| f52db3f | Thomas Mooney | 01 April 2014, 17:28:03 UTC | Remove old `gmt vcf somatic-variation-to-vcf`. It refers to a non-existent snp130.txt and is mostly a wrapper for other gmt commands. | 01 April 2014, 17:28:03 UTC |
| 27d6ef3 | Eddie Belter | 31 March 2014, 22:28:20 UTC | Remove gmt lims apipe-bridge commands | 01 April 2014, 15:57:30 UTC |
| 87229b6 | Eddie Belter | 31 March 2014, 20:34:48 UTC | Move sanger dump file system to site tgi sync sanger class | 01 April 2014, 15:57:30 UTC |
| 7fe506a | APipe Tester | 01 April 2014, 12:18:33 UTC | Updated `gmt` tab completion. | 01 April 2014, 12:18:33 UTC |
| 530f956 | APipe Tester | 01 April 2014, 12:17:52 UTC | Updated `genome` tab completion. | 01 April 2014, 12:17:52 UTC |
| 2fc8023 | APipe Tester | 01 April 2014, 12:16:24 UTC | Updated class browser cache. | 01 April 2014, 12:16:24 UTC |
| 29c7f46 | Thomas Mooney | 31 March 2014, 22:05:45 UTC | Use a pipe so that errant queries don't cause unexpected behaviour. | 31 March 2014, 22:05:45 UTC |
| b353608 | Thomas Mooney | 31 March 2014, 21:31:51 UTC | A command to grep through configurations. | 31 March 2014, 21:31:51 UTC |
| cdc78c9 | Thomas Mooney | 31 March 2014, 20:51:04 UTC | Sort by name by default in the menu item lister. | 31 March 2014, 20:51:04 UTC |
| fd3d427 | Eddie Belter | 31 March 2014, 20:34:48 UTC | Move sanger dump file system to site tgi sync sanger class | 31 March 2014, 20:35:01 UTC |
| 4f21f51 | Adam Coffman | 31 March 2014, 19:51:43 UTC | add empty command tree module | 31 March 2014, 19:51:43 UTC |
| 474e781 | Adam Coffman | 31 March 2014, 19:45:38 UTC | fix typos | 31 March 2014, 19:45:38 UTC |
| 69285dd | APipe Tester | 31 March 2014, 18:01:29 UTC | updated workflow submodule to 1108b72 | 31 March 2014, 18:01:29 UTC |
| 6c3e540 | Eddie Belter | 31 March 2014, 17:55:39 UTC | Genotype Microarray: remove use of "//" b/c LIMS is still on perl 5.8.7 | 31 March 2014, 17:55:48 UTC |
| d4018e4 | APipe Tester | 31 March 2014, 17:40:54 UTC | updated ur submodule to 38a0c0f | 31 March 2014, 17:40:54 UTC |
| c1853a9 | Thomas Mooney | 31 March 2014, 15:06:37 UTC | Remove old `gmt analysis 454 run-refcov` tool. This tool just generated a script that ran two other GMTs in sequence. The pipeline has long handled this case. | 31 March 2014, 15:06:37 UTC |
| a436ba0 | Thomas Mooney | 31 March 2014, 14:54:24 UTC | Remove old `gmt varscan compile-readcounts` with hardcoded refseq. | 31 March 2014, 14:54:24 UTC |
| 7e02286 | Thomas Mooney | 31 March 2014, 14:47:49 UTC | Remove unused model reflection subroutines. | 31 March 2014, 14:47:49 UTC |
| 4a33545 | Thomas Mooney | 31 March 2014, 14:42:40 UTC | Remove unused subs from "legacy" config. | 31 March 2014, 14:42:40 UTC |
| f424ae3 | Thomas Mooney | 31 March 2014, 14:19:42 UTC | Remove another reference to InstrumentDataStatus in the whitelist. | 31 March 2014, 14:19:42 UTC |
| 6c17b7f | Thomas Mooney | 31 March 2014, 14:17:49 UTC | Remove obsolete `gmt lims apipe-bridge instrument-data-status`. It relies on a LIMS PSE that is no longer created. | 31 March 2014, 14:17:49 UTC |
| e22787c | Thomas Mooney | 31 March 2014, 14:12:55 UTC | Remove old `gmt snp get-dbsnps` tool that relies on LIMS and build36. | 31 March 2014, 14:12:55 UTC |
| 2d4728a | Ian Ferguson | 28 March 2014, 19:22:42 UTC | Add is_output => 1 to somatic_variation_build in SomVar CreateReport | 28 March 2014, 19:23:51 UTC |
| 1aa5993 | APipe Tester | 28 March 2014, 19:21:38 UTC | updated workflow submodule to 69cd752 | 28 March 2014, 19:21:38 UTC |
| bf47213 | APipe Tester | 28 March 2014, 19:09:00 UTC | updated ur submodule to e30c533 | 28 March 2014, 19:09:00 UTC |
| d2569a3 | APipe Tester | 28 March 2014, 19:00:20 UTC | updated workflow submodule to 04245f6 | 28 March 2014, 19:00:20 UTC |
| a745bb3 | Nathaniel Nutter | 28 March 2014, 18:59:20 UTC | fix submodule pointing at personal fork | 28 March 2014, 18:59:38 UTC |
| b5c7422 | APipe Tester | 28 March 2014, 18:41:16 UTC | updated ur submodule to a14a31d | 28 March 2014, 18:41:16 UTC |
| af22e29 | APipe Tester | 28 March 2014, 17:41:04 UTC | updated ur submodule to fdb7a53 | 28 March 2014, 17:41:04 UTC |
| 2ba9894 | APipe Tester | 28 March 2014, 12:17:50 UTC | Updated `genome` tab completion. | 28 March 2014, 12:17:50 UTC |
| 6c601d3 | APipe Tester | 28 March 2014, 12:15:58 UTC | Updated class browser cache. | 28 March 2014, 12:15:58 UTC |
| 8577330 | Chris Miller | 27 March 2014, 22:11:39 UTC | setting dumpBins option to true by default | 27 March 2014, 22:11:43 UTC |
| 57c3df5 | Nathaniel Nutter | 27 March 2014, 21:13:35 UTC | fix odd number of elements in hash assignment | 27 March 2014, 21:13:35 UTC |
| 07697a4 | Nathaniel Nutter | 27 March 2014, 20:38:08 UTC | update workflow submodule URL | 27 March 2014, 20:38:08 UTC |
| 93bb906 | Chris Miller | 27 March 2014, 19:55:36 UTC | updating to reflect improved samtools file format detection present in copyCat 1.6.5 | 27 March 2014, 19:55:36 UTC |
| 9d2a9dc | Thomas Mooney | 27 March 2014, 14:07:11 UTC | Remove obsolete Oracle-dependent summary-of-builds report. | 27 March 2014, 14:07:11 UTC |
| bbcc4b4 | Avinash Ramu | 27 March 2014, 13:25:03 UTC | update blessed build to one run by jenkins | 27 March 2014, 13:25:03 UTC |
| 04d4e85 | APipe Tester | 27 March 2014, 12:18:21 UTC | Updated `gmt` tab completion. | 27 March 2014, 12:18:21 UTC |
| 620fbd1 | APipe Tester | 27 March 2014, 12:17:36 UTC | Updated `genome` tab completion. | 27 March 2014, 12:17:36 UTC |
| 3f8478d | Avinash Ramu | 27 March 2014, 05:18:08 UTC | update clinseq blessed build. | 27 March 2014, 05:18:08 UTC |
| aaeb673 | Avinash Ramu | 27 March 2014, 04:40:43 UTC | add SVGs to the list of ignored files | 27 March 2014, 04:40:43 UTC |
| 89b4aa8 | Nathaniel Nutter | 26 March 2014, 23:39:05 UTC | add instrumentation to Genome::Sys::Lock * add instrumentation when both locks acquired * use Genome::Logger instead of error_message * add instrumentation for inconsistent locking * whitespace * only error if Nessy and File locks are inconsistent * make conditional order match message order * use a message template to make it easier to add future conditionals * return early to make it easier to add additional conditions later | 26 March 2014, 23:40:28 UTC |
| 0d1277a | Nathaniel Nutter | 25 March 2014, 22:32:00 UTC | add instrumentation when both locks acquired | 26 March 2014, 23:40:27 UTC |
| 1289c33 | Nathaniel Nutter | 26 March 2014, 23:29:37 UTC | use Genome::Logger instead of error_message We were using error_message so they would show up in Logstash but we don't really consider these errors yet and we don't want users to see them. Genome::Logger is setup so debug messages go to Syslog (and therefore Logstash) so use that instead. | 26 March 2014, 23:40:26 UTC |
| 6d3b397 | Nathaniel Nutter | 25 March 2014, 22:31:30 UTC | add instrumentation for inconsistent locking | 26 March 2014, 23:40:25 UTC |
| 7d0a107 | Nathaniel Nutter | 25 March 2014, 22:27:38 UTC | whitespace | 26 March 2014, 23:40:24 UTC |
| 0b1f9f8 | Nathaniel Nutter | 25 March 2014, 22:25:15 UTC | only error if Nessy and File locks are inconsistent | 26 March 2014, 23:40:22 UTC |
| 3541f85 | Nathaniel Nutter | 25 March 2014, 22:24:09 UTC | make conditional order match message order | 26 March 2014, 23:40:21 UTC |
| 434c133 | Nathaniel Nutter | 25 March 2014, 22:23:06 UTC | use a message template to make it easier to add future conditionals | 26 March 2014, 23:40:20 UTC |
| 6b133c9 | Nathaniel Nutter | 25 March 2014, 22:18:59 UTC | return early to make it easier to add additional conditions later | 26 March 2014, 23:40:19 UTC |
| 0bf37bf | Nathaniel Nutter | 26 March 2014, 23:37:48 UTC | fix memoization sensitivity to list/scalar context * tell memoize to reuse scalar cache in list context * add failing test | 26 March 2014, 23:40:17 UTC |
| 56bad10 | Nathaniel Nutter | 26 March 2014, 23:24:23 UTC | tell memoize to reuse scalar cache in list context | 26 March 2014, 23:40:16 UTC |
| 9790f22 | Nathaniel Nutter | 26 March 2014, 23:23:34 UTC | add failing test This test shows that the memoization was independent for list and scalar contexts. | 26 March 2014, 23:40:15 UTC |
| a75969f | Nathaniel Nutter | 26 March 2014, 23:07:03 UTC | add *f methods analogous to printf | 26 March 2014, 23:40:14 UTC |
| 67003dd | Nathaniel Nutter | 26 March 2014, 23:05:34 UTC | make Genome::Logger more like a singleton | 26 March 2014, 23:40:12 UTC |
| 8b023a8 | Feiyu Du | 26 March 2014, 22:04:37 UTC | make DV2 samtools mpileup handle empty snvs/indels output | 26 March 2014, 22:04:37 UTC |
| e621fc4 | APipe Tester | 26 March 2014, 21:05:19 UTC | updated workflow submodule to 2b0880b | 26 March 2014, 21:05:19 UTC |
| 558464e | APipe Tester | 26 March 2014, 20:53:06 UTC | updated ur submodule to cdeebc5 | 26 March 2014, 20:53:06 UTC |
| aa73366 | Chris Miller | 26 March 2014, 19:07:52 UTC | passing purity as number instead of string | 26 March 2014, 19:07:52 UTC |
| f743f37 | Chris Miller | 26 March 2014, 18:45:43 UTC | exposing purity option in wrapper | 26 March 2014, 18:45:43 UTC |
| 0d871a1 | APipe Tester | 26 March 2014, 13:57:05 UTC | Updated `gmt` tab completion. | 26 March 2014, 13:57:05 UTC |
| 5279d7e | APipe Tester | 26 March 2014, 13:56:21 UTC | Updated `genome` tab completion. | 26 March 2014, 13:56:21 UTC |
| cb901a1 | APipe Tester | 26 March 2014, 13:54:08 UTC | Updated class browser cache. | 26 March 2014, 13:54:08 UTC |
| 727e99f | Nathaniel Nutter | 25 March 2014, 20:12:55 UTC | new usage logging * remove old command logging * remove command log reader * no longer log commands to log file * add usage log | 25 March 2014, 20:12:55 UTC |
| f3e543f | Nathaniel Nutter | 20 March 2014, 19:50:55 UTC | remove old command logging | 25 March 2014, 20:10:32 UTC |
| 4d6c9b5 | Nathaniel Nutter | 20 March 2014, 19:50:34 UTC | remove command log reader | 25 March 2014, 20:10:32 UTC |
| 80add4c | Nathaniel Nutter | 20 March 2014, 19:50:16 UTC | no longer log commands to log file | 25 March 2014, 20:10:31 UTC |
| dc06820 | Nathaniel Nutter | 20 March 2014, 19:48:10 UTC | add usage log | 25 March 2014, 20:10:30 UTC |
| a135962 | APipe Tester | 25 March 2014, 18:12:30 UTC | updated workflow submodule to dfccc76 | 25 March 2014, 18:12:30 UTC |
| 861de89 | APipe Tester | 25 March 2014, 18:01:48 UTC | updated workflow submodule to 57324f1 | 25 March 2014, 18:01:48 UTC |
| 597cd25 | APipe Tester | 25 March 2014, 17:56:44 UTC | updated ur submodule to 897ebcb | 25 March 2014, 17:56:44 UTC |
| 31c8afe | APipe Tester | 25 March 2014, 17:49:32 UTC | updated ur submodule to c85a88b | 25 March 2014, 17:49:32 UTC |
| 0617bd6 | Jim Weible | 25 March 2014, 14:01:21 UTC | support "no-opt" config files in AP Config (AUE-200) | 25 March 2014, 14:01:42 UTC |
| 6d14d2e | APipe Tester | 25 March 2014, 12:18:06 UTC | Updated `gmt` tab completion. | 25 March 2014, 12:18:06 UTC |
| 6538a57 | APipe Tester | 25 March 2014, 12:17:26 UTC | Updated `genome` tab completion. | 25 March 2014, 12:17:26 UTC |
| e6a5b63 | APipe Tester | 25 March 2014, 12:15:58 UTC | Updated class browser cache. | 25 March 2014, 12:15:58 UTC |
| b0880a9 | Thomas Mooney | 24 March 2014, 22:27:19 UTC | Better sorting of which workflow step to try first... Prefer steps that have an end time--this means they "Failed" instead of being stuck in "Running". In the case of a tie, prefer the child since that's usually more informative than the parent. | 24 March 2014, 22:27:19 UTC |
| 386989f | Thomas Mooney | 24 March 2014, 22:05:50 UTC | Move this include to the file in which it is used. | 24 March 2014, 22:05:50 UTC |
| d717456 | Thomas Mooney | 24 March 2014, 22:02:10 UTC | Undo the reverse... the original sort order has some merit. | 24 March 2014, 22:02:10 UTC |
| e6f2cf7 | Avinash Ramu | 24 March 2014, 20:05:49 UTC | skip test until debian package is available | 24 March 2014, 20:05:49 UTC |
| 82f850e | Thomas Mooney | 24 March 2014, 19:21:41 UTC | Fallback on finding LSF errors if no ERROR in logs. Reverse the search order in order to hit an "innermost" step when looking for failures--this is usually the most informative error step. | 24 March 2014, 19:21:41 UTC |
| c88b116 | Avinash Ramu | 24 March 2014, 18:52:34 UTC | add cnmops gmt | 24 March 2014, 18:52:45 UTC |
| 8aa12e9 | Thomas Mooney | 24 March 2014, 18:39:58 UTC | Test that the objects we created are valid. | 24 March 2014, 18:39:58 UTC |
| 14514c7 | Adam Coffman | 24 March 2014, 18:29:32 UTC | add importer for setting up somval models with apconfig | 24 March 2014, 18:29:32 UTC |
| 5464ae0 | apregier | 24 March 2014, 18:28:51 UTC | Merge branch 'updated2' into gb_master | 24 March 2014, 18:28:51 UTC |
| 78baa15 | apregier | 24 March 2014, 18:08:08 UTC | custom_domains is optional | 24 March 2014, 18:08:08 UTC |
| 487fa6c | Thomas Mooney | 24 March 2014, 16:13:09 UTC | Add a default base URL based on the environment. | 24 March 2014, 16:13:09 UTC |
| 995594c | Jim Weible | 24 March 2014, 15:21:17 UTC | Add a status to Genome::Config::Profile::Item for great justice | 24 March 2014, 15:22:13 UTC |
| 6d14fc5 | Thomas Mooney | 24 March 2014, 13:17:18 UTC | Move alignment_results_from_analysis_projects to base class. G:I:Imported steals a bunch of subs from G:I:Solexa. Rather than add another one, move this up since it could be useful for any instrument data that is aligned. | 24 March 2014, 13:17:18 UTC |
| a71d669 | Eddie Belter | 21 March 2014, 17:33:25 UTC | GM: read from inst data annotated was not filtering out genotpyes not in dbsnp build | 21 March 2014, 17:33:25 UTC |
| 7483bc8 | Eddie Belter | 21 March 2014, 17:18:53 UTC | GM: rename readers; merge tests | 21 March 2014, 17:20:31 UTC |
| 7147395 | Eddie Belter | 20 March 2014, 20:40:07 UTC | GM: add original file reader; add from base class | 21 March 2014, 17:20:29 UTC |
| 1197e55 | Eddie Belter | 20 March 2014, 19:58:18 UTC | GM: rename read unannotated csv reader | 21 March 2014, 17:20:29 UTC |
| cbb56e3 | Eddie Belter | 20 March 2014, 19:54:57 UTC | GM: rm unsed code from create gold snp file from genotypes | 21 March 2014, 17:20:28 UTC |
| abe54dc | Eddie Belter | 20 March 2014, 19:54:19 UTC | GM: speed up of read unannotated csv | 21 March 2014, 17:20:27 UTC |
| 1ae2540 | Eddie Belter | 20 March 2014, 19:53:28 UTC | GM: do not use UR in from inst data reader | 21 March 2014, 17:19:25 UTC |
| 6f2dc7c | apregier | 21 March 2014, 17:11:43 UTC | Merge branch 'updated' into gb_master | 21 March 2014, 17:11:43 UTC |
| 18a47d0 | apregier | 21 March 2014, 17:06:46 UTC | Use MutationProviders rather than parsing inside MutationDiagram | 21 March 2014, 17:08:00 UTC |
| 7e6cf37 | apregier | 21 March 2014, 17:06:05 UTC | Pull out annotation file parsing functionality to a MutationProvider class | 21 March 2014, 17:07:59 UTC |
| ebd02fc | Avinash Ramu | 21 March 2014, 16:45:59 UTC | remove inclusion of class | 21 March 2014, 16:46:25 UTC |
