| c6ed552 | APipe Tester | 07 October 2013, 20:32:12 UTC | Updated `genome` tab completion. | 07 October 2013, 20:32:12 UTC |
| 17ce44f | Eddie Belter | 07 October 2013, 19:55:53 UTC | Chimera Slayer: if nastier runs ok, but no output, return 1 | 07 October 2013, 20:02:54 UTC |
| a3e3165 | APipe Tester | 07 October 2013, 15:46:41 UTC | Updated `genome` tab completion. | 07 October 2013, 15:46:41 UTC |
| e615e71 | dmorton | 07 October 2013, 15:35:29 UTC | Updated blessed model for somatic-variation-short Only difference was due to removing references to the cached reference sequences. | 07 October 2013, 15:36:25 UTC |
| d26af2a | APipe Tester | 07 October 2013, 11:16:42 UTC | Updated `genome` tab completion. | 07 October 2013, 11:16:42 UTC |
| dc7d93a | APipe Tester | 06 October 2013, 11:18:27 UTC | Updated `genome` tab completion. | 06 October 2013, 11:18:27 UTC |
| 1113f50 | APipe Tester | 06 October 2013, 04:41:45 UTC | Updated `genome` tab completion. | 06 October 2013, 04:41:45 UTC |
| 459cab3 | APipe Tester | 06 October 2013, 04:40:20 UTC | Updated class browser cache. | 06 October 2013, 04:40:20 UTC |
| 8f9ddf3 | dmorton | 04 October 2013, 22:06:37 UTC | Sys->shellcmd sets default handler for SIGPIPE POE (used in legacy workflow) was setting it to IGNORE and thus countering our efforts to set -o pipefail and catch errors. Since we expect many errors in the wild, we're just warning on the error code 141 (PIPEFAIL) and handling cases as they pop up. | 06 October 2013, 03:59:19 UTC |
| 1afef53 | dmorton | 03 October 2013, 21:55:05 UTC | Put restriction on how long error_text can get | 06 October 2013, 03:59:18 UTC |
| 2059e6e | dmorton | 03 October 2013, 21:00:18 UTC | Redesigned genome model admin failed-model-tickets No longer uses ErrorLogEntry Handles grouping errors better (especially unstartable ones) | 06 October 2013, 03:59:18 UTC |
| 9adefbc | dmorton | 03 October 2013, 20:59:47 UTC | Added genome model build determine-error | 06 October 2013, 03:59:18 UTC |
| d700186 | dmorton | 30 September 2013, 22:29:22 UTC | Add check for model->status to suppress warnings | 06 October 2013, 03:59:18 UTC |
| ad70489 | dmorton | 30 September 2013, 22:29:01 UTC | Extract Method get_tickets | 06 October 2013, 03:59:18 UTC |
| 13e2e9e | dmorton | 30 September 2013, 22:06:16 UTC | Extract Method get_builds | 06 October 2013, 03:59:18 UTC |
| b853349 | dmorton | 30 September 2013, 21:54:56 UTC | Extract method to get events | 06 October 2013, 03:59:18 UTC |
| e2a6094 | dmorton | 30 September 2013, 19:18:42 UTC | Fix failed-model-tickets to work with new uuids | 06 October 2013, 03:59:18 UTC |
| 1df7a47 | APipe Tester | 05 October 2013, 11:17:56 UTC | Updated `genome` tab completion. | 05 October 2013, 11:17:56 UTC |
| fc68872 | APipe Tester | 04 October 2013, 22:50:57 UTC | Updated `genome` tab completion. | 04 October 2013, 22:50:57 UTC |
| c8fdc3d | Travis Abbott | 04 October 2013, 22:34:55 UTC | update test data version | 04 October 2013, 22:36:01 UTC |
| bed1cd7 | Feiyu Du | 04 October 2013, 20:27:07 UTC | bug fix | 04 October 2013, 20:27:07 UTC |
| 2ef5645 | Ian Ferguson | 04 October 2013, 20:13:39 UTC | Add invalid status to Genome::Disk::Allocation Invalid status added for Allocations. This is for allocations that exist in the database but never existed on disk. Not to be confused with the 'purged' status, which is used for allocations that were on disk but were later removed. | 04 October 2013, 20:18:20 UTC |
| 7ff98fd | Travis Abbott | 04 October 2013, 18:42:31 UTC | bump test data version for cross sample indels | 04 October 2013, 18:42:31 UTC |
| 323c920 | APipe Tester | 04 October 2013, 17:32:09 UTC | Updated `gmt` tab completion. | 04 October 2013, 17:32:09 UTC |
| dc16c0b | APipe Tester | 04 October 2013, 17:31:30 UTC | Updated `genome` tab completion. | 04 October 2013, 17:31:30 UTC |
| 32864d2 | APipe Tester | 04 October 2013, 17:29:59 UTC | Updated class browser cache. | 04 October 2013, 17:29:59 UTC |
| 931e8db | Chris Miller | 04 October 2013, 17:25:29 UTC | Merge branch 'manuscript' | 04 October 2013, 17:25:29 UTC |
| df3b88a | Chris Miller | 04 October 2013, 17:25:00 UTC | skeleton of a new tool to munge through a processing profile and spit out a text description. Still needs a ton of work | 04 October 2013, 17:25:00 UTC |
| 9cf04ed | APipe Tester | 04 October 2013, 17:17:30 UTC | Updated `genome` tab completion. | 04 October 2013, 17:17:30 UTC |
| bfda356 | Eddie Belter | 04 October 2013, 17:08:39 UTC | DV2 Filter False Indels: remove default for min_good_coverage | 04 October 2013, 17:08:47 UTC |
| 85a2286 | APipe Tester | 04 October 2013, 17:05:22 UTC | Updated `genome` tab completion. | 04 October 2013, 17:05:22 UTC |
| 9293e99 | APipe Tester | 04 October 2013, 17:02:50 UTC | Updated class browser cache. | 04 October 2013, 17:02:50 UTC |
| 159d648 | Eddie Belter | 04 October 2013, 16:56:26 UTC | AQID: update site tgi project classes | 04 October 2013, 16:56:26 UTC |
| 1bdb90e | Eddie Belter | 04 October 2013, 16:49:49 UTC | Sync: update LimsProject* classes and SQL | 04 October 2013, 16:52:01 UTC |
| 41612df | Eddie Belter | 04 October 2013, 16:48:14 UTC | Sync: rename SetupProject* classes to LimsProject* | 04 October 2013, 16:52:01 UTC |
| 2d78c49 | APipe Tester | 04 October 2013, 15:05:31 UTC | Updated `genome` tab completion. | 04 October 2013, 15:05:31 UTC |
| 7a7a807 | APipe Tester | 03 October 2013, 21:15:19 UTC | Updated `gmt` tab completion. | 03 October 2013, 21:15:19 UTC |
| 98c1abe | APipe Tester | 03 October 2013, 21:14:33 UTC | Updated `genome` tab completion. | 03 October 2013, 21:14:33 UTC |
| 896f0a7 | APipe Tester | 03 October 2013, 21:13:15 UTC | Updated class browser cache. | 03 October 2013, 21:13:15 UTC |
| 2597b78 | Feiyu Du | 03 October 2013, 21:01:53 UTC | finish IntersectSv.pm and add unit test | 03 October 2013, 21:02:44 UTC |
| e71ae35 | Feiyu Du | 02 October 2013, 18:08:36 UTC | Add IntersectSv.pm | 03 October 2013, 21:02:43 UTC |
| 86e2a88 | APipe Tester | 03 October 2013, 20:04:51 UTC | Updated `genome` tab completion. | 03 October 2013, 20:04:51 UTC |
| 77f17f7 | Gabriel Sanderson | 03 October 2013, 19:47:53 UTC | Merge branch 'ref' into gb_master | 03 October 2013, 19:47:53 UTC |
| eff63c7 | Gabriel Sanderson | 03 October 2013, 19:32:53 UTC | Remove cached reference alignments from DV2. | 03 October 2013, 19:46:49 UTC |
| dce25e0 | APipe Tester | 03 October 2013, 19:33:26 UTC | Updated `genome` tab completion. | 03 October 2013, 19:33:26 UTC |
| 1c9a2d5 | APipe Tester | 03 October 2013, 19:30:03 UTC | Updated class browser cache. | 03 October 2013, 19:30:03 UTC |
| 444d411 | APipe Tester | 03 October 2013, 19:26:39 UTC | updated ur submodule to 93fb4ce | 03 October 2013, 19:26:39 UTC |
| 375887f | APipe Tester | 03 October 2013, 18:59:04 UTC | Updated `genome` tab completion. | 03 October 2013, 18:59:04 UTC |
| 8944a5e | APipe Tester | 03 October 2013, 18:57:38 UTC | Updated class browser cache. | 03 October 2013, 18:57:38 UTC |
| 6d44c20 | Nathan Nutter | 01 October 2013, 15:31:44 UTC | account for kilobytes_requested in shadow_get_or_create If an allocation already exists it can have a different kilobytes_requested so we filter that from the get params and apply it to the gotten allocation. | 03 October 2013, 17:48:29 UTC |
| fd0afff | Nathan Nutter | 01 October 2013, 15:29:45 UTC | refactor to allow multiple params | 03 October 2013, 17:48:29 UTC |
| f26d688 | Nathan Nutter | 01 October 2013, 15:26:32 UTC | rename get_or_create to shadow_get_or_create get_or_create is going to have to change to filter out certain parameters, etc. which doesn't really make it a get_or_create anymore. | 03 October 2013, 17:48:28 UTC |
| 0f0ebed | Nathan Nutter | 01 October 2013, 18:56:08 UTC | use next volume which is not an archive volume | 03 October 2013, 17:48:27 UTC |
| 8968cca | Nathan Nutter | 01 October 2013, 18:55:17 UTC | refactor allocation test library Refactor allocation test library to make it easier to create multiple volumes. | 03 October 2013, 17:48:27 UTC |
| ae9fe17 | APipe Tester | 03 October 2013, 11:19:59 UTC | Updated `genome` tab completion. | 03 October 2013, 11:19:59 UTC |
| dc2ba46 | APipe Tester | 03 October 2013, 11:18:23 UTC | Updated class browser cache. | 03 October 2013, 11:18:23 UTC |
| 83c5795 | APipe Tester | 02 October 2013, 18:41:19 UTC | Updated `genome` tab completion. | 02 October 2013, 18:41:19 UTC |
| ff89132 | APipe Tester | 02 October 2013, 18:37:46 UTC | Updated class browser cache. | 02 October 2013, 18:37:46 UTC |
| 5a4f9be | APipe Tester | 02 October 2013, 18:28:53 UTC | Updated `genome` tab completion. | 02 October 2013, 18:31:12 UTC |
| fd588b0 | APipe Tester | 02 October 2013, 18:25:23 UTC | Updated class browser cache. | 02 October 2013, 18:31:12 UTC |
| 320560d | Ben Ainscough | 02 October 2013, 18:24:50 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 02 October 2013, 18:24:50 UTC |
| 0fd51d3 | Feiyu Du | 02 October 2013, 18:17:24 UTC | lower picard max mem to 16 gb | 02 October 2013, 18:18:06 UTC |
| ea79782 | Jim Weible | 02 October 2013, 18:13:47 UTC | cleanup | 02 October 2013, 18:13:59 UTC |
| fe80915 | Jim Weible | 02 October 2013, 16:22:25 UTC | cleanup to be more better | 02 October 2013, 18:13:58 UTC |
| 858760a | Jim Weible | 02 October 2013, 15:01:58 UTC | Add support for non-region limited data in create cross sample vcf | 02 October 2013, 18:13:58 UTC |
| ba963bf | Ben Ainscough | 02 October 2013, 17:34:39 UTC | fixed logic error in determining to use wgs or exome | 02 October 2013, 17:34:39 UTC |
| a7ff137 | APipe Tester | 02 October 2013, 17:16:32 UTC | Updated `genome` tab completion. | 02 October 2013, 17:16:32 UTC |
| f4626a4 | APipe Tester | 02 October 2013, 17:13:13 UTC | Updated class browser cache. | 02 October 2013, 17:13:13 UTC |
| 49b5534 | apregier | 02 October 2013, 16:57:12 UTC | Allow user to select subsets of clinseq inputs | 02 October 2013, 16:57:58 UTC |
| 2cdad55 | APipe Tester | 02 October 2013, 14:55:34 UTC | Updated `genome` tab completion. | 02 October 2013, 14:55:34 UTC |
| fbffb88 | APipe Tester | 02 October 2013, 14:53:31 UTC | Updated class browser cache. | 02 October 2013, 14:53:31 UTC |
| 4b2adf7 | Ben Ainscough | 02 October 2013, 14:44:21 UTC | Fixed unit test problem and added error handleing if there is no rna data | 02 October 2013, 14:44:21 UTC |
| 945332c | Ben Ainscough | 02 October 2013, 14:23:18 UTC | Updated tool to be fully functional with WGS+RNA+exome data. | 02 October 2013, 14:23:18 UTC |
| c75cf21 | APipe Tester | 02 October 2013, 13:08:05 UTC | Updated `genome` tab completion. | 02 October 2013, 13:08:05 UTC |
| fd402ad | apregier | 02 October 2013, 12:57:05 UTC | Updates from commit 7a3149dc223 | 02 October 2013, 12:57:16 UTC |
| 9721150 | APipe Tester | 02 October 2013, 11:19:20 UTC | Updated `genome` tab completion. | 02 October 2013, 11:19:20 UTC |
| 83e2ca6 | APipe Tester | 02 October 2013, 03:48:15 UTC | Updated `genome` tab completion. | 02 October 2013, 03:48:15 UTC |
| 8bd2c3d | apregier | 02 October 2013, 03:33:22 UTC | glob doesn't always work | 02 October 2013, 03:33:22 UTC |
| 1148edb | APipe Tester | 01 October 2013, 22:26:25 UTC | Updated `genome` tab completion. | 01 October 2013, 22:26:25 UTC |
| 26901e7 | APipe Tester | 01 October 2013, 22:24:05 UTC | Updated class browser cache. | 01 October 2013, 22:24:05 UTC |
| 129bd3a | Adam Coffman | 01 October 2013, 22:07:59 UTC | remove test for class that doesnt exist | 01 October 2013, 22:07:59 UTC |
| 5ff9be6 | APipe Tester | 01 October 2013, 21:55:08 UTC | updated ur submodule to 99babd9 | 01 October 2013, 21:55:08 UTC |
| b6eea9b | Adam Coffman | 01 October 2013, 21:50:30 UTC | remove do-not-archive globally in favor of delay archiving | 01 October 2013, 21:50:30 UTC |
| 07f08b0 | Eddie Belter | 01 October 2013, 21:27:22 UTC | DV2 Filter False Indels: init stats | 01 October 2013, 21:27:48 UTC |
| 7f6a86c | APipe Tester | 01 October 2013, 20:49:06 UTC | updated ur submodule to d4ddfbb | 01 October 2013, 20:49:06 UTC |
| 6ac5c3e | Adam Coffman | 01 October 2013, 20:41:20 UTC | set archive_after_time automatically on allocation creation | 01 October 2013, 20:41:20 UTC |
| 629fb68 | Gabriel Sanderson | 01 October 2013, 20:24:51 UTC | add is_optional to output_vcf because otheriwse it breaks for some reason I dont understand. | 01 October 2013, 20:25:34 UTC |
| c5db9e9 | Anthony Brummett | 01 October 2013, 20:19:32 UTC | join the outout for R into a single string before calling status_message() response to UR's change where the *_message functions work like sprintf with a format string and list | 01 October 2013, 20:19:32 UTC |
| 2ce3a54 | APipe Tester | 01 October 2013, 20:16:42 UTC | Updated `genome` tab completion. | 01 October 2013, 20:16:42 UTC |
| fd61e07 | APipe Tester | 01 October 2013, 20:14:21 UTC | Updated class browser cache. | 01 October 2013, 20:14:21 UTC |
| ce9a17d | Adam Coffman | 01 October 2013, 20:04:09 UTC | remove concept of preserved allocations | 01 October 2013, 20:04:09 UTC |
| 41033b5 | Veena Bhonagiri | 01 October 2013, 19:52:58 UTC | Rfam ace file changes for egap Merge branch 'master' of ssh://git/srv/git/genome | 01 October 2013, 19:52:58 UTC |
| 7a3149d | Veena Bhonagiri | 01 October 2013, 19:51:13 UTC | Modified rfam ace file so rfam score and rfam_product are added Also added a filter so less than 50 score rfam genes do not enter into the ace file | 01 October 2013, 19:51:13 UTC |
| 234ce83 | Adam Coffman | 01 October 2013, 19:49:45 UTC | add status column for allocations | 01 October 2013, 19:49:45 UTC |
| 1f383a8 | APipe Tester | 30 September 2013, 18:44:31 UTC | Updated `genome` tab completion. | 30 September 2013, 18:44:31 UTC |
| ec2db44 | APipe Tester | 30 September 2013, 18:42:57 UTC | Updated class browser cache. | 30 September 2013, 18:42:57 UTC |
| 7cafbe9 | apregier | 30 September 2013, 18:33:18 UTC | Merge branch 'annovar' into gb_master | 30 September 2013, 18:33:18 UTC |
| 967faac | apregier | 30 September 2013, 14:36:50 UTC | Specifically get gtf file | 30 September 2013, 18:32:07 UTC |
| 8037bec | apregier | 23 September 2013, 16:46:05 UTC | CHANGELOG Switch music model to take clinseq builds Old music models will need to be updated to take inputs named clinseq_builds and the somatic_variation_builds inputs will need to be removed. | 30 September 2013, 18:31:15 UTC |
| 4d91c04 | apregier | 23 September 2013, 16:13:49 UTC | Refactor resolve_reference_build into a utility function for reuse | 30 September 2013, 17:15:25 UTC |
