC | moved the qc result. | 27 June 2017, 19:50:13 UTC |
| a9c82de | Jason Walker | 27 June 2017, 15:35:30 UTC | Add SpeedSeq and QC results to list used for disk usage for SomVal builds. | 27 June 2017, 15:35:30 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 |
