| 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 |
| 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 |
| 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 |
| 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 |
| 882574a | Thomas B. Mooney | 11 December 2017, 16:11:39 UTC | Merge pull request #1800 from tmooney/fix_concatenatemetricfiles_test_in_testrunner Canonicalize the data path. | 11 December 2017, 16:11:39 UTC |
| b7e64be | Jason Walker | 11 December 2017, 16:10:37 UTC | Merge pull request #1799 from jasonwalker80/test_transfer PrepForTransfer Test | 11 December 2017, 16:10:37 UTC |
| 23e4ce8 | Thomas B. Mooney | 11 December 2017, 14:50:30 UTC | Canonicalize the data path. If the test is run as, e.g., "./ConcatenateMetricFiles.t", the data directory would have the "./" but the files written out would not, thwarting the replace in the comparison. | 11 December 2017, 14:50:30 UTC |
| 0357abd | Jason Walker | 08 December 2017, 14:46:13 UTC | Handle existing files/directories. Improve test to cover symlink creation. | 08 December 2017, 14:46:13 UTC |
| 845ff93 | APipe Tester | 08 December 2017, 13:17:28 UTC | Updated `gmt` tab completion. | 08 December 2017, 13:17:28 UTC |
| 5fb632a | APipe Tester | 08 December 2017, 13:16:51 UTC | Updated `genome` tab completion. | 08 December 2017, 13:16:51 UTC |
| 2dbd616 | APipe Tester | 08 December 2017, 13:15:31 UTC | Updated class browser cache. | 08 December 2017, 13:15:31 UTC |
| 9d4ee59 | Jason Walker | 07 December 2017, 20:21:38 UTC | test for PrepForTransfer. Use absolute path before symlink. | 07 December 2017, 20:21:38 UTC |
| c9390aa | Jason Walker | 07 December 2017, 18:16:56 UTC | Merge pull request #1798 from jasonwalker80/master Picard concatenate test and generic parser. | 07 December 2017, 18:16:56 UTC |
| 1357287 | Jason Walker | 07 December 2017, 18:11:15 UTC | use the sort order of the headers from reader. also write output as soon as we read each line. updated test files to correct column order. | 07 December 2017, 18:11:15 UTC |
| 6143465 | Jason Walker | 07 December 2017, 17:55:43 UTC | Use replace to avoid file path issues with test and expected files. | 07 December 2017, 17:55:43 UTC |
| 5e05fb0 | Jason Walker | 07 December 2017, 17:43:27 UTC | generic parser logic. add test case. | 07 December 2017, 17:43:27 UTC |
| 59d1d21 | Jason Walker | 07 December 2017, 16:27:34 UTC | Merge pull request #1791 from jasonwalker80/picard_metrics Picard ConcatenateMetricsFiles | 07 December 2017, 16:27:34 UTC |
| 57f1481 | Thomas B. Mooney | 07 December 2017, 16:27:20 UTC | Merge pull request #1796 from tmooney/copy_config_copies_environment_config Support copying the environment configuration in AnP CopyConfig. | 07 December 2017, 16:27:20 UTC |
| 394ec26 | Thomas B. Mooney | 07 December 2017, 16:27:06 UTC | Merge pull request #1794 from tmooney/update_expected_test_cases_for_no_genotype_data Update RefAlign test builds for run without genotype data. | 07 December 2017, 16:27:06 UTC |
| 87e1b57 | Jason Walker | 07 December 2017, 16:26:15 UTC | Merge pull request #1797 from jasonwalker80/prep_for_transfer CwlPipeline PrepForTransfer | 07 December 2017, 16:26:15 UTC |
| ada1533 | Jason Walker | 06 December 2017, 21:44:22 UTC | remove unnecessary periods | 06 December 2017, 21:44:22 UTC |
| 25b8c31 | Jason Walker | 06 December 2017, 21:43:19 UTC | changes from code review. use File::Spec and spelling error. | 06 December 2017, 21:43:19 UTC |
| 6b76450 | Jason Walker | 06 December 2017, 21:14:08 UTC | initial revision of CwlPipeline tool for prepping data transfer. | 06 December 2017, 21:14:08 UTC |
| 686d4d9 | Jason Walker | 06 December 2017, 20:15:48 UTC | Merge pull request #1793 from jasonwalker80/fastq_importer FASTQ Importer with less RAM | 06 December 2017, 20:15:48 UTC |
| f0d53b1 | Thomas B. Mooney | 06 December 2017, 16:19:04 UTC | Support copying the environment configuration in AnP CopyConfig. | 06 December 2017, 16:19:04 UTC |
| a67217f | Thomas B. Mooney | 06 December 2017, 15:49:28 UTC | Better CwlPipeline model naming. Since CwlPipeline encompasses many different workflows, it is more common to have multiple models per subject. Having them named "cwl_pipeline-1" through "cwl_pipeline-6" is less than ideal, so this provides a way to distinguish them based on the workflows they run. | 06 December 2017, 15:49:28 UTC |
| 2bb0c61 | Thomas B. Mooney | 06 December 2017, 13:57:03 UTC | Update refalign test builds for run without genotype data. (The old genotype data these test used has been purged, and the corresponding model was so old we don't run them that way anymore, anyway.) | 06 December 2017, 13:57:03 UTC |
| 87d8cb1 | Jason Walker | 05 December 2017, 18:10:43 UTC | remove BAM comparison | 05 December 2017, 18:10:43 UTC |
| bde5d93 | Jason Walker | 05 December 2017, 16:21:16 UTC | Use the original BAM file. sorting with Picard 1.82 is not necessary. | 05 December 2017, 16:21:16 UTC |
| d0e5baf | Jason Walker | 04 December 2017, 22:37:02 UTC | Fix the builder and test case to actually remove SortSam from the workflow for importing FASTQ. | 04 December 2017, 22:37:02 UTC |
| 33eaced | Jason Walker | 04 December 2017, 22:23:15 UTC | use file_is_gzipped to determine such. | 04 December 2017, 22:23:15 UTC |
| 5060360 | Jason Walker | 04 December 2017, 22:20:35 UTC | remove redundant sort command in FASTQ workflow for GMS importer. | 04 December 2017, 22:20:35 UTC |
| abe08b0 | Jason Walker | 04 December 2017, 19:07:42 UTC | Update the path to expected BAM files. | 04 December 2017, 19:07:42 UTC |
| 9703ef8 | Jason Walker | 04 December 2017, 17:36:47 UTC | Remove unarchive of FASTQ and use latest version of Picard for FastqToSam. | 04 December 2017, 17:36:47 UTC |
| 68b9904 | Thomas B. Mooney | 04 December 2017, 14:18:03 UTC | Merge pull request #1792 from tmooney/microarray_sr_classes_for_move Add GenotypeMicroarray's SR classes. | 04 December 2017, 14:18:03 UTC |
| ea79c06 | Thomas B. Mooney | 04 December 2017, 14:17:52 UTC | Merge pull request #1790 from tmooney/clinseq_sr_classes_for_move Add ClinSeq's SR classes. | 04 December 2017, 14:17:52 UTC |
| b5223bf | Thomas B. Mooney | 04 December 2017, 14:17:39 UTC | Merge pull request #1788 from tmooney/fix_purge_reason Fix setting of purge reason for `Genome::Disk::Allocation->purge` | 04 December 2017, 14:17:39 UTC |
| f7abf16 | Thomas B. Mooney | 04 December 2017, 14:17:23 UTC | Merge pull request #1789 from tmooney/fix_lqunion_testdata Hackily replace deleted test data with some that's still around. | 04 December 2017, 14:17:23 UTC |
| 2f87a49 | Jason Walker | 01 December 2017, 15:58:42 UTC | remove subclass parsing. | 01 December 2017, 15:58:42 UTC |
| dec8c35 | Jason Walker | 01 December 2017, 15:50:02 UTC | fix fatal messages. | 01 December 2017, 15:50:02 UTC |
| 58523c0 | Thomas B. Mooney | 30 November 2017, 20:55:08 UTC | Add GenotypeMicroarray's SR classes. This fixes `genome model build move-allocations` for GenotypeMicroarray builds. | 30 November 2017, 20:55:08 UTC |
| f9c1b31 | Jason Walker | 29 November 2017, 21:41:44 UTC | initial revision of ConcatenateMetricsFiles.pm | 29 November 2017, 21:41:44 UTC |
| 5467e8d | Thomas B. Mooney | 29 November 2017, 13:37:59 UTC | Add ClinSeq's SR classes. This fixes `genome model build move-allocations` for ClinSeq builds. | 29 November 2017, 13:37:59 UTC |
| 7f33d6d | APipe Tester | 29 November 2017, 13:17:25 UTC | Updated `gmt` tab completion. | 29 November 2017, 13:17:25 UTC |
| ee807c5 | APipe Tester | 29 November 2017, 13:16:33 UTC | Updated `genome` tab completion. | 29 November 2017, 13:16:33 UTC |
| 19290e1 | APipe Tester | 29 November 2017, 13:14:18 UTC | Updated class browser cache. | 29 November 2017, 13:14:18 UTC |
| 995e037 | Thomas B. Mooney | 28 November 2017, 23:22:15 UTC | Hackily replace deleted test data with some that's still around. This would still be better without relying on real data! | 28 November 2017, 23:22:15 UTC |
| 8c4e570 | Thomas B. Mooney | 28 November 2017, 19:32:57 UTC | Merge pull request #1784 from tmooney/allow_arbitrary_object_inputs_in_cwlpipeline Add a mechanism for specifying arbitrary object inputs in CwlPipeline. | 28 November 2017, 19:32:57 UTC |
| b0b2b87 | Thomas B. Mooney | 28 November 2017, 18:05:41 UTC | Add test case for new object input support. | 28 November 2017, 18:05:41 UTC |
