| 7c9a61a | Adam Coffman | 27 January 2014, 20:02:13 UTC | Add CLIA support to analysis projects. This updates analysis projects to contain an is_clia field as well as a run_as field and makes the surrounding classes aware of them. | 27 January 2014, 20:02:13 UTC |
| 56224d6 | Adam Coffman | 27 January 2014, 16:08:45 UTC | Auto-increment names for LaneQC models. We'll now auto-increment names for LaneQC models like we do other models. This is expected to have a few side effects, but we'll address them as they come up. We have a situation where a piece of instrument data could have multiple valid LaneQC models from being used in multiple analysis projects which is something that hasn't occured previously. | 27 January 2014, 16:08:45 UTC |
| 6815964 | Thomas Mooney | 27 January 2014, 15:26:53 UTC | Try to determine what error caused a build to fail. The message "Can't convert workflow errors to build errors." will no longer be displayed. If an error can't be determined, "[Unable to automatically determine error.]" will appear instead. | 27 January 2014, 15:30:11 UTC |
| f597701 | Thomas Mooney | 27 January 2014, 15:21:50 UTC | Allow the failure type to be provided. This way the error can be determined after a build is Abandoned or while it is still Running (if it is known to have a failed step). | 27 January 2014, 15:30:10 UTC |
| 1a54220 | Thomas Mooney | 27 January 2014, 15:20:46 UTC | Split out formatting and printing of the determined error. | 27 January 2014, 15:30:09 UTC |
| 9ffcce6 | Jim Weible | 10 January 2014, 14:19:11 UTC | Change status_message to debug message to remove output noise | 27 January 2014, 15:18:53 UTC |
| 6689c89 | APipe Tester | 25 January 2014, 13:18:00 UTC | Updated `gmt` tab completion. | 25 January 2014, 13:18:00 UTC |
| 37c0179 | APipe Tester | 25 January 2014, 13:17:12 UTC | Updated `genome` tab completion. | 25 January 2014, 13:17:12 UTC |
| f691d01 | APipe Tester | 25 January 2014, 13:15:29 UTC | Updated class browser cache. | 25 January 2014, 13:15:29 UTC |
| ec394ec | APipe Tester | 24 January 2014, 23:36:53 UTC | updated workflow submodule to 1824055 | 24 January 2014, 23:36:53 UTC |
| 6c81205 | APipe Tester | 24 January 2014, 23:25:42 UTC | updated ur submodule to 3570450 | 24 January 2014, 23:25:42 UTC |
| c7ded24 | Obi Griffith | 24 January 2014, 22:58:16 UTC | removed hard coding of cancer annotation db | 24 January 2014, 22:58:16 UTC |
| 9f1135a | Malachi Griffith | 24 January 2014, 22:14:00 UTC | clinseq - tolerate failure of wget for url caching | 24 January 2014, 22:14:00 UTC |
| 3128597 | Gabriel Sanderson | 24 January 2014, 21:59:42 UTC | Merge branch 'filtern' into gb_master | 24 January 2014, 21:59:42 UTC |
| 617a165 | Gabriel Sanderson | 13 January 2014, 23:42:16 UTC | CHANGELOG: Jira AT-249: Made gmt vcf FilterNonCalls to remove vcf lines with ALT = N or '.'. Added this to all create-cross-sample-vcf workflows. This should reduce the number of useless calls made by this pipeline. | 24 January 2014, 21:50:31 UTC |
| 916b91a | APipe Tester | 24 January 2014, 20:27:49 UTC | updated workflow submodule to 69ba6b1 | 24 January 2014, 20:27:49 UTC |
| 18476cf | Avinash Ramu | 24 January 2014, 18:00:42 UTC | remove unwanted variable | 24 January 2014, 18:01:02 UTC |
| a499a88 | APipe Tester | 24 January 2014, 16:33:40 UTC | updated jenkins submodule to 2ec0b5d | 24 January 2014, 16:33:40 UTC |
| 0d53c3f | APipe Tester | 24 January 2014, 16:27:45 UTC | updated jenkins submodule to c94ebc2 | 24 January 2014, 16:27:45 UTC |
| d5cf821 | APipe Tester | 24 January 2014, 16:23:17 UTC | updated jenkins submodule to a96f2e3 | 24 January 2014, 16:23:17 UTC |
| 96fb648 | APipe Tester | 24 January 2014, 16:20:48 UTC | Updated `gmt` tab completion. | 24 January 2014, 16:20:48 UTC |
| abcd244 | APipe Tester | 24 January 2014, 16:19:59 UTC | Updated `genome` tab completion. | 24 January 2014, 16:19:59 UTC |
| b77f799 | APipe Tester | 24 January 2014, 16:18:27 UTC | Updated class browser cache. | 24 January 2014, 16:18:27 UTC |
| 201b4f4 | Dave Larson | 24 January 2014, 05:44:00 UTC | revert back to regular versioning | 24 January 2014, 05:44:32 UTC |
| 6096713 | Dave Larson | 21 January 2014, 22:40:09 UTC | fix logic error on start positions | 24 January 2014, 05:44:31 UTC |
| e3598c5 | Dave Larson | 18 January 2014, 03:12:30 UTC | fix mistake where libraries not reported by bam-readcount weren't being reported. fix poort handling of NA field generations | 24 January 2014, 05:44:30 UTC |
| 1995d4f | Dave Larson | 16 January 2014, 05:40:30 UTC | add per library support | 24 January 2014, 05:44:29 UTC |
| 7e88f75 | Dave Larson | 16 January 2014, 05:22:02 UTC | per library stuff seems to be working | 24 January 2014, 05:44:28 UTC |
| b3c2d1b | Dave Larson | 16 January 2014, 04:11:35 UTC | refactor snvs to calc and print more generally | 24 January 2014, 05:44:28 UTC |
| c88c043 | Dave Larson | 16 January 2014, 03:42:36 UTC | refactor print slightly for better clarity | 24 January 2014, 05:44:27 UTC |
| 64aee09 | Dave Larson | 16 January 2014, 02:52:49 UTC | replace SNV count backend with BamReadcount interface | 24 January 2014, 05:44:26 UTC |
| 3bf0fbf | Dave Larson | 15 January 2014, 20:05:58 UTC | update Entry interface to allow access of alleles on non-per-lib entries | 24 January 2014, 05:44:25 UTC |
| 6859bd5 | Dave Larson | 15 January 2014, 06:42:46 UTC | switch to use BamReadcount File Reader for indels | 24 January 2014, 05:44:25 UTC |
| e0ee935 | Dave Larson | 15 January 2014, 05:28:50 UTC | switch backend to utilize BamReadcount 0.5 | 24 January 2014, 05:44:24 UTC |
| 203e04d | Dave Larson | 15 January 2014, 05:28:23 UTC | add some support for a test of 0.5 | 24 January 2014, 05:44:23 UTC |
| 70c4110 | Dave Larson | 15 January 2014, 02:36:38 UTC | fix logic error with regards to start position | 24 January 2014, 05:44:22 UTC |
| 9e976f8 | Obi Griffith | 24 January 2014, 04:49:57 UTC | added logic to skip clonality plot generation when snv file empty | 24 January 2014, 04:49:57 UTC |
| c527cb4 | Malachi Griffith | 24 January 2014, 01:19:01 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 24 January 2014, 01:19:01 UTC |
| 5d29752 | Malachi Griffith | 24 January 2014, 01:18:42 UTC | additional feature additions and updates to clin-seq converge snv-indel-report | 24 January 2014, 01:18:42 UTC |
| 1d24947 | Obi Griffith | 23 January 2014, 22:34:14 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 23 January 2014, 22:34:14 UTC |
| 780d28f | apregier | 23 January 2014, 22:26:06 UTC | Merge branch 'fix' into gb_master | 23 January 2014, 22:26:06 UTC |
| b6ce014 | apregier | 23 January 2014, 22:22:44 UTC | Allow gzipped files | 23 January 2014, 22:22:44 UTC |
| ace3245 | Obi Griffith | 23 January 2014, 22:16:52 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 23 January 2014, 22:16:52 UTC |
| 30a56a0 | Obi Griffith | 23 January 2014, 22:16:37 UTC | Add logic to handle zero-size indel files | 23 January 2014, 22:16:37 UTC |
| 5e62f0f | Thomas Mooney | 23 January 2014, 20:50:52 UTC | Tolerate failures to load the workflow tab of build views. Like commit 8ca8a8500c01d3748751217157cb7f4df12a2cef, but for the other tab... There's a module that no longer exists, so the Workflow cannot be instantiated. Just show an empty workflow view instead of crashing. | 23 January 2014, 20:50:52 UTC |
| 1a2fb76 | Thomas Mooney | 23 January 2014, 19:36:16 UTC | Call the column is_clia instead of is_cle. | 23 January 2014, 19:36:16 UTC |
| d177066 | Malachi Griffith | 23 January 2014, 17:59:26 UTC | further feature additions for genome model clin-seq converge snv-indel-report | 23 January 2014, 17:59:26 UTC |
| 7a4e60b | Avinash Ramu | 23 January 2014, 16:52:45 UTC | add missing $ | 23 January 2014, 16:53:03 UTC |
| 213ce31 | Nathan Nutter | 23 January 2014, 03:40:00 UTC | rename test Path to this test is hard-coded on Jenkins so will have to update. | 23 January 2014, 03:41:20 UTC |
| 2e1714d | Nathan Nutter | 23 January 2014, 03:39:23 UTC | better than an ok(1) | 23 January 2014, 03:41:17 UTC |
| c91f59b | Nathan Nutter | 23 January 2014, 03:38:44 UTC | move test so it is in a more expected location Path to this test is hard-coded on Jenkins so will have to update. | 23 January 2014, 03:40:39 UTC |
| 3ac8a49 | Nathan Nutter | 23 January 2014, 03:26:12 UTC | refactor test to not use hard-coded group Users could not chown test directory to group they did not belong to so not the test tries to pick a group that the user is a member of. | 23 January 2014, 03:26:12 UTC |
| 80b4e5d | Thomas Mooney | 22 January 2014, 16:40:58 UTC | Whitespace. | 22 January 2014, 16:40:58 UTC |
| d0b8eda | Malachi Griffith | 22 January 2014, 06:35:29 UTC | further fixes to clin-seq tests to account for reorganization of modules | 22 January 2014, 06:35:29 UTC |
| c418a2b | Malachi Griffith | 22 January 2014, 05:22:13 UTC | fix broken use lib statements | 22 January 2014, 05:22:13 UTC |
| de66553 | Malachi Griffith | 22 January 2014, 04:47:29 UTC | remove unused code from clinseq utility | 22 January 2014, 04:47:29 UTC |
| cc362c7 | dmorton | 21 January 2014, 23:09:56 UTC | Bugfix Vcf::Differ does not crash when file sizes differ | 22 January 2014, 03:10:14 UTC |
| eba9194 | dmorton | 21 January 2014, 23:09:09 UTC | Remove incorrect documentation | 22 January 2014, 03:10:14 UTC |
| 66a8693 | Malachi Griffith | 22 January 2014, 01:15:57 UTC | Remove duplicate copies of move perl modules | 22 January 2014, 01:15:57 UTC |
| 93e3e0d | Nathan Nutter | 21 January 2014, 20:03:08 UTC | GENOME_DEV_MODE and UR_DBI_NO_COMMIT are not so synonymous | 22 January 2014, 00:58:53 UTC |
| 2cc50e9 | Nathan Nutter | 10 January 2014, 22:03:45 UTC | remove defaults that are now specified in /etc/profile.d/genome.sh | 22 January 2014, 00:58:53 UTC |
| 7b1e24d | Avinash Ramu | 22 January 2014, 00:50:24 UTC | remove old original-scripts and update directory name | 22 January 2014, 00:57:07 UTC |
| 102627d | Avinash Ramu | 22 January 2014, 00:47:10 UTC | updated converge scripts inside Clinseq, reorganized original scripts | 22 January 2014, 00:51:54 UTC |
| 4f48c68 | Malachi Griffith | 22 January 2014, 00:47:54 UTC | Changing method call approach throughout clin-seq for module RnaSeqUtil.pm that has not yet been incorporated into a proper class | 22 January 2014, 00:47:54 UTC |
| 14cd926 | Malachi Griffith | 22 January 2014, 00:36:43 UTC | ClinSeq: Found another file that relied on Util.pm | 22 January 2014, 00:36:43 UTC |
| a4347f3 | Malachi Griffith | 22 January 2014, 00:35:42 UTC | Changing method call approach throughout clin-seq for module Util.pm that has not yet been incorporated into a proper class | 22 January 2014, 00:35:42 UTC |
| f7947a5 | APipe Tester | 21 January 2014, 18:54:07 UTC | updated workflow submodule to 3a6f56c | 21 January 2014, 18:54:07 UTC |
| 90e5cf9 | APipe Tester | 21 January 2014, 18:41:46 UTC | updated ur submodule to 406a3a2 | 21 January 2014, 18:41:46 UTC |
| c140938 | dmorton | 21 January 2014, 17:32:40 UTC | Add build accessor for target_region_set_name input | 21 January 2014, 17:32:40 UTC |
| 1611fc0 | dmorton | 21 January 2014, 04:24:32 UTC | Add Varscan Indel command and tests | 21 January 2014, 16:40:59 UTC |
| b97e2dd | dmorton | 21 January 2014, 04:22:52 UTC | Factor out base-class for Varscan pileup commands | 21 January 2014, 16:40:59 UTC |
| 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 |
