| 868d09a | Thomas Mooney | 03 April 2014, 22:36:49 UTC | Update expected output to match synopsis changes. | 03 April 2014, 22:36:49 UTC |
| 2c755e4 | Thomas Mooney | 03 April 2014, 22:29:12 UTC | Remove reference to /gscuser/. The FASTA doesn't need to be in one's homedir, anyway. | 03 April 2014, 22:29:12 UTC |
| dba6418 | Avinash Ramu | 03 April 2014, 20:38:58 UTC | Add some detail to bamrc wrapper help | 03 April 2014, 20:39:37 UTC |
| d894969 | Tiandao Li | 03 April 2014, 20:36:59 UTC | add Concordance. | 03 April 2014, 20:36:59 UTC |
| ded8fad | Michael J. Kiwala | 03 April 2014, 20:17:09 UTC | Update the test plan | 03 April 2014, 20:17:09 UTC |
| 74f3460 | Michael J. Kiwala | 03 April 2014, 20:09:05 UTC | Do not check for updates while running cufflinks On sGMS, when not connected to an external network, cufflinks hangs indefinitely while attempting to check for updates over the network. | 03 April 2014, 20:11:12 UTC |
| e3b0a69 | Avinash Ramu | 03 April 2014, 19:40:27 UTC | move back to older test data | 03 April 2014, 19:41:06 UTC |
| 0b12cfc | Avinash Ramu | 03 April 2014, 19:27:58 UTC | update clinseq blessed build | 03 April 2014, 19:41:05 UTC |
| 7b031b7 | Avinash Ramu | 03 April 2014, 19:27:30 UTC | switch back to DNAcopy seg algorithm but use fixed seed | 03 April 2014, 19:41:05 UTC |
| b538d08 | Eddie Belter | 03 April 2014, 18:24:06 UTC | CQID: wrap assign inst data cmd executes in eval because they may die. | 03 April 2014, 18:26:19 UTC |
| ba7cef2 | apregier | 03 April 2014, 18:26:01 UTC | Merge branch 'updated' into gb_master | 03 April 2014, 18:26:01 UTC |
| 384ef98 | apregier | 03 April 2014, 18:24:49 UTC | Don't transfer refcov result metrics to build | 03 April 2014, 18:24:49 UTC |
| faf3a19 | apregier | 03 April 2014, 15:13:56 UTC | Fix how metric value is found - it won't always be a class property | 03 April 2014, 15:14:09 UTC |
| e0c514f | APipe Tester | 03 April 2014, 12:17:37 UTC | Updated `gmt` tab completion. | 03 April 2014, 12:17:37 UTC |
| da05341 | APipe Tester | 03 April 2014, 12:16:56 UTC | Updated `genome` tab completion. | 03 April 2014, 12:16:56 UTC |
| 366d0a5 | APipe Tester | 03 April 2014, 12:15:31 UTC | Updated class browser cache. | 03 April 2014, 12:15:31 UTC |
| d4e906a | Avinash Ramu | 03 April 2014, 05:59:18 UTC | update clinseq blessed build | 03 April 2014, 05:59:18 UTC |
| 0174643 | Avinash Ramu | 03 April 2014, 05:56:06 UTC | switch to a deterministic segmentation algorithm | 03 April 2014, 05:56:06 UTC |
| 827a8f5 | Avinash Ramu | 03 April 2014, 02:54:05 UTC | update blessed build to one with exome-cnv | 03 April 2014, 02:54:40 UTC |
| 33a48b5 | Avinash Ramu | 02 April 2014, 22:01:54 UTC | update clinseq to use cnmops | 03 April 2014, 02:54:39 UTC |
| 6c75d80 | Thomas Mooney | 02 April 2014, 21:38:57 UTC | Explicitly declare our inputs and outputs. | 02 April 2014, 21:38:57 UTC |
| 0ac3c7f | Avinash Ramu | 02 April 2014, 16:45:27 UTC | enable cnmops test The previous expected-results for this test were generated using a more recent version of the cn.mops package(v1.9.5) and this caused the diffs from Jenkins which has v1.8.9. The expected-results has now been updated to one generated by v1.8.9. | 02 April 2014, 16:47:02 UTC |
| 095c12c | apregier | 02 April 2014, 16:23:00 UTC | Merge branch 'updated' into gb_master | 02 April 2014, 16:23:00 UTC |
| b1a3444 | apregier | 02 April 2014, 16:19:27 UTC | Add tests for WithMode command and clarify behavior for instances where only one sample is available | 02 April 2014, 16:21:51 UTC |
| a0f0004 | Adam Coffman | 02 April 2014, 15:50:21 UTC | improve documentation for somval import command | 02 April 2014, 15:50:21 UTC |
| 8cba870 | Avinash Ramu | 02 April 2014, 15:39:51 UTC | continue to skip this test until the package dependencies are verified | 02 April 2014, 15:39:51 UTC |
| dc88904 | Avinash Ramu | 02 April 2014, 15:32:21 UTC | remove snow and Runit libraries which are not used right now | 02 April 2014, 15:32:21 UTC |
| e6dc4e6 | Avinash Ramu | 02 April 2014, 15:02:20 UTC | cnmops has now been added to genome-snapshot-deps | 02 April 2014, 15:03:23 UTC |
| 0b530aa | apregier | 02 April 2014, 14:57:42 UTC | Merge branch 'updated' into gb_master | 02 April 2014, 14:57:42 UTC |
| b343d5e | apregier | 01 April 2014, 21:19:20 UTC | Rename GenotypeVcf | 02 April 2014, 14:55:05 UTC |
| 715f3d0 | apregier | 28 March 2014, 15:36:17 UTC | Update doc to include new filter type | 02 April 2014, 14:55:04 UTC |
| 624b165 | apregier | 28 March 2014, 15:33:51 UTC | Pass in object directly as input rather than id | 02 April 2014, 14:55:04 UTC |
| 5b0a3fc | apregier | 27 March 2014, 20:44:47 UTC | Make sample names in bam and vcf match in test data | 02 April 2014, 14:55:03 UTC |
| fed6500 | apregier | 27 March 2014, 19:49:58 UTC | Make add_metrics more generic | 02 April 2014, 14:55:02 UTC |
| 8c08bae | apregier | 27 March 2014, 19:46:28 UTC | Add metrics from verifyBamId to build | 02 April 2014, 14:55:02 UTC |
| 1302546 | apregier | 27 March 2014, 19:36:01 UTC | Add metrics to verifyBamId result | 02 April 2014, 14:55:01 UTC |
| 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 |
