| f5daa75 | Thomas B. Mooney | 12 November 2018, 19:29:01 UTC | Merge pull request #1890 from tmooney/cromwell_output_collection_fixes Some fixes for staging the final outputs from Cromwell. | 12 November 2018, 19:29:01 UTC |
| a84a1c6 | Thomas B. Mooney | 12 November 2018, 19:28:40 UTC | Merge pull request #1889 from tmooney/dont_add_empty_yaml_entries_for_missing_values Don't add empty YAML entries for missing values. | 12 November 2018, 19:28:40 UTC |
| 2220ff3 | Thomas B. Mooney | 12 November 2018, 19:28:27 UTC | Merge pull request #1888 from tmooney/use_array_form_of_shellcmd_for_readcounts Update `gmt sam readcount` to use the safer form of shellcmd(). | 12 November 2018, 19:28:27 UTC |
| 72e1bc4 | Thomas B. Mooney | 08 November 2018, 23:00:37 UTC | Use the correct query syntax. The query itself has to be in a list. A label query takes the form key:value. | 08 November 2018, 23:00:37 UTC |
| 40a99fe | Thomas B. Mooney | 08 November 2018, 22:58:35 UTC | Blindly trust the cromwell server. HTTPS here is handy for encryption... but apparently our certificate is not the most trustworthy. In a more public setting this would be a bad idea! | 08 November 2018, 22:58:35 UTC |
| 6ac5a55 | Thomas B. Mooney | 08 November 2018, 14:41:58 UTC | Merge pull request #1887 from tmooney/rename_toil_runner_to_cwl_runner Now that multiple CWL Runners are implemented, give the workflow step a generic name. | 08 November 2018, 14:41:58 UTC |
| f4ecfda | Thomas B. Mooney | 08 November 2018, 14:23:13 UTC | Don't add empty YAML entries for missing values. This implementation essentially makes everything "optional". Alternatively we could die if it's not specified as being optional and yet has no value. | 08 November 2018, 14:41:07 UTC |
| 6747e40 | Thomas B. Mooney | 07 November 2018, 21:43:35 UTC | Update `gmt sam readcount` to use the safer form of shellcmd(). A user reported an error that resulted from having a space in one of their directory names. While using spaces in directory names seems like a good way to make trouble for oneself, there's no reason we can't support it here :) | 07 November 2018, 21:43:35 UTC |
| 817764d | Thomas B. Mooney | 07 November 2018, 14:45:49 UTC | Now that multiple CWL Runners are implemented, give step a generic name. This change will be most visible in the name of the log file generated for the run step. | 07 November 2018, 14:45:49 UTC |
| effd642 | Thomas B. Mooney | 07 November 2018, 14:37:00 UTC | Merge pull request #1884 from tmooney/update_gmt_transcriptome_ercmapunaligned_defaults Demote defaults to example values; update paths. | 07 November 2018, 14:37:00 UTC |
| 5bbd305 | Thomas B. Mooney | 07 November 2018, 14:36:42 UTC | Merge pull request #1885 from tmooney/turn_off_instrumentation Turn off instrumentation | 07 November 2018, 14:36:42 UTC |
| a75fc17 | Thomas B. Mooney | 07 November 2018, 14:35:05 UTC | Merge pull request #1886 from tmooney/fix_cromwell_config Use a literal `$` and not a variable named `$"`. | 07 November 2018, 14:35:05 UTC |
| 8690126 | Thomas B. Mooney | 06 November 2018, 23:52:12 UTC | Use a literal `$` and not a variable named `$"`. | 06 November 2018, 23:52:12 UTC |
| f275446 | Thomas B. Mooney | 06 November 2018, 21:32:11 UTC | Remove statsd config variables. | 06 November 2018, 21:51:43 UTC |
| c7c46b8 | Thomas B. Mooney | 06 November 2018, 21:30:54 UTC | Remove G:U:Instrumentation. | 06 November 2018, 21:51:43 UTC |
| 461d694 | Thomas B. Mooney | 06 November 2018, 21:30:35 UTC | Stop using Genome::Utility::Instrumentation. | 06 November 2018, 21:51:42 UTC |
| 8f65dd2 | Thomas B. Mooney | 05 November 2018, 19:59:48 UTC | Use canonical truth value. "1," may be true, but let's keep it simple :) | 05 November 2018, 19:59:48 UTC |
| 7521a62 | Thomas B. Mooney | 05 November 2018, 19:44:38 UTC | Demote defaults to example values; update paths. The previously listed defaults are no longer valid paths. In the spirit of not hardcoding reference-based defaults, these are now merely examples. Closes #1882. | 05 November 2018, 19:45:46 UTC |
| 7cc4caf | Thomas B. Mooney | 01 November 2018, 00:24:37 UTC | Merge pull request #1866 from tmooney/sneaky_volume_specification_in_disk_group Tolerate specifying a mount path instead of a disk group. | 01 November 2018, 00:24:37 UTC |
| df41be3 | Thomas B. Mooney | 01 November 2018, 00:24:20 UTC | Merge pull request #1869 from tmooney/cromwell_in_gms Support Cromwell as a CWL runner. | 01 November 2018, 00:24:20 UTC |
| e2156bc | Thomas B. Mooney | 31 October 2018, 21:58:59 UTC | Merge pull request #1879 from tmooney/lamely_hardcode_new_ucsc_paths Lamely hardcode new paths for UCSC information for the Annotator. | 31 October 2018, 21:58:59 UTC |
| 38b77de | Thomas B. Mooney | 31 October 2018, 21:02:45 UTC | Merge pull request #1878 from tmooney/liftover_looks_up_chain_files Look up the chain files instead of using hardcoded paths. | 31 October 2018, 21:02:45 UTC |
| aeda023 | Thomas B. Mooney | 31 October 2018, 20:17:42 UTC | Merge pull request #1876 from tmooney/lamely_update_symlink Update symlink to point to a different hardcoded path. | 31 October 2018, 20:17:42 UTC |
| e0de257 | Thomas B. Mooney | 31 October 2018, 20:17:27 UTC | Merge pull request #1877 from tmooney/more_path_fuzzy_matches Don't match on the absolute path to the reference. | 31 October 2018, 20:17:27 UTC |
| 664211f | Thomas B. Mooney | 31 October 2018, 20:17:08 UTC | Merge pull request #1880 from tmooney/remove_lookupvariants Remove old `gmt annotate lookup-variants`. | 31 October 2018, 20:17:08 UTC |
| 8060b5d | Thomas B. Mooney | 31 October 2018, 20:15:51 UTC | Merge pull request #1881 from tmooney/type_to_two Typo: s/to/two/. | 31 October 2018, 20:15:51 UTC |
| 49b5d3d | Thomas B. Mooney | 31 October 2018, 20:04:47 UTC | Consolidate chain file logic. | 31 October 2018, 20:14:01 UTC |
| a9fde1e | Thomas B. Mooney | 31 October 2018, 17:34:38 UTC | Typo: s/to/two/. | 31 October 2018, 17:34:38 UTC |
| b5e5815 | Thomas B. Mooney | 31 October 2018, 17:33:40 UTC | Remove old `gmt annotate lookup-variants`. The test and example data is all on old disk and there has been no usage reported in the past year. | 31 October 2018, 17:33:40 UTC |
| 1bec180 | Thomas B. Mooney | 31 October 2018, 16:43:27 UTC | Lamely hardcode new paths. I wanted to make these lookups, but compile-time database access is not okay. | 31 October 2018, 16:43:27 UTC |
| c7d8cf6 | Thomas B. Mooney | 31 October 2018, 13:58:14 UTC | Look up the chain files instead of using hardcoded paths. I could imagine expanding this system to support many other chain files we have, but for now this at least works right. (I could also see removing the shortcuts and always requiring a chain file, too... how often do we need to convert to hg18 these days?) | 31 October 2018, 13:58:14 UTC |
| 61188a7 | Thomas B. Mooney | 31 October 2018, 03:33:51 UTC | Squash one more reference to gc4096. | 31 October 2018, 03:35:04 UTC |
| b744bdc | Thomas B. Mooney | 31 October 2018, 03:29:50 UTC | Don't match on the absolute path to the reference. It's a little bit silly to even worry about a real path here at all... maybe these tests should use a dummy path under the test's control. | 31 October 2018, 03:29:50 UTC |
| 8a3f339 | Thomas B. Mooney | 31 October 2018, 01:41:28 UTC | Update symlink to point to a different hardcoded path. | 31 October 2018, 01:41:28 UTC |
| ce7cecb | Thomas B. Mooney | 30 October 2018, 22:32:08 UTC | Merge pull request #1875 from tmooney/remove_viromeevent Remove ViromeEvent and ViromeScreening trees. | 30 October 2018, 22:32:08 UTC |
| 57a5f80 | Thomas B. Mooney | 30 October 2018, 20:30:42 UTC | Remove ViromeEvent and ViromeScreening trees. This removes support for Virome workflows. | 30 October 2018, 20:30:42 UTC |
| 6f226f8 | Thomas B. Mooney | 30 October 2018, 19:42:23 UTC | Merge pull request #1873 from tmooney/lamely_update_paths_for_chimeraslayer Update hardcoded paths in low-effort attempt to make tests pass. | 30 October 2018, 19:42:23 UTC |
| cbbe400 | Thomas B. Mooney | 30 October 2018, 19:41:18 UTC | Merge pull request #1859 from tmooney/cwl_pipeline_input_improvements Helper class for processing inputs in `process_inputs.pl`. | 30 October 2018, 19:41:18 UTC |
| 1310fc0 | Thomas B. Mooney | 30 October 2018, 19:39:54 UTC | Merge pull request #1872 from tmooney/use_testdir_instead_of_sata828 Use test data dir for AlignmentResult tests | 30 October 2018, 19:39:54 UTC |
| 88de106 | Thomas B. Mooney | 30 October 2018, 19:39:40 UTC | Merge pull request #1874 from tmooney/remove_hardcoded_gc4096 Remove hardcoded references to `gc4096`. | 30 October 2018, 19:39:40 UTC |
| ae162b4 | Thomas B. Mooney | 30 October 2018, 19:28:10 UTC | Look up FASTA path instead of using hardcoded value. | 30 October 2018, 19:28:10 UTC |
| 3a6237d | Thomas B. Mooney | 30 October 2018, 19:22:27 UTC | Don't match on full path--just see that our allocation path matches. This is kind of a silly test anyway. | 30 October 2018, 19:22:27 UTC |
| 5cc387a | Thomas B. Mooney | 30 October 2018, 18:27:35 UTC | Update hardcoded paths in low-effort attempt to make tests pass. | 30 October 2018, 18:27:35 UTC |
| 7fc8f36 | Thomas B. Mooney | 30 October 2018, 17:18:29 UTC | Replace hardcoded sata828 with test data dir. | 30 October 2018, 17:18:29 UTC |
| 2aba7f9 | Thomas B. Mooney | 30 October 2018, 16:55:26 UTC | Use test data dir instead of a hardcoded path. | 30 October 2018, 16:55:26 UTC |
| 0d4bcd5 | Thomas B. Mooney | 30 October 2018, 15:23:15 UTC | Merge pull request #1871 from tmooney/dont_hardcode_fasta_path_in_tests Find the reference FASTA via a database lookup instead of hardcoding. | 30 October 2018, 15:23:15 UTC |
| 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 |
| f6bccf1 | Thomas B. Mooney | 11 October 2018, 20:26:25 UTC | Use the Cromwell API to get outputs to stage to the results dir. | 11 October 2018, 20:47:28 UTC |
| 8df53f1 | Thomas B. Mooney | 11 October 2018, 20:25:34 UTC | Wrapper for the Cromwell API Server. The initial version only has two of the endpoints implemented: 1) query for a workflow 2) get a workflow's outputs | 11 October 2018, 20:47:27 UTC |
| 5d8e24c | Thomas B. Mooney | 10 October 2018, 21:39:39 UTC | Typo: s/oull/pull/. This is what I get for having comments be dark blue on black. | 10 October 2018, 21:39:39 UTC |
| 96418a7 | Thomas B. Mooney | 10 October 2018, 21:38:48 UTC | Labels file should be JSON not YAML. | 10 October 2018, 21:38:48 UTC |
| 0538cbc | Thomas B. Mooney | 10 October 2018, 19:42:02 UTC | Add labels to the workflow for the build, model, and AnP. | 10 October 2018, 19:42:02 UTC |
| 35df094 | Thomas B. Mooney | 10 October 2018, 19:18:13 UTC | Support Cromwell as a CWL runner. | 10 October 2018, 19:35:58 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 |
| fed1e78 | Thomas B. Mooney | 19 September 2018, 20:31:26 UTC | Tolerate specifying a mount path instead of a disk group. | 19 September 2018, 20:31:26 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 |
| be2b905 | Thomas B. Mooney | 12 July 2018, 15:44:34 UTC | Helper class for processing inputs in `process_inputs.pl`. | 12 July 2018, 18:10:36 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 |
