| b5ee21e | Thomas B. Mooney | 30 October 2018, 15:14:34 UTC | Find the reference FASTA via a database lookup instead of hardcoding. | 30 October 2018, 15:14:34 UTC |
| 09e4913 | Thomas B. Mooney | 10 October 2018, 14:54:55 UTC | Merge pull request #1867 from tmooney/update_testtracker_logdir Update lsf_log_dir for test-tracker configuration. | 10 October 2018, 14:54:55 UTC |
| 0c9f83c | Thomas B. Mooney | 10 October 2018, 14:54:38 UTC | Merge pull request #1868 from tmooney/rm_uploadtodacc_denovo_command Remove DeNovoAssembly UploadToDacc command. | 10 October 2018, 14:54:38 UTC |
| f344cd7 | Thomas B. Mooney | 04 October 2018, 20:33:01 UTC | Remove DeNovoAssembly UploadToDacc command. This relied on a key in someone's homedir and had a hardocded account. The key is no longer present, so now this command will be likewise. | 04 October 2018, 20:33:01 UTC |
| 1c5aa19 | Thomas B. Mooney | 26 September 2018, 16:29:11 UTC | Update lsf_log_dir for test-tracker configuration. This value still isn't useful to anyone else in the world, but at least it's more useful right here now! | 26 September 2018, 16:29:11 UTC |
| 4803c4e | Thomas B. Mooney | 21 August 2018, 20:35:28 UTC | Merge pull request #1862 from tmooney/bugfix_for_bam_lookup Make sure $self gets passed to _resolve_bam_path. | 21 August 2018, 20:35:28 UTC |
| aa83e2f | Thomas B. Mooney | 21 August 2018, 18:54:55 UTC | Make sure $self gets passed to _resolve_bam_path. | 21 August 2018, 18:54:55 UTC |
| ffd420d | Thomas B. Mooney | 16 August 2018, 19:40:21 UTC | Merge pull request #1861 from tmooney/subjectmapping_bugfix Pass the label along correctly. | 16 August 2018, 19:40:21 UTC |
| b4a1cde | Thomas B. Mooney | 16 August 2018, 19:17:27 UTC | Pass the label along correctly. Who knows what $_ is here! | 16 August 2018, 19:17:27 UTC |
| 42019b2 | APipe Tester | 01 August 2018, 16:25:04 UTC | Updated `genome` tab completion. | 01 August 2018, 16:25:04 UTC |
| 29540a4 | APipe Tester | 01 August 2018, 16:23:28 UTC | Updated class browser cache. | 01 August 2018, 16:23:28 UTC |
| e4c9000 | Thomas B. Mooney | 31 July 2018, 18:11:43 UTC | Merge pull request #1860 from tmooney/subject_mapping_importer_for_cwlpipeline New SubjectMapping Importer for Arbitrary Mappings | 31 July 2018, 18:11:43 UTC |
| 890acd4 | Thomas Mooney | 25 July 2018, 18:09:56 UTC | New importer for arbitrary SubjectMappings. The name might be "CwlPipeline" but conceivably this could be used for anything--there's no structure imposed. | 25 July 2018, 18:09:56 UTC |
| fbe0bce | Thomas Mooney | 25 July 2018, 18:09:27 UTC | Create a base class for SubjectMapping imports. | 25 July 2018, 18:09:27 UTC |
| 152e91f | Thomas B. Mooney | 02 July 2018, 16:52:22 UTC | Merge pull request #1856 from tmooney/subject_mappings_for_cwl_pipelines Allow a config to request subject mappings for input_data. | 02 July 2018, 16:52:22 UTC |
| a697743 | Thomas B. Mooney | 02 July 2018, 16:52:09 UTC | Merge pull request #1855 from tmooney/set_envvars_before_calling_lims_image Set envrionment variables to get a cleaner environment. | 02 July 2018, 16:52:09 UTC |
| e1f97cf | Thomas B. Mooney | 07 June 2018, 19:06:37 UTC | Merge pull request #1858 from tmooney/make_bam_path_a_property_again Make "bam_path" a property again. | 07 June 2018, 19:06:37 UTC |
| be6c186 | Thomas B. Mooney | 06 June 2018, 22:25:46 UTC | Make "bam_path" a property again. Calculated + constant, so it only finds the value once and otherwise treats it like a UR object property as it was before. This fixes tests (and possibly real code :) ) that expected it to be a property. | 06 June 2018, 22:25:46 UTC |
| 8412ca3 | Thomas B. Mooney | 06 June 2018, 17:10:22 UTC | Merge pull request #1843 from tmooney/ask_lims_for_bam_path Ask the LIMS system where the BAM file is. | 06 June 2018, 17:10:22 UTC |
| d5730c0 | Thomas B. Mooney | 30 May 2018, 13:17:38 UTC | Add a debug message with the found path. | 30 May 2018, 13:17:38 UTC |
| f023b7e | Thomas B. Mooney | 29 May 2018, 22:03:26 UTC | Add missing semicolon. | 29 May 2018, 22:03:26 UTC |
| c3262d7 | Thomas B. Mooney | 24 May 2018, 23:02:33 UTC | Allow a config to request subject mappings for input_data. | 24 May 2018, 23:02:33 UTC |
| 9ff0aaa | Thomas B. Mooney | 23 May 2018, 16:57:14 UTC | Set envrionment variables to get a cleaner environment. The LIMS code falls into legacy copies of the code if they are left cluttering the environment. | 23 May 2018, 16:57:14 UTC |
| ed13d28 | Thomas B. Mooney | 15 May 2018, 13:22:03 UTC | Merge pull request #1848 from tmooney/remove_print_from_sr Convert print to debug message and show only when true. | 15 May 2018, 13:22:03 UTC |
| ca06201 | Thomas B. Mooney | 15 May 2018, 13:21:29 UTC | Merge pull request #1854 from tmooney/sourcefile_only_chop_gz_extension Only remove ".gz" from the end of the filename! | 15 May 2018, 13:21:29 UTC |
| f72d959 | Thomas B. Mooney | 15 May 2018, 13:21:12 UTC | Merge pull request #1853 from tmooney/distinguish_cwl_pipeline_types_in_search Surface different CWL pipeline types in Solr search. | 15 May 2018, 13:21:12 UTC |
| 812a975 | Thomas B. Mooney | 15 May 2018, 13:21:02 UTC | Merge pull request #1852 from tmooney/disable_tests_dependent_on_removed_test_data Fix `rsync_directory` and disable some broken tests. | 15 May 2018, 13:21:02 UTC |
| 7e49d68 | Thomas B. Mooney | 15 May 2018, 13:16:53 UTC | Only remove ".gz" from the end of the filename! This was breaking on directories that contained the string ".gz". | 15 May 2018, 13:16:53 UTC |
| 0ecd017 | Thomas B. Mooney | 14 May 2018, 20:29:21 UTC | Surface different CWL pipeline types in Solr search. | 14 May 2018, 20:29:21 UTC |
| adf9dfc | Thomas B. Mooney | 14 May 2018, 14:43:08 UTC | Fix support for the "file_pattern" option in "rsync_directory". | 14 May 2018, 14:43:08 UTC |
| 7311de1 | Thomas B. Mooney | 14 May 2018, 14:08:02 UTC | Disable tests depednent on particular ClinSeq test builds. | 14 May 2018, 14:08:02 UTC |
| b866819 | Thomas B. Mooney | 14 May 2018, 14:05:50 UTC | Skip test dependent on removed SomVar test data. | 14 May 2018, 14:05:50 UTC |
| 5d16b48 | Thomas B. Mooney | 14 May 2018, 13:17:40 UTC | Merge pull request #1851 from tmooney/support_instrumentdata_inputs_in_cwlpipeline Config: Support `input_data` within `instrument_data_properties` | 14 May 2018, 13:17:40 UTC |
| 6f00484 | Thomas B. Mooney | 14 May 2018, 13:10:09 UTC | Merge pull request #1849 from tmooney/import_bam_from_lims Command for importing LIMS BAMs from the new archive system. | 14 May 2018, 13:10:09 UTC |
| b25cad6 | Thomas B. Mooney | 09 May 2018, 21:09:43 UTC | Add support for input_data from instrument data properties. This allows for dynamically determined inputs for model types that support arbitrary inputs (at this time, this is CwlPipeline only). | 09 May 2018, 21:09:43 UTC |
| 5cb8084 | Thomas B. Mooney | 09 May 2018, 21:07:43 UTC | Pass along objects as-is without further processing. If someone already created the object for the get() call, we don't want to end up creating a UR::Value of the memory address! (This will probably fail on non-UR objects unless they happen to support id(), class(), and get(). But at least that'll be noisy instead of a quiet failure.) | 09 May 2018, 21:07:43 UTC |
| dc18987 | Thomas B. Mooney | 09 May 2018, 19:43:51 UTC | Extract subroutine for looking up instrument data properties. | 09 May 2018, 19:43:51 UTC |
| c777706 | Thomas B. Mooney | 24 April 2018, 18:35:56 UTC | Rollback the new allocation on errors. With this setup, we'll continue to try to process other instrument data in the list. | 24 April 2018, 18:35:56 UTC |
| 83d5bd1 | Thomas B. Mooney | 03 April 2018, 21:52:53 UTC | Use Perl's for syntax. | 03 April 2018, 21:52:53 UTC |
| 9aa61ee | Thomas B. Mooney | 03 April 2018, 20:22:09 UTC | Merge pull request #1845 from tmooney/restart_checks_user Only allow restart by the user who originally started a build. | 03 April 2018, 20:22:09 UTC |
| 53c4886 | Thomas B. Mooney | 03 April 2018, 20:21:41 UTC | Merge pull request #1846 from tmooney/bam_cram_removes_old_index Remove the source file's index when we remove the source file. | 03 April 2018, 20:21:41 UTC |
| 1bba01d | Thomas B. Mooney | 02 April 2018, 16:29:47 UTC | Merge pull request #1850 from tmooney/reduce_expected_result_count Only two results for this test now... one was purged. | 02 April 2018, 16:29:47 UTC |
| 1824afd | APipe Tester | 30 March 2018, 12:16:58 UTC | Updated `gmt` tab completion. | 30 March 2018, 12:16:58 UTC |
| dfd580f | APipe Tester | 30 March 2018, 12:16:15 UTC | Updated `genome` tab completion. | 30 March 2018, 12:16:15 UTC |
| 2956b7b | APipe Tester | 30 March 2018, 12:14:20 UTC | Updated class browser cache. | 30 March 2018, 12:14:20 UTC |
| 6faa268 | Thomas B. Mooney | 29 March 2018, 22:32:16 UTC | Only two results for this test now... one was purged. | 29 March 2018, 22:32:16 UTC |
| 9d79c00 | Thomas B. Mooney | 29 March 2018, 20:22:19 UTC | Set the transferred data to the project's group ownership. | 29 March 2018, 20:22:19 UTC |
| 120f40a | Thomas B. Mooney | 29 March 2018, 20:10:12 UTC | Command to import LIMS BAM out of the new archive system. | 29 March 2018, 20:10:12 UTC |
| 8769b37 | Thomas B. Mooney | 29 March 2018, 20:08:55 UTC | Don't go through the shell for the `rsync` shellcmd. If the directories have any shell metacharacters, we wouldn't want crazy things to happen! | 29 March 2018, 20:08:55 UTC |
| c55a57c | Thomas B. Mooney | 29 March 2018, 16:09:46 UTC | Merge pull request #1847 from tmooney/remove_reference_sequence_directory Remove legacy `reference_sequence_directory` | 29 March 2018, 16:09:46 UTC |
| 9e9dd24 | Thomas B. Mooney | 29 March 2018, 15:36:59 UTC | Convert print to debug message and show only when true. It's a bit scary when the system says it's deleting data and you weren't expecting there to be data to delete! | 29 March 2018, 15:36:59 UTC |
| ca809cd | Thomas B. Mooney | 28 March 2018, 22:12:03 UTC | Remove obsolete spec for "model_root". | 28 March 2018, 22:12:03 UTC |
| 390b5b3 | Thomas B. Mooney | 28 March 2018, 22:11:25 UTC | Remove legacy reference_sequence_directory from config | 28 March 2018, 22:11:25 UTC |
| 9922948 | Thomas B. Mooney | 28 March 2018, 22:10:23 UTC | Remove example values for references. The supplied example was outdated (build36!). | 28 March 2018, 22:10:23 UTC |
| 127169d | Thomas B. Mooney | 28 March 2018, 22:09:59 UTC | Lookup reference to use for tests. | 28 March 2018, 22:09:59 UTC |
| 74267a6 | Thomas B. Mooney | 28 March 2018, 22:07:29 UTC | Remove default reference sequence. | 28 March 2018, 22:07:29 UTC |
| 3f557bc | Thomas B. Mooney | 28 March 2018, 22:02:42 UTC | Move test refseq link into test inputs. | 28 March 2018, 22:02:42 UTC |
| 6190691 | Thomas B. Mooney | 28 March 2018, 22:01:34 UTC | Remove redundant default value in documentation. --help already includes it. | 28 March 2018, 22:01:34 UTC |
| 0db6c66 | Thomas B. Mooney | 28 March 2018, 22:01:07 UTC | Remove default value for reference index. | 28 March 2018, 22:01:07 UTC |
| a5c99b3 | Thomas B. Mooney | 28 March 2018, 21:56:33 UTC | Remove old `gmt fasta generate-backbone` The test depended on data which is no longer available. | 28 March 2018, 21:56:33 UTC |
| 5ed0e18 | Thomas B. Mooney | 28 March 2018, 18:26:50 UTC | Remove the source file's index when we remove the source file. | 28 March 2018, 18:26:50 UTC |
| ac8b179 | Thomas B. Mooney | 27 March 2018, 20:08:49 UTC | Only allow restart by the user who originally started a build. Restricted permissions in the Toil directories will typically mean a different user would be unable to properly continue the attempt. | 27 March 2018, 20:12:08 UTC |
| 7cdbd27 | Thomas B. Mooney | 22 March 2018, 13:07:08 UTC | Merge pull request #1844 from tmooney/config_lister_shows_tags_by_default Include the tag name in the default AnP config lister. | 22 March 2018, 13:07:08 UTC |
| c35abe6 | Thomas B. Mooney | 19 March 2018, 13:56:14 UTC | Include the tag name in the default AnP config lister. | 19 March 2018, 13:56:14 UTC |
| 38acb7b | Thomas B. Mooney | 12 March 2018, 14:42:31 UTC | Ask the LIMS system where the BAM file is. It's no longer stored in a single place in the database, so we'll call their logic that examines the multiple choices. | 12 March 2018, 14:42:31 UTC |
| e3931c0 | APipe Tester | 09 March 2018, 13:15:20 UTC | Updated `genome` tab completion. | 09 March 2018, 13:15:20 UTC |
| 233d24b | APipe Tester | 09 March 2018, 13:13:47 UTC | Updated class browser cache. | 09 March 2018, 13:13:47 UTC |
| 4de380b | Thomas B. Mooney | 08 March 2018, 20:39:39 UTC | Merge pull request #1842 from tmooney/diffexp_sr_usage_classes Add empty _disk_usage_result_subclass_names for DifferentialExpression | 08 March 2018, 20:39:39 UTC |
| 045c19d | Thomas B. Mooney | 08 March 2018, 19:00:38 UTC | Merge pull request #1841 from tmooney/speedseq_to_core Update these hardcoded speedseq paths to new location. | 08 March 2018, 19:00:38 UTC |
| b5e4981 | Thomas B. Mooney | 08 March 2018, 19:00:18 UTC | Merge pull request #1838 from tmooney/remove_svn_comments Remove old "HeadURL" and "Id" comments from the bottoms of files. | 08 March 2018, 19:00:18 UTC |
| 71ca8c0 | Thomas B. Mooney | 08 March 2018, 19:00:01 UTC | Merge pull request #1837 from tmooney/cwlpipeline_command_qol_improvements `genome model cwl-pipeline` usability improvements | 08 March 2018, 19:00:01 UTC |
| 013bfe8 | Thomas B. Mooney | 08 March 2018, 18:53:48 UTC | Add empty _disk_usage_result_subclass_names for DifferentialExpression This build type didn't get SoftwareResults added. | 08 March 2018, 18:53:48 UTC |
| 16806f4 | Thomas B. Mooney | 07 March 2018, 18:53:09 UTC | Update these hardcoded speedseq paths to new location. | 07 March 2018, 18:53:09 UTC |
| 34c921e | Thomas B. Mooney | 28 February 2018, 20:02:00 UTC | Merge pull request #1840 from tmooney/converted_bed_results_are_like_references BED-related results should use `disk_group_references`. | 28 February 2018, 20:02:00 UTC |
| 9c97765 | Thomas B. Mooney | 28 February 2018, 18:42:06 UTC | Merge pull request #1839 from tmooney/stop_for_restarted_builds Look for the latest workflow or LSF job. | 28 February 2018, 18:42:06 UTC |
| b865ad1 | Thomas B. Mooney | 28 February 2018, 18:41:49 UTC | Merge pull request #1835 from tmooney/define_results_for_refseq_builds Define _disk_usage_result_subclass_names for refseq builds. | 28 February 2018, 18:41:49 UTC |
| 9f71727 | Thomas B. Mooney | 28 February 2018, 18:09:55 UTC | Bugfix: input_files should be arrayref. | 28 February 2018, 18:09:55 UTC |
| 9316a7d | Thomas B. Mooney | 28 February 2018, 18:09:27 UTC | Make sure both ConvertedBedResult and IntervalList use reference disk. | 28 February 2018, 18:09:27 UTC |
| 2231055 | Thomas B. Mooney | 26 February 2018, 16:04:11 UTC | Look for the latest workflow or LSF job. A build could have multiple processes (and workflows) since it can be restarted. For most purposes (like `genome model build stop`) the most recent process is the correct one to consider. | 28 February 2018, 15:52:10 UTC |
| ebe8535 | Thomas B. Mooney | 26 February 2018, 15:53:01 UTC | Remove old "HeadURL" and "Id" comments from the bottoms of files. | 26 February 2018, 15:53:01 UTC |
| 132f604 | Thomas B. Mooney | 22 February 2018, 14:36:05 UTC | Add base of `genome model cwl-pipeline` tree. This is necessary for `cwl-pipeline` to appear in `genome model -h` and for tab-completion to find the `cwl-pipeline` commands. | 22 February 2018, 14:36:05 UTC |
| f8e36a3 | Thomas B. Mooney | 22 February 2018, 14:31:12 UTC | Make "builds" a positional parameter for cwl-pipeline commands. | 22 February 2018, 14:31:12 UTC |
| 5206432 | Thomas B. Mooney | 21 February 2018, 22:52:08 UTC | Merge pull request #1836 from tmooney/add_unionindel_to_dv2_results Add UnionIndel as a DV2 result. | 21 February 2018, 22:52:08 UTC |
| c604d36 | Thomas B. Mooney | 21 February 2018, 21:23:03 UTC | Add UnionIndel as a DV2 result. | 21 February 2018, 21:23:03 UTC |
| ecf5357 | Thomas B. Mooney | 21 February 2018, 14:05:16 UTC | Merge pull request #1821 from tmooney/unarchive_maybe_supports_archive_path Add experimental support for instrument data with tar.gz of FASTQs. | 21 February 2018, 14:05:16 UTC |
| 2893cba | Thomas B. Mooney | 20 February 2018, 17:36:08 UTC | Merge pull request #1834 from tmooney/bamtocram_reallocate_after_unlink Unlink the old file before reallocating. | 20 February 2018, 17:36:08 UTC |
| dd82e1b | Thomas B. Mooney | 20 February 2018, 17:35:53 UTC | Merge pull request #1831 from tmooney/import_assign_fix Fix for assigning new instrument data to specified AnP. | 20 February 2018, 17:35:53 UTC |
| d5a4773 | Thomas B. Mooney | 20 February 2018, 17:35:35 UTC | Merge pull request #1830 from tmooney/input_handling_fixes_cwlpipeline Another place where we need "defined". | 20 February 2018, 17:35:35 UTC |
| 9282638 | Thomas B. Mooney | 20 February 2018, 17:35:21 UTC | Merge pull request #1828 from tmooney/more_build_restart_fixes More build restart fixes | 20 February 2018, 17:35:21 UTC |
| d78bfe1 | APipe Tester | 20 February 2018, 13:34:28 UTC | Updated `genome` tab completion. | 20 February 2018, 13:34:28 UTC |
| 579a11d | APipe Tester | 20 February 2018, 13:30:39 UTC | Updated class browser cache. | 20 February 2018, 13:30:39 UTC |
| ce625c2 | Thomas B. Mooney | 19 February 2018, 19:35:52 UTC | Define _disk_usage_result_subclass_names for refseq builds. | 19 February 2018, 19:37:47 UTC |
| a570b2f | Thomas B. Mooney | 19 February 2018, 16:47:24 UTC | Merge pull request #1832 from tmooney/featurelist_bed_to_intervallist_result New SR and Command for getting IntervalLists from FeatureLists | 19 February 2018, 16:47:24 UTC |
| aa50e94 | Thomas B. Mooney | 19 February 2018, 16:38:06 UTC | Unlink the old file before reallocating. | 19 February 2018, 16:38:06 UTC |
| 3ff4a44 | Thomas B. Mooney | 15 February 2018, 21:53:16 UTC | Command for dumping an interval list for a feature list. | 15 February 2018, 22:41:45 UTC |
| a27608d | Thomas B. Mooney | 15 February 2018, 20:26:44 UTC | New SR for storing the IntervalList version of a FeatureList. | 15 February 2018, 21:53:00 UTC |
| 8fc09a0 | Thomas B. Mooney | 15 February 2018, 19:58:00 UTC | Fix for assigning new instrument data to specified AnP. The `@data` passed in here is not the Genome object but the synch object, so we need to look up the Genome entitiy for the add command. | 15 February 2018, 19:58:00 UTC |
| c838f3a | Thomas B. Mooney | 15 February 2018, 19:47:53 UTC | Merge pull request #1770 from tmooney/disable_genotype_synch Stop synching genotype data. | 15 February 2018, 19:47:53 UTC |
| c9cb13b | Thomas B. Mooney | 14 February 2018, 20:31:35 UTC | Another place where we need "defined". | 14 February 2018, 20:31:35 UTC |
| ecc1cbb | Thomas B. Mooney | 14 February 2018, 19:35:11 UTC | Merge pull request #1829 from tmooney/input_handling_fixes_cwlpipeline Fixes for CwlPipeline Input Processing | 14 February 2018, 19:35:11 UTC |
