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 |
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 |
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 |
ab62e0a | Thomas B. Mooney | 28 November 2017, 14:52:09 UTC | Merge pull request #1787 from tmooney/update_test_data_for_fasta_removen_test Point to test inputs for test FASTA file. | 28 November 2017, 14:52:09 UTC |
e16b01b | Thomas B. Mooney | 28 November 2017, 14:51:58 UTC | Merge pull request #1786 from tmooney/remove_gmt_ber Remove GMT::Predictor::Ber tree. | 28 November 2017, 14:51:58 UTC |
77a2df1 | Thomas B. Mooney | 27 November 2017, 19:34:33 UTC | Add a testcase for the purge command. | 27 November 2017, 19:34:33 UTC |
a286d85 | Thomas B. Mooney | 27 November 2017, 19:27:32 UTC | G:D:A->purge expects only a string. This was setting all reasons to the literal string "reason". | 27 November 2017, 19:27:32 UTC |
26c1c7c | Thomas B. Mooney | 16 November 2017, 23:51:44 UTC | Point to test data for test FASTA file. We don't really use it in this test, anyway, but at least this location exists! | 16 November 2017, 23:51:44 UTC |
4d6983f | Thomas B. Mooney | 16 November 2017, 23:46:16 UTC | Remove GMT::Predictor::Ber tree. This depends on a now-removed directory. | 16 November 2017, 23:46:16 UTC |
0612a7c | Thomas B. Mooney | 16 November 2017, 22:31:54 UTC | Merge pull request #1785 from tmooney/fix_tophat1_result_users_again The param is called "users" not "result_users" in results themselves. | 16 November 2017, 22:31:54 UTC |
35a4144 | Thomas B. Mooney | 14 November 2017, 20:14:11 UTC | The param is called "users" not "result_users" in results themselves. | 14 November 2017, 20:14:11 UTC |
e1ced8f | Thomas B. Mooney | 08 November 2017, 15:54:36 UTC | Merge pull request #1783 from tmooney/add_result_users_to_tophat1_alignment Fill in `result_users` hash before getting/creating alignments | 08 November 2017, 15:54:36 UTC |
5851d14 | Thomas B. Mooney | 01 November 2017, 19:02:20 UTC | Add a mechanism for specifying arbitrary object inputs in CwlPipeline. | 01 November 2017, 19:02:20 UTC |
b2dce86 | APipe Tester | 01 November 2017, 12:17:33 UTC | Updated `gmt` tab completion. | 01 November 2017, 12:17:33 UTC |
7654e19 | APipe Tester | 01 November 2017, 12:16:43 UTC | Updated `genome` tab completion. | 01 November 2017, 12:16:43 UTC |
e766331 | APipe Tester | 01 November 2017, 12:14:48 UTC | Updated class browser cache. | 01 November 2017, 12:14:48 UTC |
2c45734 | Thomas B. Mooney | 31 October 2017, 18:49:30 UTC | Whitespace. | 31 October 2017, 18:49:30 UTC |
2f74c00 | Thomas B. Mooney | 31 October 2017, 18:48:43 UTC | Fill in result users before attempting to get_or_create Tophat1 result. | 31 October 2017, 18:48:43 UTC |
47ddd6d | Chris Miller | 31 October 2017, 16:20:41 UTC | Merge pull request #1781 from genome/chrisamiller-gmbqueue adding some feedback to gmb queue | 31 October 2017, 16:20:41 UTC |
c7b07ec | Thomas B. Mooney | 31 October 2017, 14:59:29 UTC | Merge pull request #1779 from tmooney/more_reliable_cram_paths AlignedBamResult: Try delegating to get the bam_path first. | 31 October 2017, 14:59:29 UTC |
cd387d3 | Thomas B. Mooney | 31 October 2017, 14:59:09 UTC | Merge pull request #1782 from tmooney/remove_gmt_beagle Remove GMT Beagle tree. | 31 October 2017, 14:59:09 UTC |
cbf5991 | Thomas B. Mooney | 31 October 2017, 14:08:25 UTC | Remove GMT Beagle tree. The "installed" path to the JAR file was a user directory which has been removed. | 31 October 2017, 14:08:25 UTC |
cbca02d | Chris Miller | 26 October 2017, 18:23:07 UTC | adding some feedback to gmb queue | 26 October 2017, 18:23:07 UTC |
7424d29 | Thomas B. Mooney | 25 October 2017, 15:23:46 UTC | Merge pull request #1694 from tmooney/possible_fix_for_index_timestamp_order Sort the files to be promoted. | 25 October 2017, 15:23:46 UTC |
fa3935b | Thomas B. Mooney | 18 October 2017, 19:48:23 UTC | Try delegating to get the bam path first. Still fall back on calculating the name ourselves. This is to handle that some subclasses can "convert" now and store the file in other formats. | 18 October 2017, 19:48:52 UTC |
4302558 | Jason Walker | 12 October 2017, 18:54:05 UTC | Merge pull request #1771 from tmooney/update_dgidb_url Use new canonical DGIdb.org domain. | 12 October 2017, 18:54:05 UTC |
ed70878 | Thomas B. Mooney | 12 October 2017, 18:48:58 UTC | Merge pull request #1769 from tmooney/workorder_import_supports_specifying_anp Option to Specify an AnP When Importing Work Order | 12 October 2017, 18:48:58 UTC |
9b88094 | Thomas B. Mooney | 12 October 2017, 18:48:38 UTC | Merge pull request #1774 from tmooney/index_after_alignment_conversion (Re)index the converted alignment file. | 12 October 2017, 18:48:38 UTC |
4584d17 | Thomas B. Mooney | 12 October 2017, 18:48:24 UTC | Merge pull request #1775 from tmooney/turn_off_genotype_import Disable importing genotype data in `import-data-for-work-order`. | 12 October 2017, 18:48:24 UTC |
244cf4a | Thomas B. Mooney | 12 October 2017, 18:48:10 UTC | Merge pull request #1776 from tmooney/build_purge_is_anp_aware Ignore our own AnP when deciding if a result is still in use. | 12 October 2017, 18:48:10 UTC |
5d58953 | Thomas B. Mooney | 12 October 2017, 18:47:55 UTC | Merge pull request #1777 from tmooney/db_result_for_gnomad First version of a gnomad file importer. | 12 October 2017, 18:47:55 UTC |
8e24670 | Thomas B. Mooney | 12 October 2017, 18:47:43 UTC | Merge pull request #1778 from tmooney/dont_hardcode_smtp_address Don't hardcode the SMTP server location. | 12 October 2017, 18:47:43 UTC |
25e7af1 | Thomas B. Mooney | 11 October 2017, 17:39:15 UTC | Don't hardcode the SMTP server location. | 11 October 2017, 17:39:15 UTC |
142bc9b | Thomas B. Mooney | 09 October 2017, 21:19:32 UTC | First version of a Gnomad file importer. | 09 October 2017, 21:19:32 UTC |
f998211 | Thomas B. Mooney | 05 October 2017, 13:54:37 UTC | Ignore our own AnP when deciding if a result is still in use. If other builds in the AnP are still using the result, they'll still be in the active users. This does mean a result used by two AnPs still cannot be purged via this mechanism. | 05 October 2017, 13:54:37 UTC |
88f9041 | Thomas B. Mooney | 04 October 2017, 20:34:16 UTC | Disable importing genotype data in `import-data-for-work-order`. The normal synch process loads PIDFAs to find the file paths, but those are not guaranteed to exist for these data. | 04 October 2017, 20:36:05 UTC |
37756a8 | Thomas B. Mooney | 04 October 2017, 18:01:19 UTC | Reallocate after manipulating the result files. | 04 October 2017, 18:01:19 UTC |
9eecfa3 | Thomas B. Mooney | 04 October 2017, 14:23:25 UTC | (Re)index the converted alignment file. The conversion process may not produce an identical file, so we can't trust the existing index to still be valid. Closes #1773. | 04 October 2017, 14:26:01 UTC |