| 0a25a7a | Nathaniel Nutter | 27 February 2014, 00:29:09 UTC | prototype logger to split messages (by type) The goal would be to delegate UR::ModuleBase's *_message to this so that we can send different types of messages to syslog than to the screen. Log::Dispatch enables this but log4perl does not. | 27 February 2014, 00:29:09 UTC |
| b4be7f1 | Nathaniel Nutter | 11 February 2014, 00:34:34 UTC | add test | 27 February 2014, 00:26:00 UTC |
| 15cd5b2 | Nathaniel Nutter | 11 February 2014, 00:33:29 UTC | extract should_color_screen | 27 February 2014, 00:26:00 UTC |
| 9919883 | Nathaniel Nutter | 11 February 2014, 00:16:42 UTC | fall back on non-color screen when color package is not available | 27 February 2014, 00:25:59 UTC |
| 1008700 | Nathaniel Nutter | 11 February 2014, 00:07:27 UTC | fall back on non-color screen when STDERR is not a TTY | 27 February 2014, 00:25:58 UTC |
| 67773df | Nathaniel Nutter | 11 February 2014, 00:06:56 UTC | extract color_screen | 27 February 2014, 00:25:58 UTC |
| 615018e | Nathaniel Nutter | 10 February 2014, 21:22:28 UTC | move syslog dispatcher to TGI site | 27 February 2014, 00:25:57 UTC |
| cca2ab5 | Nathaniel Nutter | 10 February 2014, 20:56:38 UTC | Genome::Logger | 27 February 2014, 00:25:56 UTC |
| 653a658 | Eddie Belter | 26 February 2014, 22:07:34 UTC | CQID: does not require user to verify when running w/ inst data | 26 February 2014, 22:07:34 UTC |
| c4aab94 | Thomas Mooney | 26 February 2014, 20:58:32 UTC | Replace reserved function debug_file with debug_file_path. | 26 February 2014, 20:58:32 UTC |
| 4ecf27a | Gabriel Sanderson | 26 February 2014, 19:23:57 UTC | Clarified comments | 26 February 2014, 19:24:42 UTC |
| 6569b3b | Gabriel Sanderson | 26 February 2014, 19:23:23 UTC | Sort builds by date_completed so things are consistent. | 26 February 2014, 19:24:42 UTC |
| 526c28d | Malachi Griffith | 26 February 2014, 16:45:09 UTC | clin-seq fix sorting before getting bam read counts | 26 February 2014, 16:45:09 UTC |
| abe63e4 | APipe Tester | 26 February 2014, 13:18:19 UTC | Updated `gmt` tab completion. | 26 February 2014, 13:18:19 UTC |
| a0e3ad5 | APipe Tester | 26 February 2014, 13:17:33 UTC | Updated `genome` tab completion. | 26 February 2014, 13:17:33 UTC |
| 057b182 | APipe Tester | 26 February 2014, 13:15:49 UTC | Updated class browser cache. | 26 February 2014, 13:15:49 UTC |
| a944de4 | Eddie Belter | 25 February 2014, 23:23:31 UTC | InstData Import: use correct seq-grind | 25 February 2014, 23:24:03 UTC |
| eba20ec | Eddie Belter | 11 February 2014, 22:57:19 UTC | Import InstData: use seq-grind to sanitize bams | 25 February 2014, 23:24:02 UTC |
| 327dd3b | Eddie Belter | 11 February 2014, 22:06:17 UTC | Import InstData: update sort bam test data | 25 February 2014, 23:24:01 UTC |
| b671301 | Eddie Belter | 11 February 2014, 21:50:30 UTC | Import InstData: Add sanitize workflow step | 25 February 2014, 23:24:01 UTC |
| e37ae35 | Eddie Belter | 25 February 2014, 23:02:25 UTC | InstData Import: hacky way to get read_lenth and set on instdata #FIXME! | 25 February 2014, 23:02:25 UTC |
| 5b8ef4d | Nathaniel Nutter | 25 February 2014, 21:23:29 UTC | remove unused method, execute_with_bsub I am trying to improve a related method and discovered that this method is not used. I believe it is unused because `ack execute_with_bsub` returned no matches and running an event model (ReferenceAlignment) did not call the method. Also, all tests pass with it removed. | 25 February 2014, 21:27:58 UTC |
| 2b665a1 | Malachi Griffith | 25 February 2014, 19:14:20 UTC | add conditions to CallR.pm.MutationSpectrum.R so that mutation-spectrum plots created in clin-seq will work with ggplot2 <= 0.8.9 and ggplot2 >= 0.9.X | 25 February 2014, 19:14:20 UTC |
| f5b98b5 | Ian Ferguson | 25 February 2014, 18:45:06 UTC | Allpaths assemblies >3GB should run on 1TB machine | 25 February 2014, 18:46:08 UTC |
| 6b04d72 | dmorton | 25 February 2014, 18:36:13 UTC | Add ability for gmt Park::Base to run rex processes | 25 February 2014, 18:36:46 UTC |
| 5c3e119 | dmorton | 25 February 2014, 17:00:32 UTC | Add gmt Park base class for Park based tools | 25 February 2014, 18:36:46 UTC |
| 293f385 | Charles Lu | 25 February 2014, 17:56:20 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 25 February 2014, 17:56:20 UTC |
| f5261b5 | Charles Lu | 25 February 2014, 17:56:15 UTC | added the ability to specify base quality | 25 February 2014, 17:56:15 UTC |
| 46ac116 | Susanna Siebert | 25 February 2014, 16:44:17 UTC | updated test data version and REBUILD because new instrument data came through | 25 February 2014, 16:44:17 UTC |
| 03c13ab | Nathaniel Nutter | 24 February 2014, 21:48:43 UTC | set config to test config | 24 February 2014, 21:48:43 UTC |
| b0c1b0f | Feiyu Du | 24 February 2014, 20:37:45 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 24 February 2014, 20:37:45 UTC |
| 651352e | Feiyu Du | 24 February 2014, 20:37:16 UTC | bug fixed | 24 February 2014, 20:37:16 UTC |
| a3d1fc4 | apregier | 24 February 2014, 20:32:31 UTC | Merge branch 'updated' into gb_master | 24 February 2014, 20:32:31 UTC |
| 6cf9e49 | apregier | 14 February 2014, 20:36:36 UTC | Remove trailing tabs introduced by intersectBed | 24 February 2014, 20:30:46 UTC |
| 7a5b51f | apregier | 14 February 2014, 18:43:04 UTC | Add -v intersect type | 24 February 2014, 20:30:45 UTC |
| bd97a5b | apregier | 13 February 2014, 20:21:09 UTC | Add option to keep header in bed/vcf file | 24 February 2014, 20:30:45 UTC |
| 42b7625 | Thomas Mooney | 24 February 2014, 18:45:58 UTC | Remove trailing whitespace. | 24 February 2014, 18:45:58 UTC |
| 7e5dd38 | Chris Miller | 22 February 2014, 23:46:42 UTC | Fixing an edge case where indel readcounts can be reported incorrectly when there are multiple alleles at a single position | 22 February 2014, 23:46:55 UTC |
| 2cdf01b | APipe Tester | 22 February 2014, 13:17:59 UTC | Updated `gmt` tab completion. | 22 February 2014, 13:17:59 UTC |
| f71bac1 | APipe Tester | 22 February 2014, 13:17:15 UTC | Updated `genome` tab completion. | 22 February 2014, 13:17:15 UTC |
| 92dd197 | Chris Miller | 21 February 2014, 22:19:54 UTC | add samtools vcf file support | 21 February 2014, 22:20:14 UTC |
| 77bb9e3 | dmorton | 18 February 2014, 17:32:09 UTC | Fix message typo | 21 February 2014, 19:27:45 UTC |
| 212225b | Susanna Siebert | 21 February 2014, 19:09:00 UTC | bugfix: Genome::Model::Tools::FastTier::AddTiers expects a anno file, not bed file delete annoFileToBedFile conversion before calling Genome::Model::Tools::FastTier::AddTiers because the anno file format is correct delete bedFileToAnnoFile after addTiering because the file is already in anno format | 21 February 2014, 19:09:00 UTC |
| 426c15e | Travis Abbott | 21 February 2014, 18:40:16 UTC | Sort VEP output after annotating sometimes VEP puts out unsorted data. | 21 February 2014, 18:40:16 UTC |
| 502a0a8 | APipe Tester | 21 February 2014, 16:06:22 UTC | updated workflow submodule to a98122e | 21 February 2014, 16:06:22 UTC |
| dc11ee1 | APipe Tester | 21 February 2014, 13:17:40 UTC | Updated `gmt` tab completion. | 21 February 2014, 13:17:40 UTC |
| 1e1eb32 | APipe Tester | 21 February 2014, 13:16:52 UTC | Updated `genome` tab completion. | 21 February 2014, 13:16:52 UTC |
| 79576e5 | Adam Coffman | 20 February 2014, 22:58:10 UTC | change clia to cle | 20 February 2014, 22:58:10 UTC |
| 3abd50f | Gabriel Sanderson | 14 February 2014, 17:08:12 UTC | Update all tools with a joinx_version parameter to have no default and instead ask G:M:T::Joinx for its current default value. This is not ideal because of the copypasted _resolve_joinx_version duplication. But at least the default version is centralized now. | 20 February 2014, 22:10:15 UTC |
| fd3e880 | Chris Miller | 20 February 2014, 19:42:45 UTC | removing stupid header | 20 February 2014, 19:42:45 UTC |
| 1f1b84e | APipe Tester | 20 February 2014, 13:16:56 UTC | Updated `genome` tab completion. | 20 February 2014, 13:16:56 UTC |
| 6ef656a | Malachi Griffith | 19 February 2014, 22:49:58 UTC | Fix clinseq module definition to address warnings in Command/Services/WebApp/Core.t | 19 February 2014, 22:49:58 UTC |
| 74cb597 | APipe Tester | 19 February 2014, 22:45:32 UTC | updated graphite submodule to ac4c603 | 19 February 2014, 22:45:32 UTC |
| b070eea | Malachi Griffith | 19 February 2014, 22:19:29 UTC | clin-seq - add check for cancer_annotation_db method on rna-seq models before attempting to use | 19 February 2014, 22:19:29 UTC |
| a8dc0e7 | Nathaniel Nutter | 19 February 2014, 20:19:09 UTC | add test case for ro intermediate dir | 19 February 2014, 21:17:40 UTC |
| f33e73b | Nathaniel Nutter | 19 February 2014, 20:12:15 UTC | preserve errno to prevent an bug if an intermediate system call gets added | 19 February 2014, 21:17:40 UTC |
| f269d80 | Thomas Mooney | 19 February 2014, 20:37:50 UTC | Disconnect from DB before running workflow. | 19 February 2014, 20:37:50 UTC |
| aeca638 | Malachi Griffith | 19 February 2014, 20:17:28 UTC | clin-seq - minor update to analysis plan | 19 February 2014, 20:17:28 UTC |
| 8f3c3aa | Jim Weible | 19 February 2014, 19:05:13 UTC | add description to the correct analysis menu item table | 19 February 2014, 19:15:20 UTC |
| 6bed63c | Thomas Mooney | 19 February 2014, 17:29:33 UTC | Remove extra quotation marks. Previously Genome::Sys->bsub_and_wait was putting this into ``s, so the quotation marks were necessary. Now it's using IPC::System::Simple, so each string is already a single token in the array of parameters. (This fix is similar to commit 2fa2de5dcd3b9cf470461c7124f7accfd35686a7dd) | 19 February 2014, 17:29:33 UTC |
| 2fa2de5 | Thomas Mooney | 19 February 2014, 17:14:38 UTC | Remove extra quotation marks. Previously Genome::Sys->bsub_and_wait was putting this into ``s, so the quotation marks were necessary. Now it's using IPC::System::Simple, so each string is already a single token in the array of parameters. | 19 February 2014, 17:14:38 UTC |
| bc2da62 | apregier | 19 February 2014, 17:00:11 UTC | Merge branch 'my_annotation' into gb_master | 19 February 2014, 17:00:11 UTC |
| 764f139 | apregier | 18 February 2014, 23:59:04 UTC | Update docs | 19 February 2014, 16:59:54 UTC |
| 6b30685 | apregier | 18 February 2014, 23:56:33 UTC | Add custom annotation option for vep | 19 February 2014, 16:59:53 UTC |
| 1cab51b | Jim Weible | 19 February 2014, 16:49:21 UTC | add description to Analysis menu items | 19 February 2014, 16:54:13 UTC |
| 21856e8 | APipe Tester | 19 February 2014, 13:18:58 UTC | Updated `gmt` tab completion. | 19 February 2014, 13:18:58 UTC |
| d301024 | APipe Tester | 19 February 2014, 13:18:16 UTC | Updated `genome` tab completion. | 19 February 2014, 13:18:16 UTC |
| e58a1f1 | APipe Tester | 19 February 2014, 13:16:44 UTC | Updated class browser cache. | 19 February 2014, 13:16:44 UTC |
| b2e5ee0 | Malachi Griffith | 19 February 2014, 03:33:02 UTC | clin-seq - add variant filter option to snv-indel-report | 19 February 2014, 03:33:02 UTC |
| a4afa7b | Adam Coffman | 18 February 2014, 22:14:52 UTC | remove useless command | 18 February 2014, 22:14:52 UTC |
| 9ce3064 | Thomas Mooney | 18 February 2014, 21:36:32 UTC | More robustly tolerate special characters in protein names. | 18 February 2014, 21:36:32 UTC |
| c6e3787 | Nathaniel Nutter | 18 February 2014, 21:33:28 UTC | set never rerunnable on build workflow job | 18 February 2014, 21:33:54 UTC |
| fa4f87a | Nathaniel Nutter | 18 February 2014, 21:32:29 UTC | add option for rerunnable and never_rerunnable | 18 February 2014, 21:33:53 UTC |
| f2f2555 | Adam Coffman | 18 February 2014, 21:32:13 UTC | remove clia column now that it is unused | 18 February 2014, 21:32:13 UTC |
| 5c715dd | Adam Coffman | 18 February 2014, 20:30:03 UTC | change user_name to run_as in config profile | 18 February 2014, 20:30:18 UTC |
| 42f85d9 | Jim Weible | 18 February 2014, 20:28:27 UTC | add a backfill option for adding a menu item to an analysis project | 18 February 2014, 20:28:34 UTC |
| 499b1f9 | Dave Larson | 18 February 2014, 19:38:46 UTC | This partially reverts commit 77e03be534ab4b424140bc95879dd9d6d5041b4c. But only the stupid parts that I didn't mean to commit in the first part. Conflicts: lib/perl/Genome/Model/Tools/Analysis/Coverage/AddReadcounts.pm | 18 February 2014, 19:38:46 UTC |
| 33f2e00 | Dave Larson | 18 February 2014, 19:28:03 UTC | actually pass the min_quality_score option to BamReadcount.pm | 18 February 2014, 19:28:03 UTC |
| a56d3a7 | Dave Larson | 18 February 2014, 19:02:28 UTC | remove counting with varscan as an option | 18 February 2014, 19:03:02 UTC |
| e0f27b4 | Dave Larson | 18 February 2014, 18:59:14 UTC | fix regex which could identify the wrong indel allele if there were multiple indels that could match the allele string | 18 February 2014, 19:03:02 UTC |
| 03ef2f4 | Nathaniel Nutter | 18 February 2014, 17:31:10 UTC | add support for launching builds as the run_as user | 18 February 2014, 17:31:10 UTC |
| 8caf4ec | Nathaniel Nutter | 11 February 2014, 21:23:50 UTC | support launching builds as the run_as user | 18 February 2014, 17:31:02 UTC |
| c7e2a8e | Nathaniel Nutter | 13 February 2014, 22:46:58 UTC | remove space between option and value We need to keep the option, e.g. `-g`, connected to the value, e.g. `/apipe-builder`, so that the wrapper that we use to sudo can allow us to securely run commands like: sudo -i bsub [options] annotate-log \ genome model services build run [options] | 18 February 2014, 17:31:01 UTC |
| 0f3549b | Nathaniel Nutter | 12 February 2014, 00:13:36 UTC | _capture already lazy loads IPC::System::Simple | 18 February 2014, 17:31:01 UTC |
| 0ce9c15 | Nathaniel Nutter | 11 February 2014, 21:23:20 UTC | support passing in the bsub executable We need to be able to pass in `sudo bsub` so we can't hard-code the executable as `bsub`. | 18 February 2014, 17:31:00 UTC |
| d983c46 | Nathaniel Nutter | 11 February 2014, 19:40:28 UTC | refactor to use Genome::Sys::LSF::bsub | 18 February 2014, 17:30:59 UTC |
| c3fe6e7 | Nathaniel Nutter | 11 February 2014, 19:39:45 UTC | extract _job_group | 18 February 2014, 17:30:59 UTC |
| aec9d1b | Thomas Mooney | 18 February 2014, 17:09:52 UTC | Renaming pairing to mapping. | 18 February 2014, 17:09:52 UTC |
| 12892a1 | Chris Miller | 18 February 2014, 14:38:36 UTC | updating docs to be more clear on version number | 18 February 2014, 14:38:56 UTC |
| 1adcd5f | APipe Tester | 18 February 2014, 13:16:54 UTC | Updated `genome` tab completion. | 18 February 2014, 13:16:54 UTC |
| db7b25e | APipe Tester | 18 February 2014, 13:15:27 UTC | Updated class browser cache. | 18 February 2014, 13:15:27 UTC |
| 35afe69 | Dave Larson | 18 February 2014, 06:32:28 UTC | Make the following changes to BreakDancer DetectVariants module: * no longer die if fastqs are empty, but instead throw a warning * add test producing no ctx output | 18 February 2014, 06:34:40 UTC |
| beb7406 | Nathaniel Nutter | 18 February 2014, 00:45:40 UTC | tagged deploy | 18 February 2014, 00:45:40 UTC |
| 15c5a3b | Nathaniel Nutter | 17 February 2014, 23:44:47 UTC | drop m_m_id_user_name_build_requested_index | 18 February 2014, 00:42:08 UTC |
| d85056a | Nathaniel Nutter | 17 February 2014, 22:52:10 UTC | drop uniq_m_m_idun index | 18 February 2014, 00:42:07 UTC |
| 8b2a595 | Nathaniel Nutter | 17 February 2014, 22:37:54 UTC | add index to created_by column | 18 February 2014, 00:42:06 UTC |
| 954fcb3 | Nathaniel Nutter | 17 February 2014, 21:53:01 UTC | add index to run_as column | 18 February 2014, 00:42:05 UTC |
| 7e6e826 | Nathaniel Nutter | 18 February 2014, 00:41:53 UTC | remove hostname so password is not required on gms-postgres | 18 February 2014, 00:42:03 UTC |
| 9197564 | Nathaniel Nutter | 17 February 2014, 22:20:48 UTC | begin migration of Model's user_name to created_by and run_as CHANGELOG: Model now has created_by and run_as properties to distinguish the different use cases user_name was being used for. At this stage of the migration user_name is still functional but it is now deprecated and may be removed in the near future. You should review any scripts you have that might be getting Models with the user_name property and update them to use created_by or run_as instead. | 18 February 2014, 00:09:23 UTC |
| 0e02e29 | Nathaniel Nutter | 11 February 2014, 21:32:34 UTC | assume run_as is a better replacement than created_by | 18 February 2014, 00:09:22 UTC |
