| 7024e36 | APipe Tester | 21 January 2014, 13:18:07 UTC | Updated `genome` tab completion. | 21 January 2014, 13:18:07 UTC |
| ea92e14 | APipe Tester | 21 January 2014, 13:16:18 UTC | Updated class browser cache. | 21 January 2014, 13:16:18 UTC |
| ab181a1 | Malachi Griffith | 21 January 2014, 02:38:27 UTC | ClinSeq - fix update-analysis to handle cases where a suitable somatic-variation model exists but no build have been started | 21 January 2014, 02:38:27 UTC |
| 13ee0a3 | Malachi Griffith | 21 January 2014, 01:26:51 UTC | minor fix to installation of databases from github needed for standalone gms | 21 January 2014, 01:26:51 UTC |
| 7c34919 | Malachi Griffith | 20 January 2014, 21:59:47 UTC | Add methods for installation of file based databases (db-var, genome-db-dbsnp, ucsc) from github. Similar to those already available for cosmic, tgi/misc-annotation and tgi/cancer-annotation | 20 January 2014, 21:59:47 UTC |
| 56965a2 | Malachi Griffith | 19 January 2014, 22:53:44 UTC | Remove call to ->get() in scalar context to prevent non-fatal error messages as describe in https://github.com/genome/gms/issues/73. | 19 January 2014, 22:53:44 UTC |
| d3e1d46 | Malachi Griffith | 19 January 2014, 20:59:40 UTC | Blessing new cli-seq build to account for updated meta-data for the AML109 case | 19 January 2014, 20:59:40 UTC |
| 8b0b7cf | APipe Tester | 18 January 2014, 13:17:30 UTC | Updated `genome` tab completion. | 18 January 2014, 13:17:30 UTC |
| 958c367 | Obi Griffith | 17 January 2014, 21:03:45 UTC | use alternate paths to ucsc conservation files when in standalone | 17 January 2014, 21:03:45 UTC |
| 1cb1b08 | Adam Coffman | 17 January 2014, 19:43:42 UTC | db migration for new clia fields in analysis projects | 17 January 2014, 19:43:42 UTC |
| 268d26c | Malachi Griffith | 17 January 2014, 17:20:37 UTC | Clin-Seq - process aml trios - Add notes on use of per library bam readcount tools from DL | 17 January 2014, 17:20:37 UTC |
| bf60ce1 | Malachi Griffith | 17 January 2014, 17:18:57 UTC | Make cosmic and misc annotations configurable options for clin-seq update analysis and tidy up use of these | 17 January 2014, 17:18:57 UTC |
| 96dca6f | APipe Tester | 17 January 2014, 13:16:42 UTC | Updated `genome` tab completion. | 17 January 2014, 13:16:42 UTC |
| 2c286f6 | APipe Tester | 17 January 2014, 13:15:08 UTC | Updated class browser cache. | 17 January 2014, 13:15:08 UTC |
| 820c809 | dmorton | 17 January 2014, 04:53:04 UTC | Start using TestHelpers::Data to get at shared test data | 17 January 2014, 04:54:16 UTC |
| 276c359 | dmorton | 17 January 2014, 04:52:09 UTC | Add TestHelpers::Data for getting at shared test data | 17 January 2014, 04:54:15 UTC |
| 9ce3626 | dmorton | 17 January 2014, 04:51:12 UTC | Remove unused subroutine parameter | 17 January 2014, 04:54:15 UTC |
| 3541491 | dmorton | 17 January 2014, 04:50:57 UTC | Add get_test_data to TestHelpers::General | 17 January 2014, 04:54:15 UTC |
| b9eaa5d | dmorton | 17 January 2014, 04:48:48 UTC | Stop using Genome::Utility::Test for test_dir I wanted to be able to get a test_dir for things that aren't ur classes | 17 January 2014, 04:54:15 UTC |
| 6c86cef | APipe Tester | 17 January 2014, 00:15:57 UTC | updated jenkins submodule to 4070700 | 17 January 2014, 00:15:57 UTC |
| da26fde | dmorton | 17 January 2014, 00:05:26 UTC | Replace test-helpers in Dindel with general-purpose versions | 17 January 2014, 00:06:37 UTC |
| 40722c0 | dmorton | 17 January 2014, 00:04:17 UTC | Create some general test-helpers | 17 January 2014, 00:06:37 UTC |
| c6d9f12 | Adam Coffman | 16 January 2014, 23:27:20 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 16 January 2014, 23:27:20 UTC |
| c7118cb | Avinash Ramu | 16 January 2014, 23:09:23 UTC | remove unwanted print | 16 January 2014, 23:09:34 UTC |
| f054b3f | Adam Coffman | 16 January 2014, 22:39:57 UTC | remove unused command | 16 January 2014, 22:39:57 UTC |
| 0d4fd6f | Adam Coffman | 16 January 2014, 22:16:28 UTC | Refactor purge orphans cron. The previous version had a hardcoded limit of 2,500,000 documents and took hours to run as a result of fetching objects from the database one at a time and doing a linear search of documents to compare ids each time. The new version uses a lookup hash and fetches the ids in bulk directly from the DB. There is no document limit and run time is well under an hour. | 16 January 2014, 22:16:28 UTC |
| 37c616a | Adam Coffman | 16 January 2014, 22:15:04 UTC | Add utility helper to grab single column values while bypassing object creation | 16 January 2014, 22:15:04 UTC |
| bcc229e | Avinash Ramu | 16 January 2014, 21:56:05 UTC | update exporter to export annotation indexes for the aligners we are interested in to shortcut rnaseq tophat indexing | 16 January 2014, 21:56:21 UTC |
| 35fcb79 | Michael J. Kiwala | 16 January 2014, 21:24:51 UTC | removing file which is tracked in another repo The genome_view script also is tracked in puppet-modules.git and belongs there: /srv/git/puppet-modules.git as site/imp_apipe/files/genome_view | 16 January 2014, 21:26:24 UTC |
| d338eb6 | Adam Coffman | 16 January 2014, 19:22:37 UTC | remove outdated dgi references | 16 January 2014, 19:22:37 UTC |
| 08e17a0 | Michael J. Kiwala | 16 January 2014, 17:08:04 UTC | Merge branch 'ar375' https://jira.gsc.wustl.edu/browse/AR-375 | 16 January 2014, 17:08:04 UTC |
| 12e69c9 | Michael J. Kiwala | 16 January 2014, 16:05:42 UTC | placing 6-Post-Promote shell script under vcs previously only existed at: http://apipe-ci.gsc.wustl.edu/job/6%20Post%20Promote%20(restart%20genome-view)/configure Planning to deploy to: /gsc/scripts/bin/genome_view_init_wrapper | 16 January 2014, 17:07:45 UTC |
| 397b872 | Michael J. Kiwala | 16 January 2014, 16:46:51 UTC | updating git with currently deployed script Deployed script found at: /gsc/scripts/sbin/genome_view | 16 January 2014, 17:07:45 UTC |
| e74728f | Michael J. Kiwala | 16 January 2014, 16:45:06 UTC | updating git with currently deployed script Deployed script found at: imp-apipe.gsc.wustl.edu:/etc/init.d/genome_view | 16 January 2014, 17:07:44 UTC |
| d203d77 | Feiyu Du | 16 January 2014, 16:49:07 UTC | update blessed build for som-var | 16 January 2014, 16:49:07 UTC |
| 421c728 | Anthony Brummett | 16 January 2014, 15:22:06 UTC | Remove unused data source From https://jira.gsc.wustl.edu/browse/AR-322 | 16 January 2014, 15:22:06 UTC |
| b879a9a | Avinash Ramu | 15 January 2014, 23:13:56 UTC | updated exporter to export alignment indexes | 15 January 2014, 23:14:26 UTC |
| faa1218 | Adam Coffman | 15 January 2014, 21:39:52 UTC | add helper method to get counts of indexed documents by class | 15 January 2014, 21:40:31 UTC |
| e7b25ff | Adam Coffman | 15 January 2014, 21:38:48 UTC | include user_name in config hashes for CQID tests | 15 January 2014, 21:38:48 UTC |
| c11023f | Adam Coffman | 15 January 2014, 21:37:35 UTC | Cache correct sub | 15 January 2014, 21:37:35 UTC |
| 5a4e018 | Adam Coffman | 15 January 2014, 21:34:34 UTC | The config Translator now wraps bare config hashes in array refs. This normalization keeps all information regarding the underlying structure of config file in the Translator and allows us to move it out of the Profile object. | 15 January 2014, 21:34:34 UTC |
| 5f914cb | Thomas Mooney | 15 January 2014, 19:36:54 UTC | Assume that we're running on at least 5.10.1 now. | 15 January 2014, 19:37:50 UTC |
| e4a15b5 | Feiyu Du | 15 January 2014, 19:02:46 UTC | update blessed build for refalign-germline-short and som-val-sv | 15 January 2014, 19:02:46 UTC |
| 338ad4c | Thomas Mooney | 15 January 2014, 18:55:23 UTC | Don't try to look up chromosomes that aren't present in the reference. | 15 January 2014, 18:55:23 UTC |
| 55c302d | Thomas Mooney | 15 January 2014, 18:45:57 UTC | s/genotpe/genotype/ | 15 January 2014, 18:45:57 UTC |
| 902561b | Thomas Mooney | 15 January 2014, 16:37:08 UTC | IDs are 32 characters long. | 15 January 2014, 16:37:08 UTC |
| 5d079d4 | APipe Tester | 15 January 2014, 14:43:57 UTC | updated workflow submodule to a43bedf | 15 January 2014, 14:43:57 UTC |
| 45a4f51 | APipe Tester | 15 January 2014, 13:55:06 UTC | Updated `genome` tab completion. | 15 January 2014, 13:55:06 UTC |
| 20cef40 | Avinash Ramu | 14 January 2014, 23:01:17 UTC | dgidb has a new source ClearityFoundationClinicalTrial | 14 January 2014, 23:01:51 UTC |
| f199e49 | Michael J. Kiwala | 14 January 2014, 22:05:25 UTC | updated test data with Avi The old strelka bed file had incorrect coordinates | 14 January 2014, 22:06:16 UTC |
| 59bff41 | Michael J. Kiwala | 14 January 2014, 21:14:42 UTC | change build id for test; see rt 97150 | 14 January 2014, 22:06:16 UTC |
| 7f24e47 | Malachi Griffith | 14 January 2014, 22:03:13 UTC | Further modifications to AML trio SNV/Indel summary clin-seq command | 14 January 2014, 22:03:13 UTC |
| 6f31f98 | APipe Tester | 14 January 2014, 20:41:11 UTC | updated ur submodule to 16bcd51 | 14 January 2014, 20:41:11 UTC |
| 5125685 | Adam Coffman | 14 January 2014, 19:53:13 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 14 January 2014, 19:53:13 UTC |
| 2cda558 | Adam Coffman | 14 January 2014, 19:53:02 UTC | Add function to get total number of indexed documents in solr | 14 January 2014, 19:53:02 UTC |
| 956d446 | Thomas Mooney | 14 January 2014, 19:51:25 UTC | Add messages when updating the status of pairs. The intention of this change is to make it easy for Jenkins to detect when processing a particular pair has failed so that the build can be marked "Unstable". ("Failure" is then reserved for CQID crashing.) | 14 January 2014, 19:51:25 UTC |
| 31c7cf3 | Avinash Ramu | 14 January 2014, 17:07:40 UTC | sort using a temporary file before intersect | 14 January 2014, 17:08:33 UTC |
| c1106a6 | Thomas Mooney | 14 January 2014, 14:30:53 UTC | Allow other users to clean up their builds; apipe-builder anyone's. | 14 January 2014, 14:30:53 UTC |
| 92f99c6 | APipe Tester | 14 January 2014, 01:39:50 UTC | updated jenkins submodule to 287b23c | 14 January 2014, 01:39:50 UTC |
| c6dffbb | APipe Tester | 14 January 2014, 01:06:01 UTC | updated workflow submodule to bfa5f3c | 14 January 2014, 01:06:01 UTC |
| ed5df38 | APipe Tester | 14 January 2014, 00:19:07 UTC | updated workflow submodule to b6ef377 | 14 January 2014, 00:19:07 UTC |
| fa7755a | APipe Tester | 13 January 2014, 22:43:31 UTC | updated ur submodule to 6926bc8 | 13 January 2014, 22:43:31 UTC |
| 5ebea1c | Thomas Mooney | 13 January 2014, 21:12:38 UTC | Update expected output to account for an allocation that moved. | 13 January 2014, 21:12:38 UTC |
| 5d06db5 | Michael J. Kiwala | 13 January 2014, 20:40:33 UTC | Revert "joinx-sort caller files before calling joinx-intersect" This reverts commit 53838007d0344660e803fdd2cff54dc36a119b92. | 13 January 2014, 20:41:06 UTC |
| 935164b | Nathan Nutter | 13 January 2014, 20:01:32 UTC | remove CLIA config, this will be done outside of code We're migrating to using shell environment for configuration (source, not just as globals) with /etc/profile.d/genome.sh serving as the defaults. Changes for CLIA will be implemented in the executing user's environment. | 13 January 2014, 20:01:32 UTC |
| dd53cba | Thomas Mooney | 13 January 2014, 14:31:29 UTC | Pass the log file into the subroutine that processes it. | 13 January 2014, 14:31:29 UTC |
| 90ed697 | APipe Tester | 13 January 2014, 13:16:14 UTC | Updated `genome` tab completion. | 13 January 2014, 13:16:14 UTC |
| 8c05503 | APipe Tester | 13 January 2014, 13:14:34 UTC | Updated class browser cache. | 13 January 2014, 13:14:34 UTC |
| 31d7f2b | Malachi Griffith | 13 January 2014, 06:39:04 UTC | Add snv-indel trio clin-seq converge tool | 13 January 2014, 06:39:04 UTC |
| 5bb6238 | APipe Tester | 12 January 2014, 13:16:56 UTC | Updated `gmt` tab completion. | 12 January 2014, 13:16:56 UTC |
| 2a98cc7 | APipe Tester | 12 January 2014, 13:16:12 UTC | Updated `genome` tab completion. | 12 January 2014, 13:16:12 UTC |
| 833f7b8 | APipe Tester | 12 January 2014, 13:14:35 UTC | Updated class browser cache. | 12 January 2014, 13:14:35 UTC |
| cc33ce3 | Feiyu Du | 12 January 2014, 00:11:38 UTC | change it back until sample meta into bug fixed | 12 January 2014, 00:11:38 UTC |
| a4ad333 | Feiyu Du | 10 January 2014, 22:56:01 UTC | update build id for ref-align som-var-short and som-val | 10 January 2014, 22:56:01 UTC |
| f930578 | Feiyu Du | 10 January 2014, 22:10:25 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 10 January 2014, 22:10:25 UTC |
| c5de63b | Malachi Griffith | 10 January 2014, 21:39:55 UTC | use consistently names misc-annotation databases in CopyNumber/PlotSegments.pm | 10 January 2014, 21:39:55 UTC |
| 0ff2ec6 | Feiyu Du | 10 January 2014, 21:29:36 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 10 January 2014, 21:29:36 UTC |
| e56e7f4 | Veena Bhonagiri | 10 January 2014, 20:41:27 UTC | Had to fix issues Merge branch 'master' of ssh://git/srv/git/genome | 10 January 2014, 20:41:27 UTC |
| ad32587 | Veena Bhonagiri | 10 January 2014, 20:40:29 UTC | Fixed ace file issues for rna genes | 10 January 2014, 20:40:29 UTC |
| 9ba7a93 | Veena Bhonagiri | 10 January 2014, 20:39:17 UTC | Added snap models for T. nativa | 10 January 2014, 20:39:17 UTC |
| 85d573b | Feiyu Du | 10 January 2014, 19:19:19 UTC | 1.increment vcf version due to the change of samtools snv vcf null ALT column; 2. create a new gmt tool and plug into CreateSubmissionArchive.pm | 10 January 2014, 19:19:19 UTC |
| b4ac230 | Dave Larson | 10 January 2014, 19:12:22 UTC | only skip complex indels, rather than die | 10 January 2014, 19:13:43 UTC |
| 7d46ee6 | Dave Larson | 27 December 2013, 17:34:04 UTC | update the documentation | 10 January 2014, 19:13:41 UTC |
| 0ea8fa4 | apregier | 10 January 2014, 18:33:51 UTC | Merge branch 'my_annotation' into gb_master | 10 January 2014, 18:33:51 UTC |
| 71a7911 | apregier | 10 January 2014, 18:30:45 UTC | CHANGELOG VEP will always print gene symbol The --hgnc parameter will be ignored, and vep will always be asked to print the gene symbol, if available. In versions pre-74, the --hgnc parameter will always be appended to the vep command. In 74+, the --symbol parameter replaced --hgnc and will always be appended to the vep command. | 10 January 2014, 18:32:56 UTC |
| 04ca46a | APipe Tester | 10 January 2014, 17:50:17 UTC | updated workflow submodule to 77cc763 | 10 January 2014, 17:50:17 UTC |
| b379296 | APipe Tester | 10 January 2014, 17:37:10 UTC | updated ur submodule to a051290 | 10 January 2014, 17:37:10 UTC |
| 8f1a50b | APipe Tester | 10 January 2014, 16:46:06 UTC | updated jenkins submodule to 1764003 | 10 January 2014, 16:46:06 UTC |
| c6f81fc | APipe Tester | 10 January 2014, 13:18:03 UTC | Updated `genome` tab completion. | 10 January 2014, 13:18:03 UTC |
| fe1dec8 | Ben Ainscough | 09 January 2014, 22:01:26 UTC | updated test files | 09 January 2014, 22:01:26 UTC |
| 3fb1813 | Avinash Ramu | 09 January 2014, 20:44:07 UTC | updated microarray_cnv to handle exome models without microarrays, added min_cnv_diff param | 09 January 2014, 20:44:31 UTC |
| 6113610 | Ben Ainscough | 09 January 2014, 20:10:41 UTC | added cancer_annotation_db command to rna-seq creation in updateAnalysis | 09 January 2014, 20:10:41 UTC |
| 8ca8a85 | Thomas Mooney | 09 January 2014, 19:36:28 UTC | Tolerate failures to load the events tab of build views. The specific failure we encountered here is the necessary data to reconstruct the events is no longer in the system, but the event tab isn't that useful anymore, so just let it be blank instead of preventing the remainder of the view from loading. | 09 January 2014, 19:36:28 UTC |
| d166320 | Feiyu Du | 09 January 2014, 17:15:27 UTC | set ALT column to N instead of . if genotype is N | 09 January 2014, 17:15:27 UTC |
| 8540f4c | APipe Tester | 09 January 2014, 13:17:34 UTC | Updated `genome` tab completion. | 09 January 2014, 13:17:34 UTC |
| 0544d3a | APipe Tester | 09 January 2014, 13:15:53 UTC | Updated class browser cache. | 09 January 2014, 13:15:53 UTC |
| 2e98fcf | Adam Coffman | 08 January 2014, 22:23:33 UTC | update expected test output | 08 January 2014, 22:23:33 UTC |
| f67bb5c | Thomas Mooney | 08 January 2014, 22:11:01 UTC | Update blessed velvet build per kkyung | 08 January 2014, 22:11:01 UTC |
| 7b46989 | Adam Coffman | 08 January 2014, 22:08:33 UTC | add support for bisulfite_conversion field in libraries | 08 January 2014, 22:08:33 UTC |
| c981111 | Adam Coffman | 08 January 2014, 19:46:09 UTC | sqitch: add bisulfite_conversion column | 08 January 2014, 19:46:09 UTC |
