| 9f5098a | Thomas B. Mooney | 14 January 2019, 18:27:55 UTC | Merge pull request #1907 from tmooney/yet_even_more_stager_updates More Tolerant Staging and Handling of Strange Outputs | 14 January 2019, 18:27:55 UTC |
| e6dfd5a | Thomas B. Mooney | 14 January 2019, 17:14:50 UTC | Merge pull request #1908 from tmooney/dumb_default_value_for_volume_hostname Set a default for disk volume hostname. | 14 January 2019, 17:14:50 UTC |
| 1959431 | Thomas B. Mooney | 14 January 2019, 16:25:53 UTC | Set a default for disk volume hostname. New disk volumes are coming through with this value undefined. A better solution would probably be to make a sqitch migration to drop this column and then not worry about it. This is an expedient solution instead. | 14 January 2019, 16:25:53 UTC |
| 8b026ba | Thomas B. Mooney | 10 January 2019, 22:19:09 UTC | Merge pull request #1906 from tmooney/lookup_sambamba_path Eliminate hard-coded sambamba path by looking up allocation. | 10 January 2019, 22:19:09 UTC |
| a9bbefa | Thomas B. Mooney | 10 January 2019, 21:05:02 UTC | Can't change the permissions of a dangling symlink. | 10 January 2019, 21:05:02 UTC |
| c284851 | Thomas B. Mooney | 10 January 2019, 21:04:28 UTC | Ignore simple values. They're definitely not files! | 10 January 2019, 21:04:28 UTC |
| 63640da | Thomas B. Mooney | 10 January 2019, 21:04:04 UTC | Tolerate duplicate file names as long as the files are identical. | 10 January 2019, 21:04:04 UTC |
| 7b635a6 | Thomas B. Mooney | 08 January 2019, 21:23:27 UTC | Eliminate hard-coded sambamba path by looking up allocation. | 08 January 2019, 21:23:27 UTC |
| 73dfdc2 | Thomas B. Mooney | 07 January 2019, 22:11:16 UTC | Merge pull request #1905 from tmooney/more_staging_fixes Better handling of arbitrary array structures when extracting files. | 07 January 2019, 22:11:16 UTC |
| 90b753d | Thomas B. Mooney | 07 January 2019, 22:11:05 UTC | Merge pull request #1904 from tmooney/control_cwlpipeline_runner_memory_usage Make LSF Resource for CWL Runner job configurable. | 07 January 2019, 22:11:05 UTC |
| 15553e4 | Thomas B. Mooney | 07 January 2019, 21:52:12 UTC | Add a very minimal test for walking the output data structure. | 07 January 2019, 21:52:12 UTC |
| c040344 | Thomas B. Mooney | 07 January 2019, 19:10:17 UTC | Better handling of arbitrary array structures when extracting files. We've encountered some workflows that like to have arrays of arrays of files as outputs. Rather than coerce everything into a single level of arrays, let's just recurse until we find the individual entries we're after. | 07 January 2019, 19:10:17 UTC |
| 4fdee1c | Thomas B. Mooney | 06 January 2019, 05:17:53 UTC | Make LSF Resource for CWL Runner job configurable. We've encountered some workflows where Cromwell needs more than the default amount to survive pre-processing, but it's probably better to only request more memory if we really need it. | 06 January 2019, 05:17:53 UTC |
| 7f5f173 | Thomas B. Mooney | 03 January 2019, 20:54:59 UTC | Merge pull request #1863 from tmooney/interval_list_dumping_has_strip_chr_option Add new option whether or not to remove "chr"s during conversion. | 03 January 2019, 20:54:59 UTC |
| e6f709c | Thomas B. Mooney | 03 January 2019, 20:52:37 UTC | Merge pull request #1903 from tmooney/fix_batch_mode This will work better if we specify the necessary key. | 03 January 2019, 20:52:37 UTC |
| 393180a | Thomas B. Mooney | 03 January 2019, 20:52:22 UTC | Merge pull request #1900 from tmooney/import_fastqs_too Support importing LIMS data that may or may not be BAMs. | 03 January 2019, 20:52:22 UTC |
| db26766 | Thomas B. Mooney | 03 January 2019, 19:10:06 UTC | This will work better if we specify the necessary key. Otherwise the value is ignored and `batch` mode is identical to `queued` mode. | 03 January 2019, 19:10:06 UTC |
| 2dff766 | Thomas B. Mooney | 03 January 2019, 16:52:58 UTC | Merge pull request #1901 from tmooney/stage_dangling_symlinks_too Use lower-level `move` for staging results. | 03 January 2019, 16:52:58 UTC |
| 583a718 | Thomas B. Mooney | 02 January 2019, 15:26:00 UTC | Use lower-level move for staging results. When moving symlinks, their targets may or may not exist depending if what they point to already got moved. We need to faithfully relocate them in either circumstance, so verifying `-e` is bad. | 02 January 2019, 15:26:00 UTC |
| 47a7806 | Thomas B. Mooney | 26 December 2018, 14:25:00 UTC | Merge pull request #1899 from tmooney/lsf_bsub_test_doesnt_hardcode_queues Don't use hardcoded queue names in LSF bsub test. | 26 December 2018, 14:25:00 UTC |
| 86eede3 | Thomas B. Mooney | 20 December 2018, 20:55:17 UTC | Support importing LIMS data that may or may not be BAMs. | 20 December 2018, 20:55:17 UTC |
| 30a5a3e | Thomas B. Mooney | 19 December 2018, 21:49:33 UTC | Don't use hardcoded queue names in LSF bsub test. Use the config! Also... don't inject a method into our module that only gets used in this test... just use an array directly. | 19 December 2018, 21:49:33 UTC |
| eaf2cd8 | Thomas B. Mooney | 19 December 2018, 18:42:03 UTC | Merge pull request #1898 from tmooney/more_tolerant_subject_mappings Allow individual configs for a model type to mismatch. | 19 December 2018, 18:42:03 UTC |
| 9991256 | Thomas B. Mooney | 19 December 2018, 15:44:29 UTC | Merge pull request #1892 from tmooney/add_batch_mode_to_search_index Add batch mode to search indexer. | 19 December 2018, 15:44:29 UTC |
| 44bc711 | Thomas B. Mooney | 12 December 2018, 22:08:03 UTC | Really skip when the tags don't match instead of processing as unmapped! Otherwise this generates bogus models in addition to the correct ones. | 12 December 2018, 22:08:03 UTC |
| 6a2d564 | Thomas B. Mooney | 12 December 2018, 21:13:04 UTC | Allow individual configs for a model type to mismatch. When using tags to distinguish between otherwise matching configurations to limit to certain subject mappings, this will occasionally return no result for a given config. For now, let's optimsitically assume that we should always get at least one match for a model type, even though it's possible even this assumption is not valid either. | 12 December 2018, 21:13:04 UTC |
| 01ac9bb | Thomas B. Mooney | 11 December 2018, 17:15:27 UTC | Fix BED file chromosome name for test. The seqdict says `Y` but the BED file said `chrY`. Now both say `Y`. | 11 December 2018, 17:15:27 UTC |
| 4ed3944 | Thomas B. Mooney | 11 December 2018, 16:44:39 UTC | Merge pull request #1896 from tmooney/use_local_disk_tables Use Local `disk.` Tables | 11 December 2018, 16:44:39 UTC |
| cba0458 | Thomas B. Mooney | 11 December 2018, 16:43:58 UTC | Merge pull request #1897 from tmooney/set_cromwell_db_threads Limit threads instead of connections. | 11 December 2018, 16:43:58 UTC |
| 4685f1b | Thomas B. Mooney | 22 August 2018, 13:31:11 UTC | Add new option whether or not to remove "chr"s during conversion. The original behavior was a holdover from when we assumed human build36 or 37. | 11 December 2018, 16:00:05 UTC |
| ab70dee | Thomas B. Mooney | 04 December 2018, 21:36:52 UTC | New synchronize classes for getting disk information from LIMS. | 10 December 2018, 23:06:14 UTC |
| 3a7818d | Thomas B. Mooney | 04 December 2018, 19:41:34 UTC | Use our own bridge table for groups and volumes. | 10 December 2018, 23:06:14 UTC |
| 9137eda | Thomas B. Mooney | 04 December 2018, 19:37:49 UTC | Use our own disk.group table instead of reading out. | 10 December 2018, 23:06:13 UTC |
| d282293 | Thomas B. Mooney | 03 December 2018, 23:31:09 UTC | Use our own disk.volume table instead of reading out. | 10 December 2018, 23:06:13 UTC |
| b87b445 | Thomas B. Mooney | 10 December 2018, 22:54:55 UTC | Limit threads instead of connections. Slick will automatically limit connections based on the thread count but not vice versa. Therefore to get sane numbers let's set the thread count instead. | 10 December 2018, 22:54:55 UTC |
| f80cbae | Thomas B. Mooney | 04 December 2018, 22:14:37 UTC | Merge pull request #1895 from tmooney/better_cromwell_output_staging Handle array outputs and non-file outputs when staging results. | 04 December 2018, 22:14:37 UTC |
| a3fc168 | Thomas B. Mooney | 27 November 2018, 20:08:16 UTC | Handle array outputs and non-file outputs when staging results. | 27 November 2018, 20:10:09 UTC |
| 84a787f | Thomas B. Mooney | 27 November 2018, 19:29:07 UTC | Merge pull request #1894 from tmooney/deal_with_lims_permissions Handle `000`-mode files for BAM imports. | 27 November 2018, 19:29:07 UTC |
| 9ce9cf1 | Thomas B. Mooney | 26 November 2018, 17:56:25 UTC | Merge pull request #1893 from tmooney/set_max_connections_in_cromwell Restrict the number of DB connections for a single Cromwell run. | 26 November 2018, 17:56:25 UTC |
| 91e775b | Thomas B. Mooney | 20 November 2018, 22:13:32 UTC | Set explicit permissions and group on imported BAMs. | 20 November 2018, 22:13:32 UTC |
| a40fb27 | Thomas B. Mooney | 20 November 2018, 22:06:26 UTC | rsync_directory support for chown. | 20 November 2018, 22:06:26 UTC |
| 59503e9 | Thomas B. Mooney | 20 November 2018, 21:48:10 UTC | New option for rsync_directory to overwrite permissions. | 20 November 2018, 22:05:47 UTC |
| c7c5e89 | Thomas B. Mooney | 20 November 2018, 20:49:04 UTC | Restrict the number of DB connections for a single Cromwell run. This was the advice provided in: https://gatkforums.broadinstitute.org/gatk/discussion/12330/call-catching-cromwell-exhausts-all-connection-to-mysqld | 20 November 2018, 20:49:04 UTC |
| b6f577e | Thomas B. Mooney | 19 November 2018, 23:19:07 UTC | Merge pull request #1891 from tmooney/import_bam_from_lims_updates Make the `import-bam-from-lims` command apply to more situations | 19 November 2018, 23:19:07 UTC |
| 8457ee9 | Thomas B. Mooney | 13 November 2018, 17:55:55 UTC | Add batch mode to search indexer. Adds items from the queue up to the specified maximum. (Contrast with the "queued" option that processes everything.) | 13 November 2018, 17:55:55 UTC |
| 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 |
| a7b8c9a | Thomas B. Mooney | 12 November 2018, 19:25:07 UTC | Don't require bam_path to already be set. We can now do an initial import of BAMs for new instrument data. | 12 November 2018, 19:25:07 UTC |
| e38968b | Thomas B. Mooney | 12 November 2018, 19:24:36 UTC | Use polling version of waiting for LSF job. bsub -K doesn't work right inside of other interactive jobs. | 12 November 2018, 19:24:36 UTC |
| dea5a5c | Thomas B. Mooney | 12 November 2018, 19:23:58 UTC | Don't mount a version of /gsc in the LIMS call. lims-env tries to use this version if it's present, and it fails under xenial. | 12 November 2018, 19:23:58 UTC |
| 76b9675 | Thomas B. Mooney | 12 November 2018, 19:23:09 UTC | Use gerald_bam_path lookup. The LIMS system now checks both active and archive locations under this call. | 12 November 2018, 19:23:09 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 |
