| 3223367 | Nathan Nutter | 09 October 2013, 22:31:31 UTC | update UR submodule to point at Gerrit | 09 October 2013, 22:33:37 UTC |
| 1cbbd84 | APipe Tester | 09 October 2013, 21:42:13 UTC | Updated `genome` tab completion. | 09 October 2013, 21:42:13 UTC |
| 0abe9d4 | APipe Tester | 09 October 2013, 21:35:25 UTC | updated jenkins submodule to 74bd768 | 09 October 2013, 21:35:25 UTC |
| 5267b9e | APipe Tester | 09 October 2013, 21:34:48 UTC | Updated `gmt` tab completion. | 09 October 2013, 21:34:48 UTC |
| f6f6ade | APipe Tester | 09 October 2013, 21:34:05 UTC | Updated `genome` tab completion. | 09 October 2013, 21:34:05 UTC |
| 743a39e | APipe Tester | 09 October 2013, 21:32:29 UTC | Updated class browser cache. | 09 October 2013, 21:32:29 UTC |
| f7f2d54 | APipe Tester | 09 October 2013, 19:53:29 UTC | updated ur submodule to a394ba1 | 09 October 2013, 19:53:29 UTC |
| 83e62b4 | dmorton | 09 October 2013, 18:16:14 UTC | Justify constant's value | 09 October 2013, 19:42:04 UTC |
| 8475221 | dmorton | 09 October 2013, 18:15:20 UTC | Ensure MakeDindelWindows only makes one window This is done by concatinating all the windows together, since dindel makes one file per chromosome. | 09 October 2013, 19:42:04 UTC |
| f72550a | dmorton | 09 October 2013, 17:11:12 UTC | Ease the permissions on the log dir created when unarchiving builds. | 09 October 2013, 18:59:33 UTC |
| e6554fb | Adam Coffman | 09 October 2013, 18:51:03 UTC | add event logging to disk/allocation | 09 October 2013, 18:51:03 UTC |
| 60a2044 | Adam Coffman | 09 October 2013, 18:20:41 UTC | update Timeline/Event to use the subclass preprocessor rather than inheritance | 09 October 2013, 18:20:41 UTC |
| d837402 | Thomas Mooney | 09 October 2013, 17:43:34 UTC | Bring version4 to life. | 09 October 2013, 17:43:34 UTC |
| 9f6270f | Thomas Mooney | 09 October 2013, 17:40:04 UTC | New annotator version Primary to re-order the priority of Ensembl annotations. | 09 October 2013, 17:40:04 UTC |
| f09f381 | Thomas Mooney | 09 October 2013, 15:11:04 UTC | sprintf-ify debug messages. *_message has been changed to sprintf() in UR::ModuleBase. | 09 October 2013, 15:11:04 UTC |
| 2fab13e | APipe Tester | 09 October 2013, 14:18:12 UTC | Updated `genome` tab completion. | 09 October 2013, 14:18:12 UTC |
| 80d2ba9 | Thomas Mooney | 09 October 2013, 14:09:31 UTC | Remove trailing characters from things that look like RSIDs. | 09 October 2013, 14:09:31 UTC |
| 55afea8 | APipe Tester | 09 October 2013, 11:17:02 UTC | Updated `genome` tab completion. | 09 October 2013, 11:17:02 UTC |
| d7515cb | APipe Tester | 08 October 2013, 22:52:30 UTC | Updated `genome` tab completion. | 08 October 2013, 22:52:30 UTC |
| 924f5f9 | APipe Tester | 08 October 2013, 22:50:05 UTC | Updated class browser cache. | 08 October 2013, 22:50:05 UTC |
| 23a5d9c | Adam Coffman | 08 October 2013, 22:41:53 UTC | add initial Timeline tree for event logging | 08 October 2013, 22:41:53 UTC |
| 7d066ba | APipe Tester | 08 October 2013, 22:35:28 UTC | Updated `genome` tab completion. | 08 October 2013, 22:35:28 UTC |
| 7fa89c3 | APipe Tester | 08 October 2013, 22:23:49 UTC | Updated `genome` tab completion. | 08 October 2013, 22:25:30 UTC |
| 06d8194 | Adam Coffman | 08 October 2013, 22:15:04 UTC | auto populate archive after time on both creation and unarchiving | 08 October 2013, 22:15:04 UTC |
| d5530a3 | APipe Tester | 08 October 2013, 22:09:56 UTC | updated ur submodule to a5b9b4b | 08 October 2013, 22:09:56 UTC |
| 136aa1c | APipe Tester | 08 October 2013, 21:37:48 UTC | Updated `genome` tab completion. | 08 October 2013, 21:37:48 UTC |
| 442aa4e | Eddie Belter | 08 October 2013, 21:22:32 UTC | Sync: Resume expunging instrument data that was removed from LIMS | 08 October 2013, 21:23:39 UTC |
| d95721e | Eddie Belter | 08 October 2013, 20:50:36 UTC | Sync: update UAC locking | 08 October 2013, 21:23:38 UTC |
| 657376c | Eddie Belter | 08 October 2013, 20:45:52 UTC | Sync: Commit between creating objects in genome. | 08 October 2013, 21:23:38 UTC |
| 5dd8909 | APipe Tester | 08 October 2013, 19:47:01 UTC | Updated `genome` tab completion. | 08 October 2013, 19:47:01 UTC |
| f903721 | Eddie Belter | 08 October 2013, 18:59:25 UTC | Sync Index Illumina: make joins to work order etc left joins | 08 October 2013, 19:38:06 UTC |
| bfd9f41 | APipe Tester | 08 October 2013, 19:15:37 UTC | Updated `genome` tab completion. | 08 October 2013, 19:15:37 UTC |
| c6b98e0 | Gabriel Sanderson | 08 October 2013, 19:07:06 UTC | Merge branch 'master' into gb_master | 08 October 2013, 19:07:06 UTC |
| e7c1675 | Gabriel Sanderson | 08 October 2013, 19:06:22 UTC | Update somatic-validation blessed build | 08 October 2013, 19:06:22 UTC |
| b9fcc69 | APipe Tester | 08 October 2013, 17:51:09 UTC | Updated `genome` tab completion. | 08 October 2013, 17:51:09 UTC |
| 6c32d2d | Gabriel Sanderson | 08 October 2013, 17:41:40 UTC | Merge branch 'ccsvcf' into gb_master | 08 October 2013, 17:41:40 UTC |
| 74a3702 | Gabriel Sanderson | 08 October 2013, 17:41:26 UTC | added exact_pos to the initial merge for indels so we dont crash because a single input file has overlapping indels. | 08 October 2013, 17:41:26 UTC |
| c8edef3 | APipe Tester | 08 October 2013, 16:17:22 UTC | Updated `genome` tab completion. | 08 October 2013, 16:17:22 UTC |
| 1f588dd | Eddie Belter | 08 October 2013, 15:41:35 UTC | Sync: Use LIMS admin projects instead of research projects | 08 October 2013, 16:06:15 UTC |
| 4fe5602 | APipe Tester | 08 October 2013, 15:44:46 UTC | Updated `genome` tab completion. | 08 October 2013, 15:44:46 UTC |
| 005f2fb | Kyung Kim | 08 October 2013, 15:35:17 UTC | Increased newbler assemble stage memory to 30G otherwise most builds fail currently | 08 October 2013, 15:35:17 UTC |
| 7068dfb | APipe Tester | 08 October 2013, 11:18:59 UTC | Updated `genome` tab completion. | 08 October 2013, 11:18:59 UTC |
| 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 |
