| 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 |
| 841614c | APipe Tester | 21 March 2014, 12:18:03 UTC | Updated `gmt` tab completion. | 21 March 2014, 12:18:03 UTC |
| 8859022 | APipe Tester | 21 March 2014, 12:17:24 UTC | Updated `genome` tab completion. | 21 March 2014, 12:17:24 UTC |
| b5de2b7 | APipe Tester | 21 March 2014, 12:15:44 UTC | Updated class browser cache. | 21 March 2014, 12:15:44 UTC |
| 02a4ec6 | apregier | 21 March 2014, 03:16:10 UTC | Merge branch 'updated' into gb_master | 21 March 2014, 03:16:10 UTC |
| f9ca04b | apregier | 21 March 2014, 03:13:11 UTC | Move dependency on annotation build out of diagram object The MutationDiagram object now uses the DomainProvider API to get the domains. The command creates the DomainProvider object and passes it to the MutationDiagram object. This way we can write another command that creates a different type of DomainProvider that doesn't use ImportedAnnotationBuild | 21 March 2014, 03:13:11 UTC |
| 190076f | apregier | 21 March 2014, 02:42:26 UTC | Remove breakpoints | 21 March 2014, 02:42:26 UTC |
| 32880f3 | apregier | 21 March 2014, 02:40:59 UTC | First attempt at separating out domain provider | 21 March 2014, 02:40:59 UTC |
| 542a035 | Thomas Mooney | 20 March 2014, 22:58:31 UTC | Remove old "ListOld" directories of obsolete listers. | 20 March 2014, 22:58:31 UTC |
| 9347b7a | Thomas Mooney | 20 March 2014, 22:56:49 UTC | Remove old `gmt manual-review` suite of tools. These relied on modules removed in an earlier commit: 14077cd58c96d2a72d95f2b0f173fff1e67a00f7. | 20 March 2014, 22:56:49 UTC |
