| 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 |
| bd3ff13 | Thomas Mooney | 20 March 2014, 22:21:57 UTC | Remove redundant `genome model services summarize-outstanding-builds`. See `genome model admin model-summary` instead. | 20 March 2014, 22:21:57 UTC |
| 84f2d2d | apregier | 20 March 2014, 22:17:40 UTC | Merge branch 'cover' into gb_master | 20 March 2014, 22:17:40 UTC |
| 6404423 | apregier | 20 March 2014, 21:12:10 UTC | Cache number of samples to speed up | 20 March 2014, 22:17:15 UTC |
| ce43cb1 | Thomas Mooney | 20 March 2014, 22:16:41 UTC | Remove execute bit from G/M/Command/Status.pm | 20 March 2014, 22:16:41 UTC |
| 999e2eb | Thomas Mooney | 20 March 2014, 22:05:19 UTC | Remove obsolete `gmt bacterial-contamination-screen`. The script this produces won't even run correctly any more. | 20 March 2014, 22:07:00 UTC |
| 6f02aa1 | Veena Bhonagiri | 20 March 2014, 22:00:30 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 20 March 2014, 22:00:30 UTC |
| 818fcbf | Thomas Mooney | 20 March 2014, 21:58:45 UTC | Remove root of empty tree `gmt blast`. | 20 March 2014, 21:58:45 UTC |
| 3d5a565 | Veena Bhonagiri | 20 March 2014, 21:58:43 UTC | Added Ostertagi models Merge branch 'master' of ssh://git/srv/git/genome | 20 March 2014, 21:58:43 UTC |
| 3934517 | Veena Bhonagiri | 20 March 2014, 21:57:13 UTC | Added snap models for Ostertagi | 20 March 2014, 21:57:13 UTC |
| 6a1e500 | Thomas Mooney | 20 March 2014, 21:55:27 UTC | Remove redundant `gmt list-reference-sequences`. Use `genome model reference-sequence list-builds` instead. | 20 March 2014, 21:55:27 UTC |
| c661016 | Thomas Mooney | 20 March 2014, 21:52:22 UTC | Remove root of empty tree `gmt sample`. | 20 March 2014, 21:52:22 UTC |
| b0a54e3 | Thomas Mooney | 20 March 2014, 21:50:21 UTC | Remove empty root of tree `gmt solexa`. | 20 March 2014, 21:50:21 UTC |
| 09ddc73 | Thomas Mooney | 20 March 2014, 21:47:12 UTC | Remove obsolete `gmt library check-libs` command. | 20 March 2014, 21:47:12 UTC |
| 84f7906 | Thomas Mooney | 20 March 2014, 21:37:26 UTC | Remove execute permissions on .pm files. | 20 March 2014, 21:37:26 UTC |
| d286993 | Thomas Mooney | 20 March 2014, 20:57:10 UTC | Don't redeclare the variable. | 20 March 2014, 20:57:24 UTC |
| 1e582b5 | apregier | 20 March 2014, 20:16:14 UTC | Merge branch 'cover' into gb_master | 20 March 2014, 20:16:14 UTC |
| b3776f0 | apregier | 19 March 2014, 22:05:40 UTC | Stop using SVR because it is slow | 20 March 2014, 20:15:17 UTC |
| 80c6b3f | apregier | 19 March 2014, 21:23:22 UTC | Only compile regexes once | 20 March 2014, 20:15:16 UTC |
| 5aafbdb | apregier | 19 March 2014, 21:06:44 UTC | Use compare_ok | 20 March 2014, 20:15:16 UTC |
| ff5b3ae | Thomas Mooney | 20 March 2014, 20:07:19 UTC | Prefer results generated using Analysis Projects. | 20 March 2014, 20:07:19 UTC |
| 01d051c | Avinash Ramu | 20 March 2014, 18:38:24 UTC | update clinseq blessed build - LIMS report | 20 March 2014, 18:38:24 UTC |
| 1b1fea4 | apregier | 20 March 2014, 16:46:47 UTC | Merge branch 'my_annotation' into gb_master | 20 March 2014, 16:46:47 UTC |
| 6c318ae | apregier | 18 March 2014, 21:02:02 UTC | Stop trying to guess paired status since the importer sets it appropriately now | 20 March 2014, 16:45:43 UTC |
| 1bc1810 | Chris Miller | 20 March 2014, 16:04:25 UTC | removing old half-baked attempt at a Processing profile to text parser | 20 March 2014, 16:04:25 UTC |
| c787f2a | Kyung Kim | 20 March 2014, 16:01:20 UTC | test for gmt sx dedup by-sequence tool | 20 March 2014, 16:01:20 UTC |
| f7dc68d | Kyung Kim | 20 March 2014, 15:44:52 UTC | Updated phdball file CHEM for unknown types to solexa | 20 March 2014, 15:44:52 UTC |
