| 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 |
| 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 |
| 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 |
| b45f322 | Thomas B. Mooney | 25 September 2017, 19:01:21 UTC | Merge pull request #1772 from tmooney/use_ipcsystemsimple_for_pindel_faidx Properly handle chromosome names with shell metacharacters in ProcessPindelReads | 25 September 2017, 19:01:21 UTC |
| 991f723 | Thomas B. Mooney | 25 September 2017, 18:33:06 UTC | Use Genome::Sys's array form instead of system(). This does make the logs a lot noisier with "RUN:" messages, but it also makes it a lot more likely to work! | 25 September 2017, 18:33:06 UTC |
| 0999139 | Thomas B. Mooney | 25 September 2017, 18:23:45 UTC | Use IPC::System::Simple to capture samtools view. | 25 September 2017, 18:23:45 UTC |
| 8bf30f8 | Thomas B. Mooney | 25 September 2017, 18:17:34 UTC | Use IPC::System::Simple since chr names may include shell characters. | 25 September 2017, 18:17:34 UTC |
| 9e56e48 | Thomas B. Mooney | 20 September 2017, 20:29:00 UTC | Update canonical DGIdb URL. | 20 September 2017, 20:29:00 UTC |
| a157fec | Thomas B. Mooney | 13 September 2017, 20:24:46 UTC | Merge pull request #1768 from tmooney/oltp_and_dwrac_are_lowercase Set Dwrac and Oltp datasources to lowercase names. | 13 September 2017, 20:24:46 UTC |
| 00f730f | APipe Tester | 12 September 2017, 12:17:55 UTC | Updated `genome` tab completion. | 12 September 2017, 12:17:55 UTC |
| 3e871ec | APipe Tester | 12 September 2017, 12:16:13 UTC | Updated class browser cache. | 12 September 2017, 12:16:13 UTC |
| da63394 | Thomas B. Mooney | 11 September 2017, 18:46:02 UTC | Merge pull request #1764 from tmooney/genome_model_build_purge New command to purge allocations for a build. | 11 September 2017, 18:46:02 UTC |
| 6b98a84 | Thomas B. Mooney | 11 September 2017, 18:45:34 UTC | Merge pull request #1758 from tmooney/convert_debugf_to_debug_message Use the ordinary "debug_message" so they appear in the normal logs. | 11 September 2017, 18:45:34 UTC |
| 17bb7c7 | Thomas B. Mooney | 11 September 2017, 18:45:19 UTC | Merge pull request #1762 from tmooney/vcf_finalpass_receives_correct_vcf_name Pass the corrected sample name to the FinalPassOnly tool. | 11 September 2017, 18:45:19 UTC |
| 40525cb | Thomas B. Mooney | 11 September 2017, 18:44:59 UTC | Merge pull request #1763 from tmooney/cleanup_model_rename Cleanup `genome model rename`. | 11 September 2017, 18:44:59 UTC |
| ac31985 | Thomas B. Mooney | 11 September 2017, 18:44:23 UTC | Merge pull request #1760 from tmooney/fixes_for_cwlpipeline_restart Fixes for restarting CwlPipeline builds | 11 September 2017, 18:44:23 UTC |
| b6b9a04 | Thomas B. Mooney | 11 September 2017, 18:44:07 UTC | Merge pull request #1759 from tmooney/stop_stats_collection_in_cwlpipeline Stop using cwltoil's --stats option. | 11 September 2017, 18:44:07 UTC |
| 9ed7c4c | Thomas B. Mooney | 11 September 2017, 18:34:02 UTC | Merge pull request #1767 from tmooney/synclimsandgenome_test_fixes_for_1766 Test Fixes for #1766. | 11 September 2017, 18:34:02 UTC |
| 4fc785a | Thomas B. Mooney | 11 September 2017, 14:45:01 UTC | Set Dwrac and Oltp datasources to lowercase names. This fixes the error committing changes to misc_update. | 11 September 2017, 14:45:01 UTC |
| 9d67586 | Thomas B. Mooney | 11 September 2017, 13:31:27 UTC | Update test to reflect b642a1a9cdb14d44754d1f80ce3e72abe68dde14. One fewer class to synch for now! | 11 September 2017, 13:31:27 UTC |
| 9bb1052 | Thomas B. Mooney | 11 September 2017, 13:27:11 UTC | "missing" is now only filled for instrument data if --expunge enabled. | 11 September 2017, 13:27:11 UTC |
| e54b46a | Jason Walker | 08 September 2017, 18:09:33 UTC | Merge pull request #1766 from tmooney/synch_efficiencies More Efficient Synch; Temporarily Stop LimsProjectInstrumentData Synch | 08 September 2017, 18:09:33 UTC |
| 9fcd16d | Jason Walker | 08 September 2017, 18:09:20 UTC | Merge pull request #1756 from tmooney/import_associations_for_workorder Import Genotype Data, AnP links, and Sample links for Work Order. | 08 September 2017, 18:09:20 UTC |
| b642a1a | Thomas B. Mooney | 07 September 2017, 21:22:51 UTC | Temporarily stop synching LimsProjectInstrumentData. This table takes too long to examine. Any needed associations can be imported using the `import-data-for-work-order` command. | 07 September 2017, 21:22:51 UTC |
| d5bf028 | Thomas B. Mooney | 07 September 2017, 21:21:22 UTC | Streamlined handling of IndexIllumina and PIDFA. * Unless we're looking for data to remove, don't bother loading the entire PIDFA history. * Use the PIDFAs to decide what IndexIllumina to examine to avoid loading the whole table. | 07 September 2017, 21:21:22 UTC |
| 87379b9 | Thomas B. Mooney | 07 September 2017, 21:20:48 UTC | Pluck the IDs for tables with a single ID column. | 07 September 2017, 21:20:48 UTC |
| a10ad02 | Thomas B. Mooney | 07 September 2017, 16:36:52 UTC | Remove un-needed sprintf. | 07 September 2017, 16:40:25 UTC |
| 3d7f308 | Thomas B. Mooney | 07 September 2017, 16:36:37 UTC | Add more information to error message. | 07 September 2017, 16:40:25 UTC |
| 8a5fe9b | Thomas B. Mooney | 06 September 2017, 18:15:04 UTC | Merge pull request #1765 from tmooney/disconnect_oltp_handle_when_disconnecting Also disconnect the OLTP handle when disconnecting for long-running ops. | 06 September 2017, 18:15:04 UTC |
| d27c243 | Thomas B. Mooney | 05 September 2017, 15:12:42 UTC | Also disconnect the OLTP handle when disconnecting for long-running ops. | 05 September 2017, 15:12:42 UTC |
| bf734ab | Thomas B. Mooney | 05 September 2017, 15:11:45 UTC | Add explicit return value for success case. | 05 September 2017, 15:11:45 UTC |
| b9751bb | Thomas B. Mooney | 31 August 2017, 21:29:23 UTC | New command to purge allocations for a build. | 31 August 2017, 21:29:23 UTC |
| 50e2c85 | Thomas B. Mooney | 31 August 2017, 18:25:59 UTC | Allow specification of an AnP to which to assign all data for a WO. | 31 August 2017, 18:25:59 UTC |
| 33a0f1b | Thomas B. Mooney | 31 August 2017, 18:24:28 UTC | Remove extra "s": s/asssign/assign/. | 31 August 2017, 18:24:28 UTC |
| 81af684 | Thomas B. Mooney | 31 August 2017, 17:49:35 UTC | Remove old version-control comments. | 31 August 2017, 17:49:35 UTC |
| a584c31 | Thomas B. Mooney | 31 August 2017, 17:49:04 UTC | Use status_message and builtin printf form of error_message. | 31 August 2017, 17:49:04 UTC |
| cd754d9 | Thomas B. Mooney | 31 August 2017, 17:32:26 UTC | Pass the corrected sample name to the FinalPassOnly tool. | 31 August 2017, 17:32:26 UTC |
| 8d43ad0 | Thomas B. Mooney | 30 August 2017, 20:26:00 UTC | Handle multiple processes per build (i.e. build restarts) We'll now display every attempt to run the build from earliest to most recent. | 30 August 2017, 20:26:00 UTC |
| be2e4cc | Thomas B. Mooney | 30 August 2017, 20:16:34 UTC | Workflow names must be unique for Ptero, so change it up before launch. | 30 August 2017, 20:16:34 UTC |
| a632599 | Thomas B. Mooney | 30 August 2017, 20:11:05 UTC | Stop using cwltoil's --stats option. It's not worth the additional disk usage. | 30 August 2017, 20:11:05 UTC |
| c7004dd | Thomas B. Mooney | 24 August 2017, 14:48:10 UTC | Support synching project-sample associations. | 29 August 2017, 21:23:10 UTC |
| aab4715 | Thomas B. Mooney | 24 August 2017, 14:24:04 UTC | Add support for importing genotype data. | 29 August 2017, 21:23:10 UTC |
| 45f7a80 | Thomas B. Mooney | 24 August 2017, 14:17:55 UTC | Import any AnP associations for the instrument data. | 29 August 2017, 21:23:09 UTC |
| 122fae5 | Thomas B. Mooney | 29 August 2017, 19:16:24 UTC | Use the ordinary "debug_message" so they appear in the normal logs. | 29 August 2017, 19:16:24 UTC |
| 941a234 | APipe Tester | 25 August 2017, 13:50:07 UTC | Updated `genome` tab completion. | 25 August 2017, 13:50:07 UTC |
| 1ae98ce | APipe Tester | 25 August 2017, 13:33:37 UTC | Updated class browser cache. | 25 August 2017, 13:33:37 UTC |
| 376c6dd | Thomas B. Mooney | 24 August 2017, 16:30:42 UTC | Merge pull request #1757 from tmooney/revert_changing_column_type_for_anp_id Change columntype for AnP ID back to text. | 24 August 2017, 16:30:42 UTC |
| 884f084 | Jason Walker | 24 August 2017, 16:30:23 UTC | Merge pull request #1731 from jasonwalker80/somval_speedseq_qc_move Somval speedseq qc move | 24 August 2017, 16:30:23 UTC |
| 32f9135 | Thomas B. Mooney | 24 August 2017, 15:36:35 UTC | Change columntype for AnP ID back to text. This one really holds non-numeric data, so no need to have changed it in the first place :) | 24 August 2017, 15:36:35 UTC |
| d81d5b2 | Thomas B. Mooney | 24 August 2017, 12:49:19 UTC | Merge pull request #1751 from tmooney/refactor_anpbridge_synch_sql Synch: SQL refactor for AnP bridge class | 24 August 2017, 12:49:19 UTC |
| 270eef9 | Thomas B. Mooney | 24 August 2017, 12:48:22 UTC | Merge pull request #1752 from tmooney/remove_proteinannotation_uploadresults Remove obsolete `genome model protein-annotation upload-results` command | 24 August 2017, 12:48:22 UTC |
| ce86f95 | Thomas B. Mooney | 24 August 2017, 12:47:49 UTC | Merge pull request #1750 from tmooney/remove_obsolete_adaptor_path Stop filling in some obsolete properties for Illumina data | 24 August 2017, 12:47:49 UTC |
| acaafae | Thomas B. Mooney | 24 August 2017, 12:47:35 UTC | Merge pull request #1749 from tmooney/remove_dw_crossdb_link More Postgres fixes for Synchronization classes | 24 August 2017, 12:47:35 UTC |
| 536c273 | Thomas B. Mooney | 24 August 2017, 12:47:18 UTC | Merge pull request #1753 from tmooney/fix_bam_cram_conversion A few fixes to BAM <=> CRAM conversion | 24 August 2017, 12:47:18 UTC |
