| 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 |
| c14a1fa | Thomas B. Mooney | 14 February 2018, 19:32:54 UTC | We got an input if it's defined. Some inputs might have the value "0"... and that's okay! | 14 February 2018, 19:32:54 UTC |
| b549c3b | Thomas B. Mooney | 14 February 2018, 19:32:41 UTC | Fix error message to include value. | 14 February 2018, 19:32:41 UTC |
| f6c3665 | Thomas B. Mooney | 09 February 2018, 17:15:01 UTC | Include the process ID in the workflow name. Since builds can be restarted, they may end up with multiple processes, so the workflow name is not unique using the build's choice of name alone. | 12 February 2018, 14:38:01 UTC |
| 4f0d0a2 | Thomas B. Mooney | 09 February 2018, 17:09:08 UTC | Activate AnP environment before restarting. | 12 February 2018, 14:38:01 UTC |
| 4a8f2a0 | Thomas B. Mooney | 09 February 2018, 23:14:37 UTC | Merge pull request #1827 from tmooney/somval_identifydnp Add IdentifyDnpResult as a SomaticValidation result class. | 09 February 2018, 23:14:37 UTC |
| 7881dfa | Thomas B. Mooney | 09 February 2018, 17:08:18 UTC | Remove renaming that gets ignored by Ptero launch process. | 09 February 2018, 17:08:18 UTC |
| 42168ef | Thomas B. Mooney | 07 February 2018, 21:22:35 UTC | Add IdentifyDnpResult as a SomaticValidation result class. | 07 February 2018, 21:22:35 UTC |
| 1690353 | Chris Miller | 28 January 2018, 20:12:54 UTC | handle old data where md5 exists but is an empty file | 28 January 2018, 20:12:54 UTC |
| 36fe7fd | APipe Tester | 24 January 2018, 13:18:01 UTC | Updated `gmt` tab completion. | 24 January 2018, 13:18:01 UTC |
| 625f9dd | APipe Tester | 24 January 2018, 13:17:08 UTC | Updated `genome` tab completion. | 24 January 2018, 13:17:08 UTC |
| 7316b90 | APipe Tester | 24 January 2018, 13:15:23 UTC | Updated class browser cache. | 24 January 2018, 13:15:23 UTC |
| d549b24 | Thomas B. Mooney | 23 January 2018, 21:58:12 UTC | Merge pull request #1820 from tmooney/only_check_for_the_directory_if_there_is_one Only check for directory existence if we got a path back. | 23 January 2018, 21:58:12 UTC |
| 2119e19 | Thomas B. Mooney | 23 January 2018, 21:57:18 UTC | Merge pull request #1825 from tmooney/add_build_id_and_timestamp_to_prepfortransfer Add build ID and completion time to the PrepForTransfer MANIFEST. | 23 January 2018, 21:57:18 UTC |
| 1a405f9 | Thomas B. Mooney | 23 January 2018, 21:56:25 UTC | Merge pull request #1822 from tmooney/remove_pp_dependency Eliminate dependency on `PP::LSF` module | 23 January 2018, 21:56:25 UTC |
