| a30b76f | APipe Tester | 01 March 2014, 13:17:15 UTC | Updated `gmt` tab completion. | 01 March 2014, 13:17:15 UTC |
| c06b2a3 | APipe Tester | 01 March 2014, 13:16:31 UTC | Updated `genome` tab completion. | 01 March 2014, 13:16:31 UTC |
| 6370cec | APipe Tester | 01 March 2014, 13:14:55 UTC | Updated class browser cache. | 01 March 2014, 13:14:55 UTC |
| 138d971 | Thomas Mooney | 01 March 2014, 02:05:07 UTC | "Update" the model before scheduling a build for it. There are a lot of TODOs surrounding this update method. If it ever is turned into an observer this call may be obsoleted. | 01 March 2014, 02:05:07 UTC |
| 544e2a2 | Thomas Mooney | 01 March 2014, 02:03:16 UTC | Move build queueing out of instrument data assignment method. | 01 March 2014, 02:03:16 UTC |
| 327ed53 | dmorton | 28 February 2014, 20:09:30 UTC | Allow --logs to be separate from --workflow in WorkflowMixin | 28 February 2014, 20:29:19 UTC |
| 0dc4b2d | dmorton | 28 February 2014, 20:08:52 UTC | Add summary_threshold to WorkflowMixin (genome model build view) | 28 February 2014, 20:10:39 UTC |
| 094a18e | Gabriel Sanderson | 27 February 2014, 22:08:21 UTC | Add gmt cross-sample indel command This command uses the Park system under the hood. The tests only test up to that handoff. | 28 February 2014, 19:14:29 UTC |
| 5be0b4f | Gabriel Sanderson | 27 February 2014, 21:55:08 UTC | Capture stderr as well as stdout in Park::Base::_run_generic_process | 28 February 2014, 19:14:28 UTC |
| a3e8ced | Gabriel Sanderson | 27 February 2014, 20:35:59 UTC | rex_process_link/start scripts pass on all arguments | 28 February 2014, 19:14:28 UTC |
| ff94e8c | Gabriel Sanderson | 27 February 2014, 20:28:48 UTC | Add _link_process function | 28 February 2014, 19:14:27 UTC |
| 484c0e4 | Gabriel Sanderson | 27 February 2014, 20:28:21 UTC | Add additional message about viewing progress | 28 February 2014, 19:14:26 UTC |
| f4c753c | APipe Tester | 28 February 2014, 19:01:25 UTC | updated workflow submodule to d7e2b3b | 28 February 2014, 19:01:25 UTC |
| f235290 | APipe Tester | 28 February 2014, 18:48:13 UTC | updated ur submodule to b0d8d06 | 28 February 2014, 18:48:13 UTC |
| 5abef98 | Jim Weible | 28 February 2014, 15:38:29 UTC | Revert "create a dummy expected output file as standard for cnv detectors" This reverts commit 5041fff7478e7dd4211d9bde52898c2bbf70262b. | 28 February 2014, 15:38:29 UTC |
| 6055056 | Jim Weible | 28 February 2014, 15:38:27 UTC | Revert "fix up some copy pasta error messages" This reverts commit 2c1accd40beae7891fab44091ad819e16149f18d. | 28 February 2014, 15:38:27 UTC |
| 3cd0df3 | Jim Weible | 28 February 2014, 15:38:24 UTC | Revert "write our temp files to a reasonable place" This reverts commit e30cd6f01e8a48a1bb624f6a4835b23ba410b148. | 28 February 2014, 15:38:24 UTC |
| e06fc4e | Jim Weible | 28 February 2014, 15:38:10 UTC | Revert "do the right thing with the copycat annotation" This reverts commit 65dbe38a62362bdea69937309a585340ae60fa5f. | 28 February 2014, 15:38:10 UTC |
| 5041fff | Jim Weible | 26 February 2014, 19:13:36 UTC | create a dummy expected output file as standard for cnv detectors | 28 February 2014, 14:22:05 UTC |
| 2c1accd | Jim Weible | 25 February 2014, 16:38:26 UTC | fix up some copy pasta error messages | 28 February 2014, 14:22:04 UTC |
| e30cd6f | Jim Weible | 18 February 2014, 14:05:46 UTC | write our temp files to a reasonable place | 28 February 2014, 14:22:03 UTC |
| 65dbe38 | Jim Weible | 18 February 2014, 14:05:23 UTC | do the right thing with the copycat annotation | 28 February 2014, 14:22:02 UTC |
| eb1e406 | APipe Tester | 28 February 2014, 13:16:57 UTC | Updated `genome` tab completion. | 28 February 2014, 13:16:57 UTC |
| afd9af3 | apregier | 27 February 2014, 23:18:02 UTC | Merge branch 'updated' into gb_master | 27 February 2014, 23:18:02 UTC |
| 7e9968e | apregier | 27 February 2014, 23:16:29 UTC | New import sources | 27 February 2014, 23:17:01 UTC |
| 78e86d2 | Nathaniel Nutter | 27 February 2014, 20:29:18 UTC | Merge branch 'pinch' into AR-597 * pinch: inject queue into rusage pull AlignmentResult's LSF queue out of rusage use event's lsf_queue add lsf_queue to PrepareReferenceSequenceIndex event pull queue param out of bsub_rusage (for events) add lsf_queue to AlignReads should_use_alignment_pd if model's run_as =~ /^apipe/ add lsf_queue got Genome::Model::Event | 27 February 2014, 20:29:35 UTC |
| d555c3b | Nathaniel Nutter | 27 February 2014, 20:26:21 UTC | inject queue into rusage To decide whether to use the production alignment queue we need knowledge of the model so we have to inject the queue into the alignment result. | 27 February 2014, 20:26:21 UTC |
| 1bc83fd | Thomas Mooney | 27 February 2014, 19:52:19 UTC | Add back missing letter. | 27 February 2014, 19:52:19 UTC |
| ca6f9d0 | Nathaniel Nutter | 26 February 2014, 21:43:13 UTC | pull AlignmentResult's LSF queue out of rusage | 27 February 2014, 19:35:03 UTC |
| a1f668d | Nathaniel Nutter | 27 February 2014, 19:17:30 UTC | define status for buildless, unneeded, unrequested models This will probably mostly apply to lane QC models which get created but aren't needed until the genotype microarray data comes through. | 27 February 2014, 19:32:38 UTC |
| d178570 | Thomas Mooney | 27 February 2014, 19:23:51 UTC | Delay needing a build until genotype build is completed. This will greatly reduce our quantity of Unstartable builds when the genotype data hasn't been processed yet. | 27 February 2014, 19:23:51 UTC |
| 025834d | Malachi Griffith | 27 February 2014, 17:48:06 UTC | further patches to work with old/new versions of ggplot2 | 27 February 2014, 17:48:06 UTC |
| bb41c8d | APipe Tester | 27 February 2014, 13:16:17 UTC | Updated `genome` tab completion. | 27 February 2014, 13:16:17 UTC |
| 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 |
| c4e2c6f | Nathaniel Nutter | 26 February 2014, 21:39:18 UTC | use event's lsf_queue | 26 February 2014, 21:43:37 UTC |
| 4436043 | Nathaniel Nutter | 26 February 2014, 20:26:57 UTC | add lsf_queue to PrepareReferenceSequenceIndex event The boundary between events and software results is not clear so this mostly just makes more explicit what I believe was implicit. | 26 February 2014, 21:43:36 UTC |
| 1cc18b6 | Nathaniel Nutter | 26 February 2014, 20:25:50 UTC | pull queue param out of bsub_rusage (for events) | 26 February 2014, 21:43:35 UTC |
| f1d85ff | Nathaniel Nutter | 26 February 2014, 20:25:08 UTC | add lsf_queue to AlignReads | 26 February 2014, 21:43:34 UTC |
| 2a1504b | Nathaniel Nutter | 26 February 2014, 20:24:41 UTC | should_use_alignment_pd if model's run_as =~ /^apipe/ | 26 February 2014, 21:43:33 UTC |
| 92a353f | Nathaniel Nutter | 26 February 2014, 20:22:53 UTC | add lsf_queue got Genome::Model::Event | 26 February 2014, 21:43:32 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 |
