| 1e7a3a4 | apregier | 27 March 2014, 18:48:31 UTC | Move genotype vcf result creation so it doesn't happen during shortcut | 02 April 2014, 14:55:01 UTC |
| 91ccbee | apregier | 27 March 2014, 16:47:57 UTC | Add test for genotype vcf result | 02 April 2014, 14:55:00 UTC |
| 6d62703 | apregier | 27 March 2014, 16:47:27 UTC | Fix filter config | 02 April 2014, 14:54:59 UTC |
| 269c8b3 | apregier | 27 March 2014, 16:46:48 UTC | Remove unnecessary line | 02 April 2014, 14:54:59 UTC |
| fd0b473 | apregier | 27 March 2014, 16:46:28 UTC | Fix filter | 02 April 2014, 14:54:58 UTC |
| 14f342d | apregier | 27 March 2014, 16:05:36 UTC | Add a test for the build step | 02 April 2014, 14:54:57 UTC |
| f774129 | apregier | 27 March 2014, 16:05:18 UTC | Fix parameters | 02 April 2014, 14:54:57 UTC |
| 7e3774d | apregier | 27 March 2014, 16:04:40 UTC | Fix error message | 02 April 2014, 14:54:56 UTC |
| eb716d2 | apregier | 27 March 2014, 16:04:06 UTC | Create directory for links if it doesn't exist already | 02 April 2014, 14:54:56 UTC |
| bfba6cc | apregier | 27 March 2014, 16:03:37 UTC | Add verify_bam_id_version to the processing profile | 02 April 2014, 14:54:55 UTC |
| 6b5fb2b | apregier | 27 March 2014, 16:02:53 UTC | Make GenotypeVcf a stageable result | 02 April 2014, 14:54:54 UTC |
| 93fd5d6 | apregier | 26 March 2014, 22:33:30 UTC | reference instead of reference_sequence_build | 02 April 2014, 14:54:54 UTC |
| 85c9316 | apregier | 26 March 2014, 22:32:49 UTC | Don't check region_of_interest on the base class | 02 April 2014, 14:54:53 UTC |
| 5bec724 | apregier | 26 March 2014, 22:00:42 UTC | VerifyBam command is WithMode | 02 April 2014, 14:54:53 UTC |
| d2f2143 | apregier | 26 March 2014, 20:34:04 UTC | Update test data | 02 April 2014, 14:54:52 UTC |
| 28db1ab | apregier | 26 March 2014, 20:33:44 UTC | Additional model is created in test factory | 02 April 2014, 14:54:51 UTC |
| ae8ffde | apregier | 26 March 2014, 20:22:00 UTC | Ignore all diffs for files ending with *.stderr | 02 April 2014, 14:54:51 UTC |
| e927903 | apregier | 26 March 2014, 19:13:06 UTC | Update define docs | 02 April 2014, 14:54:50 UTC |
| a7a4c59 | apregier | 26 March 2014, 16:34:58 UTC | Run verifyBam in tumor and normal modes | 02 April 2014, 14:54:49 UTC |
| 200196f | apregier | 26 March 2014, 16:07:40 UTC | Extract parent class SomaticValidation::Command::WithMode allows commands to run in tumor or normal mode. | 02 April 2014, 14:54:49 UTC |
| 5043b51 | apregier | 26 March 2014, 15:21:29 UTC | Check to see whether genotype data is available | 02 April 2014, 14:54:48 UTC |
| 1fbc546 | apregier | 26 March 2014, 15:07:50 UTC | Add verify-bam to somatic validation workflow | 02 April 2014, 14:54:48 UTC |
| 1bacfba | apregier | 26 March 2014, 14:53:35 UTC | Add a build step for verifyBamId | 02 April 2014, 14:54:47 UTC |
| 5c89e5e | apregier | 26 March 2014, 14:53:06 UTC | Make a software result for the vcf version of the genotype file | 02 April 2014, 14:54:46 UTC |
| b4c0729 | apregier | 24 March 2014, 21:38:51 UTC | Make verifyBamIdResult better -Takes an aligned bam input instead of instrument data -Get the allosomes from the reference sequence -Use a method that will always get a vcf file so it works for older builds as well | 02 April 2014, 14:54:46 UTC |
| 0eb0fbf | apregier | 24 March 2014, 21:30:07 UTC | Reference build has allosome_names | 02 April 2014, 14:54:45 UTC |
| 893cb56 | apregier | 24 March 2014, 21:29:43 UTC | Add a by-chromosome filter | 02 April 2014, 14:54:44 UTC |
| f15a76a | apregier | 21 March 2014, 22:09:38 UTC | Add a test factory for merged alignment results | 02 April 2014, 14:54:43 UTC |
| 9efbb2a | apregier | 21 March 2014, 22:09:00 UTC | Put a reference sequence on the imported variation list | 02 April 2014, 14:54:42 UTC |
| 0d26b85 | Nathaniel Nutter | 02 April 2014, 13:57:28 UTC | add some dv2 instrumentation | 02 April 2014, 13:57:43 UTC |
| 6b46308 | Thomas Mooney | 02 April 2014, 13:54:22 UTC | Remove commented-out references to no-longer-extant datasets. | 02 April 2014, 13:54:22 UTC |
| bea07ab | Thomas Mooney | 02 April 2014, 13:49:59 UTC | Remove old `gmt analysis detect-recurrence`. | 02 April 2014, 13:49:59 UTC |
| 429f9cd | Thomas Mooney | 02 April 2014, 13:45:30 UTC | Remove more references to "/gscuser/". | 02 April 2014, 13:45:30 UTC |
| 9285ef1 | Thomas Mooney | 02 April 2014, 13:35:08 UTC | Remove old `gmt copy-number graph` and `gmt copy-number u-test`. These modules are a mess but are disused, so just remove them. | 02 April 2014, 13:35:08 UTC |
| 032d172 | Thomas Mooney | 02 April 2014, 13:29:03 UTC | Remove reference to /gscuser/ | 02 April 2014, 13:29:03 UTC |
| cfe1363 | Thomas Mooney | 02 April 2014, 13:26:53 UTC | Remove disused `gmt germline finish-music-clinical-correlation`. | 02 April 2014, 13:26:53 UTC |
| 1c5938a | Thomas Mooney | 02 April 2014, 13:26:24 UTC | Remove commented-out debugging code. | 02 April 2014, 13:26:24 UTC |
| d6c5a5c | Thomas Mooney | 02 April 2014, 13:22:03 UTC | whitespace | 02 April 2014, 13:22:03 UTC |
| 4574e63 | Thomas Mooney | 02 April 2014, 13:20:45 UTC | Remove duplicated comment with command-line. (Cleaning up references to home directories.) | 02 April 2014, 13:20:45 UTC |
| 9e8253e | APipe Tester | 02 April 2014, 12:18:39 UTC | Updated `gmt` tab completion. | 02 April 2014, 12:18:39 UTC |
| a24d156 | APipe Tester | 02 April 2014, 12:17:58 UTC | Updated `genome` tab completion. | 02 April 2014, 12:17:58 UTC |
| a38f9f0 | APipe Tester | 02 April 2014, 12:16:32 UTC | Updated class browser cache. | 02 April 2014, 12:16:32 UTC |
| c9aac88 | Nathaniel Nutter | 01 April 2014, 23:24:17 UTC | looks like a new input named allosome_names was added to builds | 01 April 2014, 23:24:17 UTC |
| f9881e4 | Nathaniel Nutter | 01 April 2014, 23:10:34 UTC | only check allocation owner_class_name if it got an allocation This could maybe do more in the case that the allocation doesn't exist but for now at least keep it from crashing. | 01 April 2014, 23:11:34 UTC |
| 350f225 | Nathaniel Nutter | 01 April 2014, 22:38:48 UTC | add more instrumentation to file-based lock/unlock | 01 April 2014, 22:38:48 UTC |
| fbda7db | Nathaniel Nutter | 01 April 2014, 22:35:32 UTC | add instrumentation to file-based lock/unlock | 01 April 2014, 22:35:41 UTC |
| 356748d | Thomas Mooney | 01 April 2014, 21:44:59 UTC | Update tophat2 to set itself in /etc/alternatives | 01 April 2014, 21:44:59 UTC |
| 5c8e6a9 | Thomas Mooney | 01 April 2014, 17:57:46 UTC | Remove examples that point to a home directory. | 01 April 2014, 21:29:57 UTC |
| 4dd942f | Thomas Mooney | 01 April 2014, 17:55:20 UTC | Remove half-baked `gmt simulation generate-reads`. | 01 April 2014, 21:29:57 UTC |
| a1ffede | Adam Coffman | 01 April 2014, 21:04:30 UTC | get rid of now unused properties | 01 April 2014, 21:04:30 UTC |
| 6a4e3fd | Adam Coffman | 01 April 2014, 20:46:09 UTC | Temporarily add "add_*" methods for indirect input accessors We will be modifying UR to handle this case correctly, but this is a stopgap until then | 01 April 2014, 20:46:09 UTC |
| c597bde | Adam Coffman | 01 April 2014, 20:45:26 UTC | Add "id" properties for object-based inputs for use in config | 01 April 2014, 20:45:26 UTC |
| 6165892 | Adam Coffman | 01 April 2014, 20:44:56 UTC | set the labels to the object properties rather than the id ones | 01 April 2014, 20:44:56 UTC |
| 069091b | Adam Coffman | 01 April 2014, 20:43:18 UTC | dont pull back instrument data when the AnP is on hold | 01 April 2014, 20:43:18 UTC |
| 82e523e | Thomas Mooney | 01 April 2014, 17:34:17 UTC | Remove old and deprecated `gmt somatic strand-filter`. It refers to an executable with "test" in the name in a home directory. | 01 April 2014, 17:34:17 UTC |
| 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 |
