| 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 |
| 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 |
| 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 |
| 666c89e | Thomas B. Mooney | 23 January 2018, 21:55:42 UTC | Merge pull request #1823 from tmooney/add_unioncnv_to_dv2_results Add UnionCnv to list of DV2 results that should get moved. | 23 January 2018, 21:55:42 UTC |
| d70c313 | Thomas B. Mooney | 23 January 2018, 21:31:29 UTC | Add build ID and completion time to the PrepForTransfer MANIFEST. | 23 January 2018, 21:31:29 UTC |
| 8ff1bfe | Thomas B. Mooney | 16 January 2018, 21:43:16 UTC | Add UnionCnv to list of DV2 results that should get moved. | 16 January 2018, 21:43:16 UTC |
| 9ce1638 | Thomas B. Mooney | 16 January 2018, 16:14:35 UTC | Remvoe `gmt bacterial core-gene-coverage`. No usage is shown in the log in the past year. This tool relies on the old "PP::LSF" module. | 16 January 2018, 16:14:35 UTC |
| fe35589 | Thomas B. Mooney | 16 January 2018, 15:40:55 UTC | Remove old MetricsBatchToLsf report. This relied on the long-removed `gmt maq` tree. | 16 January 2018, 15:40:55 UTC |
| 86f0aa8 | Thomas B. Mooney | 09 January 2018, 21:36:08 UTC | Add experimental support for instrument data with tar.gz of FASTQs. | 09 January 2018, 21:36:08 UTC |
| 56216e6 | Thomas B. Mooney | 08 January 2018, 23:49:32 UTC | Only check for directory existence if we got a path back. Some builds never had data directories to begin with. | 08 January 2018, 23:49:32 UTC |
| 8017e30 | Jason Walker | 05 January 2018, 16:23:33 UTC | Merge pull request #1819 from tmooney/update_blessed_clinseq_f1add76001974a54b45a754eddb439f1 Update blessed clinseq-wer build. | 05 January 2018, 16:23:33 UTC |
| 018a8b5 | Thomas B. Mooney | 04 January 2018, 17:09:39 UTC | Update blessed clinseq-wer build. Files are being moved, so the paths in the IGV XML are changing. (This seems likely to be a recurring issue for awhile as data is migrated.) | 04 January 2018, 17:09:39 UTC |
| 35e8ab3 | APipe Tester | 04 January 2018, 13:16:55 UTC | Updated `genome` tab completion. | 04 January 2018, 13:16:55 UTC |
| 142b8e2 | Thomas B. Mooney | 03 January 2018, 14:49:08 UTC | Merge pull request #1815 from tmooney/cleanup_intermediate_output_dirs_in_cwlpipeline Remove intermediate output directories after CwlPipeline run. | 03 January 2018, 14:49:08 UTC |
| a80fce0 | Thomas B. Mooney | 03 January 2018, 14:48:52 UTC | Merge pull request #1816 from tmooney/remove_solexa_specific_ignored_updater Remove "ignored" from solexa update tree. | 03 January 2018, 14:48:52 UTC |
| cc1621a | Thomas B. Mooney | 03 January 2018, 14:48:40 UTC | Merge pull request #1817 from tmooney/only_purge_results_with_allocations Don't consider purging results without allocations. | 03 January 2018, 14:48:40 UTC |
| 48a20a8 | Thomas B. Mooney | 03 January 2018, 14:48:27 UTC | Merge pull request #1795 from tmooney/cwlpipeline_naming Better CwlPipeline model naming. | 03 January 2018, 14:48:27 UTC |
| 9d2515d | Thomas B. Mooney | 02 January 2018, 22:25:49 UTC | Don't consider purging results without allocations. There's nothing to purge :) | 02 January 2018, 22:25:49 UTC |
| 20aa146 | Eddie Belter | 02 January 2018, 21:51:43 UTC | Merge pull request #1814 from ebelter/dna-disk DeNovoAssembly | 02 January 2018, 21:51:43 UTC |
| fd1e512 | Thomas B. Mooney | 02 January 2018, 21:02:16 UTC | Remove "ignored" from solexa update tree. This always has an initial value so cannot be updated due to the `only_if_null` restriction on solexa updates. The generic instrument-data updater can be used to modify this value. | 02 January 2018, 21:02:16 UTC |
| 34fc759 | Thomas B. Mooney | 28 December 2017, 18:37:29 UTC | Remove intermediate output directories after CwlPipeline run. | 28 December 2017, 18:37:29 UTC |
| b91af4c | Eddie Belter | 23 December 2017, 00:47:35 UTC | DeNovoAssembly add disk usage result classes | 23 December 2017, 00:47:35 UTC |
| e7486e9 | APipe Tester | 20 December 2017, 13:37:09 UTC | Updated `genome` tab completion. | 20 December 2017, 13:37:09 UTC |
| ec8f3c3 | APipe Tester | 20 December 2017, 13:35:18 UTC | Updated class browser cache. | 20 December 2017, 13:35:18 UTC |
| 1cf8eeb | Thomas B. Mooney | 19 December 2017, 21:33:15 UTC | Merge pull request #1812 from tmooney/abandon_purges_data_directory Build `abandon()` purges the Build's Allocation(s) | 19 December 2017, 21:33:15 UTC |
| 76bb3a1 | Thomas B. Mooney | 19 December 2017, 19:00:22 UTC | Build abandon purges the build's allocation(s). | 19 December 2017, 19:00:22 UTC |
| f765d30 | Thomas B. Mooney | 19 December 2017, 18:59:55 UTC | Use a create()d rather than a __define__()d allocation. | 19 December 2017, 18:59:55 UTC |
| 08cc107 | Jason Walker | 19 December 2017, 18:47:47 UTC | Merge pull request #1811 from jasonwalker80/import_set_env use anp env when importing data. | 19 December 2017, 18:47:47 UTC |
| ec53a7a | Jason Walker | 19 December 2017, 18:32:28 UTC | Add config directory to each AnP used in Basic import tests. | 19 December 2017, 18:32:28 UTC |
| 038c34e | Jason Walker | 19 December 2017, 16:58:41 UTC | Merge pull request #1801 from jasonwalker80/fix_duplicate_move Fix Allocation Move with Existing Path | 19 December 2017, 16:58:41 UTC |
| d4d52cf | Jason Walker | 19 December 2017, 16:40:39 UTC | use existing variable name. | 19 December 2017, 16:40:39 UTC |
| 87f9a79 | Jason Walker | 19 December 2017, 16:33:54 UTC | use anp env when importing data. | 19 December 2017, 16:33:54 UTC |
| b389ba2 | Jason Walker | 19 December 2017, 16:27:43 UTC | Merge pull request #1804 from jasonwalker80/anp_disk_group_usage AnP Disk Group Usage | 19 December 2017, 16:27:43 UTC |
| eec12ad | Jason Walker | 19 December 2017, 15:59:58 UTC | optionally add allocation IDs for all disk groups. | 19 December 2017, 15:59:58 UTC |
| ebaab76 | Thomas B. Mooney | 19 December 2017, 15:47:57 UTC | Merge pull request #1809 from tmooney/move_allocations_ok_with_null_sets Avoid calling delete() on a Set::Scalar::Null. | 19 December 2017, 15:47:57 UTC |
| a647d27 | Thomas B. Mooney | 19 December 2017, 15:47:42 UTC | Merge pull request #1810 from tmooney/anp_has_method_for_setting_env Add `set_env` to Analysis Projects | 19 December 2017, 15:47:42 UTC |
| 9c1b2fa | Thomas B. Mooney | 18 December 2017, 21:35:38 UTC | Use new `set_env` in Analysis Projects. | 18 December 2017, 21:35:38 UTC |
| a5e3c96 | Thomas B. Mooney | 18 December 2017, 21:16:41 UTC | Method for setting the configuration directory for an AnP. | 18 December 2017, 21:16:41 UTC |
| ef8b66d | Thomas B. Mooney | 18 December 2017, 20:37:24 UTC | Avoid calling delete() on a Set::Scalar::Null. Although one can create a null Set::Scalar which can have delete() called on it, the difference() method of Set::Scalar returns a special subclass, Set::Scalar::Null, that doesn't have delete() defined. This avoids this possibility by skipping the deletion if the set is already null. (In that case, there's nothing to delete, anyway!) | 18 December 2017, 20:37:24 UTC |
| d8a981e | Thomas B. Mooney | 18 December 2017, 20:11:02 UTC | Merge pull request #1802 from tmooney/warn_if_build_datadir_without_allocation Warn about build data directories that lack allocations. | 18 December 2017, 20:11:02 UTC |
| 85e48ae | Thomas B. Mooney | 18 December 2017, 20:05:06 UTC | Merge pull request #1803 from tmooney/even_more_logging_of_allocation_attempts Add debug message with current stats when volume too full. | 18 December 2017, 20:05:06 UTC |
| 0ac86c4 | Jason Walker | 18 December 2017, 19:30:01 UTC | Use a real disk group object to print allocation IDs. Including alias by name. | 18 December 2017, 19:30:01 UTC |
| 00462bd | Jason Walker | 18 December 2017, 19:12:37 UTC | update docs to refelect current command. | 18 December 2017, 19:12:37 UTC |
| 31e8625 | Jason Walker | 18 December 2017, 19:10:15 UTC | remove config_item loop. | 18 December 2017, 19:10:15 UTC |
| e9d9547 | Jason Walker | 18 December 2017, 19:04:16 UTC | Merge pull request #1806 from jasonwalker80/version_samtools_flagstat GMS Import use GMT samtools for flagstat | 18 December 2017, 19:04:16 UTC |
| eec56a7 | Jason Walker | 15 December 2017, 18:03:54 UTC | remove comments | 15 December 2017, 18:03:54 UTC |
| 7034ff1 | Jason Walker | 15 December 2017, 18:02:02 UTC | Use the GMT to run samtools to ensure a standard version is used. | 15 December 2017, 18:02:02 UTC |
| c0f2372 | Jason Walker | 14 December 2017, 15:31:50 UTC | initial revision. | 14 December 2017, 15:31:50 UTC |
| f8bfa0a | Thomas B. Mooney | 14 December 2017, 14:10:17 UTC | Add debug message with current stats when volume too full. The current logging tells us how big the request was that failed, but often the state of the volumes has changed to where the request seems fulfillable. This will hopefully help capture how much space pressure is being felt. | 14 December 2017, 14:10:17 UTC |
| c470943 | Thomas B. Mooney | 13 December 2017, 17:39:09 UTC | Warn about build data directories that lack allocations. This command can't move them, which may be surprising to the user! | 13 December 2017, 17:39:09 UTC |
| 3a13795 | Jason Walker | 12 December 2017, 18:12:58 UTC | Remove existing new path if confirmed redundant with original path. | 12 December 2017, 18:12:58 UTC |
