| dc1ce25 | Eddie Belter | 12 August 2015, 18:03:03 UTC | GC: spell check | 12 August 2015, 18:03:03 UTC |
| ff8e1f6 | APipe Tester | 12 August 2015, 12:18:45 UTC | Updated `gmt` tab completion. | 12 August 2015, 12:18:45 UTC |
| 25841d1 | APipe Tester | 12 August 2015, 12:17:56 UTC | Updated `genome` tab completion. | 12 August 2015, 12:17:56 UTC |
| 8de0838 | APipe Tester | 12 August 2015, 12:16:26 UTC | Updated class browser cache. | 12 August 2015, 12:16:26 UTC |
| fbf5aba | Eddie Belter | 11 August 2015, 23:06:13 UTC | Disk Volume Sync Usage: update messages | 11 August 2015, 23:06:13 UTC |
| 1576437 | Eddie Belter | 11 August 2015, 22:54:22 UTC | Disk Volume Sync Usage: do not use try::tiny | 11 August 2015, 22:54:22 UTC |
| f137e0e | Eddie Belter | 11 August 2015, 22:52:42 UTC | Disk Volume Sync Usage: do not use tranactions | 11 August 2015, 22:52:47 UTC |
| ed4fc46 | Eddie Belter | 11 August 2015, 22:51:52 UTC | Disk Volume Sync Usage: do not use role logger | 11 August 2015, 22:52:14 UTC |
| 8129e08 | Eddie Belter | 11 August 2015, 22:48:22 UTC | Disk Volume Sync Usage: use loop to go through sync types | 11 August 2015, 22:48:22 UTC |
| f78c928 | Eddie Belter | 11 August 2015, 22:26:49 UTC | Disk Volume Sync Usage: use meta doc for help detail to remove redundancy | 11 August 2015, 22:47:53 UTC |
| 1007466 | Eddie Belter | 11 August 2015, 22:24:18 UTC | Disk Volume Sync Usage: set tie_stderr in test to false to remove warning msg | 11 August 2015, 22:24:18 UTC |
| f7a0ec9 | Eddie Belter | 11 August 2015, 22:22:31 UTC | Disk Volume: remove sync args | 11 August 2015, 22:23:13 UTC |
| 1244824 | Eddie Belter | 11 August 2015, 22:17:50 UTC | Disk Volume: return total_kb/unallocated_kb when synching | 11 August 2015, 22:17:50 UTC |
| 92dd291 | Eddie Belter | 11 August 2015, 22:09:31 UTC | Genotype Concordance: add method to get/createsorted vcf file | 11 August 2015, 22:09:31 UTC |
| 8b3261b | Eddie Belter | 11 August 2015, 22:08:53 UTC | Genotype Concordance: add tests for getting sorted vcf file | 11 August 2015, 22:08:58 UTC |
| 3535464 | Thomas Mooney | 11 August 2015, 22:01:11 UTC | Remove unused variables and the logic to set them. *These are controlled by PP params in SomaticValidation. | 11 August 2015, 22:01:11 UTC |
| 6126200 | apregier | 11 August 2015, 19:13:22 UTC | move file | 11 August 2015, 19:13:22 UTC |
| 045d09f | Allison Penner Regier | 11 August 2015, 18:40:34 UTC | Merge pull request #869 from Origamigirl11/SpeedseqSv Speedseq sv | 11 August 2015, 18:40:34 UTC |
| 3f301f7 | apregier | 11 August 2015, 18:38:57 UTC | Add script to prime testdb for cle test | 11 August 2015, 18:38:57 UTC |
| 8418c57 | Jason Walker | 11 August 2015, 17:24:15 UTC | Add test case. | 11 August 2015, 17:24:15 UTC |
| ffd39e3 | Miranda Fulton | 11 August 2015, 16:17:10 UTC | Deleted a data file that wasn't needed | 11 August 2015, 16:17:10 UTC |
| 61e12a7 | Thomas Mooney | 11 August 2015, 15:47:32 UTC | Quiet warnings about get()ting software results. | 11 August 2015, 15:47:32 UTC |
| a89b898 | Thomas Mooney | 11 August 2015, 15:17:48 UTC | Quite redefinition warnings in TestTool1. This version is still a bit odd, since subroutine declaration is still happening in advance. | 11 August 2015, 15:17:48 UTC |
| fed5264 | APipe Tester | 11 August 2015, 12:18:19 UTC | Updated `gmt` tab completion. | 11 August 2015, 12:18:19 UTC |
| c4194e8 | APipe Tester | 11 August 2015, 12:17:16 UTC | Updated `genome` tab completion. | 11 August 2015, 12:17:16 UTC |
| d308676 | APipe Tester | 11 August 2015, 12:15:13 UTC | Updated class browser cache. | 11 August 2015, 12:15:13 UTC |
| a072669 | mkiwala | 10 August 2015, 21:47:44 UTC | Merge pull request #906 from davidlmorton/rnaseq_spawned_workflows Rnaseq spawned workflows | 10 August 2015, 21:47:44 UTC |
| 68ba404 | Eddie Belter | 10 August 2015, 19:21:28 UTC | Merge pull request #921 from ebelter/novo-realign DV2 Novo Realign: Allow to run with sample names that have parens | 10 August 2015, 19:21:28 UTC |
| 646540f | Thomas B. Mooney | 10 August 2015, 13:29:49 UTC | Merge pull request #872 from tmooney/speedseq_result_doesnt_depend_on_inconsequential_options Filter out thread count, max memory, and verbosity from lookup hash. | 10 August 2015, 13:29:49 UTC |
| 7b4b6fe | Thomas B. Mooney | 10 August 2015, 13:28:39 UTC | Merge pull request #915 from tmooney/remove_old_gmt_somatic_runreports Remove old `gmt somatic run-reports`. | 10 August 2015, 13:28:39 UTC |
| 21be8cf | dmorton | 09 August 2015, 04:12:10 UTC | Fix test data (inputproperty lines are now ordered alphabetically) | 09 August 2015, 04:26:18 UTC |
| 5b07744 | dmorton | 08 August 2015, 07:01:36 UTC | Add missing test data file | 08 August 2015, 07:01:36 UTC |
| a3add35 | dmorton | 08 August 2015, 06:01:18 UTC | Deduplicate links as they are added to a DAG | 08 August 2015, 06:01:18 UTC |
| 1a60a87 | dmorton | 08 August 2015, 06:00:08 UTC | Improve die message | 08 August 2015, 06:00:08 UTC |
| cf310c3 | dmorton | 08 August 2015, 05:57:28 UTC | Bugfix: specify properties as command inputs | 08 August 2015, 05:57:28 UTC |
| 9a4f3f5 | dmorton | 08 August 2015, 04:23:26 UTC | Support 'isOptional' DAG inputproperties This change only allows for xml round-trip support. Executing workflows with these types of inputproperties with anything other than legacy workflow is still unsupported. | 08 August 2015, 04:23:26 UTC |
| 28288de | dmorton | 08 August 2015, 04:18:16 UTC | Add convienent way to write contents to temp file This is especially useful in testing. | 08 August 2015, 04:18:16 UTC |
| d474e43 | dmorton | 08 August 2015, 03:29:47 UTC | stop doing "die $self->error_message(...)" There is no way to supress the error message from being emitted in the case where you trap the die in an eval or a try block. Therefore it just leads to potentially confusing noise. | 08 August 2015, 03:29:47 UTC |
| 4c01660 | Eddie Belter | 07 August 2015, 21:10:04 UTC | Merge pull request #920 from ebelter/recreate-per-lane-bam Recreate Per Lane Bam: function name typo | 07 August 2015, 21:10:04 UTC |
| 7bcc878 | Eddie Belter | 07 August 2015, 19:15:53 UTC | Recreate Per Lane Bam: function name typo | 07 August 2015, 19:15:53 UTC |
| 2d9ba60 | Jason Walker | 07 August 2015, 16:23:15 UTC | Initial revision of a command to inactivate config files. | 07 August 2015, 16:23:15 UTC |
| 5f1c4ce | Adam Coffman | 07 August 2015, 14:36:55 UTC | Merge pull request #913 from acoffman/remove_file_summary_creation Remove FileSummary creation when allocations are purged | 07 August 2015, 14:36:55 UTC |
| 635cf1c | APipe Tester | 07 August 2015, 12:19:44 UTC | Updated `gmt` tab completion. | 07 August 2015, 12:19:44 UTC |
| f32bd05 | APipe Tester | 07 August 2015, 12:18:53 UTC | Updated `genome` tab completion. | 07 August 2015, 12:18:53 UTC |
| d7510cf | Eddie Belter | 06 August 2015, 22:28:22 UTC | Picard: make sort vcf use base class | 06 August 2015, 22:28:22 UTC |
| 3ba5b8f | Eddie Belter | 06 August 2015, 22:27:46 UTC | Picard: quote for shell param values | 06 August 2015, 22:27:50 UTC |
| ddc063f | Eddie Belter | 06 August 2015, 22:26:27 UTC | Genotype Concordance: sanitize sample name in file path | 06 August 2015, 22:26:27 UTC |
| c994b86 | Eddie Belter | 06 August 2015, 22:24:54 UTC | Genotype Concordance: store sorted genotype microarray vcfs | 06 August 2015, 22:24:54 UTC |
| 6313d4f | Avinash Ramu | 06 August 2015, 21:43:27 UTC | Merge pull request #916 from gatoravi/add_CRC_to_clinseq_update_analysis Add CRC as a valid tumor common-name | 06 August 2015, 21:43:27 UTC |
| 6b53af9 | Jason Walker | 06 August 2015, 20:51:43 UTC | Initial revision of a command to dump build QC metrics. | 06 August 2015, 20:51:43 UTC |
| bde6164 | Avinash Ramu | 06 August 2015, 20:00:44 UTC | Add CRC as a valid tumor common-name | 06 August 2015, 20:00:44 UTC |
| ddbc793 | Thomas Mooney | 06 August 2015, 19:31:47 UTC | Remove old `gmt germline tier-variants`. It used the `gmt somatic run-reports` that is being removed for using something that was removed. | 06 August 2015, 19:31:47 UTC |
| b69232e | Chris Miller | 06 August 2015, 18:54:01 UTC | Merge pull request #911 from chrisamiller/concordance adding example file, changing 'reference-genome' param to 'reference-fasta', | 06 August 2015, 18:54:01 UTC |
| f83db71 | Thomas Mooney | 06 August 2015, 18:43:41 UTC | Remove old `gmt somatic run-reports`. It refers to some other modules that were removed in commit d08d6b84701442346ccfd9076c1be997c608732b in 2013, so it doesn't work, anyway! | 06 August 2015, 18:45:22 UTC |
| b329f94 | Adam Coffman | 06 August 2015, 16:42:45 UTC | Remove FileSummary creation when allocations are purged | 06 August 2015, 17:26:42 UTC |
| cfaf2ed | Thomas B. Mooney | 06 August 2015, 13:32:15 UTC | Merge pull request #907 from tmooney/sr_users_save_hash Save a copy of the users hash. | 06 August 2015, 13:32:15 UTC |
| b21d2f3 | APipe Tester | 06 August 2015, 12:18:18 UTC | Updated `genome` tab completion. | 06 August 2015, 12:18:18 UTC |
| 8c52658 | Chris Miller | 06 August 2015, 01:47:39 UTC | changing reference param suitable | 06 August 2015, 01:47:39 UTC |
| b1c3376 | Chris Miller | 06 August 2015, 01:12:01 UTC | adding example file, changing 'reference-genome' param to 'reference-fasta', and cleaning up extraneous comments | 06 August 2015, 01:12:01 UTC |
| 7ce64c4 | Thomas B. Mooney | 05 August 2015, 22:43:04 UTC | Merge pull request #894 from tmooney/allow_perl_access_to_model_summary Allow Programmatic Access to ModelSummary information | 05 August 2015, 22:43:04 UTC |
| 76acb86 | Miranda Fulton | 05 August 2015, 20:13:30 UTC | Some final tidying up | 05 August 2015, 20:13:30 UTC |
| 9039bf6 | Allison Penner Regier | 05 August 2015, 20:03:13 UTC | Merge pull request #908 from apregier/add_cle_test2 Add cle test2 | 05 August 2015, 20:03:13 UTC |
| 3677770 | Eddie Belter | 05 August 2015, 19:39:14 UTC | DV2 NovoRealign: use file::copy to move file | 05 August 2015, 19:39:14 UTC |
| 4307858 | apregier | 05 August 2015, 18:58:17 UTC | Simplify | 05 August 2015, 18:58:17 UTC |
| 31d7636 | apregier | 05 August 2015, 18:54:38 UTC | Use yaml block literal Makes it easier to read, and found a missing \n | 05 August 2015, 18:54:38 UTC |
| a4f871b | Eddie Belter | 05 August 2015, 18:31:36 UTC | Merge pull request #903 from ebelter/gm-rm-instrument-type Genotype Microarray: Remove instrument type param | 05 August 2015, 18:31:36 UTC |
| a200f39 | apregier | 05 August 2015, 18:24:21 UTC | Add cle test config | 05 August 2015, 18:24:21 UTC |
| 024f387 | apregier | 03 August 2015, 18:22:36 UTC | Add has_diffs convenience method | 05 August 2015, 17:56:25 UTC |
| fc94f67 | Miranda Fulton | 05 August 2015, 16:07:41 UTC | Versions options added and minor adjustments | 05 August 2015, 16:11:28 UTC |
| 2c5d5de | Miranda Fulton | 05 August 2015, 16:06:02 UTC | Removed unneeded files | 05 August 2015, 16:06:02 UTC |
| 958e4ba | Thomas Mooney | 05 August 2015, 15:23:28 UTC | Call a method that exists! | 05 August 2015, 15:23:28 UTC |
| ba6ef84 | Thomas B. Mooney | 05 August 2015, 14:59:47 UTC | Merge pull request #905 from tmooney/existance A Great Vowel Shift | 05 August 2015, 14:59:47 UTC |
| 3fc5e15 | Thomas Mooney | 05 August 2015, 14:46:11 UTC | Save a copy of the users hash. This fixes a bug where someone else with the reference was manipulating the hash between passing it and us using it, making our users disappear. | 05 August 2015, 14:47:59 UTC |
| 4993382 | APipe Tester | 05 August 2015, 12:18:35 UTC | Updated `genome` tab completion. | 05 August 2015, 12:18:35 UTC |
| a69ae17 | APipe Tester | 05 August 2015, 12:16:47 UTC | Updated class browser cache. | 05 August 2015, 12:16:47 UTC |
| dd2f127 | dmorton | 03 August 2015, 19:22:57 UTC | Add ability to view spawned PTero workflows | 05 August 2015, 03:51:13 UTC |
| 63ed20e | dmorton | 03 August 2015, 19:21:29 UTC | gmt BamQc::Run uses WorkflowBuilder | 05 August 2015, 03:51:13 UTC |
| 068165f | dmorton | 03 August 2015, 18:22:40 UTC | Name RnaSeq workflow step consistently This was the only step in the model's workflow that didn't have RnaSeq at the begining of its name. | 05 August 2015, 03:51:12 UTC |
| 7b32148 | dmorton | 25 July 2015, 05:03:58 UTC | Bugfix: Block methods don't have parameters This was copied over from converge, but shouldn't have been. | 05 August 2015, 03:50:52 UTC |
| 2e504f2 | Eddie Belter | 04 August 2015, 21:06:43 UTC | DV2 NovoRealign: use array shellcmd to run samtools commands | 04 August 2015, 21:06:43 UTC |
| 398d13a | Eddie Belter | 04 August 2015, 21:04:58 UTC | DV2 NovoRealign: join cmd using quote for shell for novo2sam command | 04 August 2015, 21:04:58 UTC |
| 7cff907 | Eddie Belter | 04 August 2015, 21:02:36 UTC | DV2 NovoRealign: use array shellcmd to run novo align | 04 August 2015, 21:02:36 UTC |
| a7907a4 | Eddie Belter | 04 August 2015, 20:59:19 UTC | DV2 NovoRealign: use join to create file names and store in variable | 04 August 2015, 20:59:19 UTC |
| 2e9df47 | Eddie Belter | 04 August 2015, 20:48:57 UTC | DV2 NovoRealign: do not add slashes to library names and fastq paths | 04 August 2015, 20:48:57 UTC |
| 2440afb | Thomas B. Mooney | 04 August 2015, 20:15:39 UTC | Merge pull request #902 from tmooney/handle_inactive_status_in_purge Account for the existence of other non-disabled statuses. | 04 August 2015, 20:15:39 UTC |
| 481d8ff | Thomas B. Mooney | 04 August 2015, 19:33:50 UTC | Merge pull request #900 from tmooney/only_disconnect_if_waiting_on_lock Don't disconnect if we're not going to wait on the lock. | 04 August 2015, 19:33:50 UTC |
| 30370d1 | Thomas Mooney | 04 August 2015, 19:03:00 UTC | Remove a c. | 04 August 2015, 19:03:00 UTC |
| a8ef952 | Thomas Mooney | 04 August 2015, 19:01:00 UTC | Anglicize "existance" to "existence". | 04 August 2015, 19:01:00 UTC |
| 433e762 | Eddie Belter | 04 August 2015, 17:55:08 UTC | Merge pull request #899 from ebelter/picard-versions Picard | 04 August 2015, 17:55:08 UTC |
| 1099c65 | Eddie Belter | 04 August 2015, 17:54:55 UTC | Merge pull request #898 from ebelter/test-doc Utility Test data_dir: add doc, use validate_pos | 04 August 2015, 17:54:55 UTC |
| 9a9d080 | Miranda Fulton | 04 August 2015, 16:41:41 UTC | fixed more bugs | 04 August 2015, 16:41:41 UTC |
| 1d2eb1b | Miranda Fulton | 04 August 2015, 15:57:44 UTC | spelling mistake | 04 August 2015, 15:57:44 UTC |
| 115ca1a | Miranda Fulton | 04 August 2015, 15:52:13 UTC | Made some minor adjustments to improve preformance | 04 August 2015, 15:52:13 UTC |
| 0b671eb | Indraniel | 04 August 2015, 13:38:25 UTC | Merge pull request #876 from indraniel/CLE-BIO-1491-addons CLE "variant-reporting wrappers gold-evaluation" addons - add fixes to the 'GoldEvaluation' variant reporting wrapper - introduce tests for both the 'GoldEvaluation' and 'ModelReport' variant reporting wrappers - introduce an abstract base class 'Utils' for common logic to all variant reports | 04 August 2015, 13:38:25 UTC |
| 7106cf1 | Eddie Belter | 03 August 2015, 22:02:33 UTC | Genotype Microarray: Remove instrument type param | 03 August 2015, 22:02:33 UTC |
| 1621125 | Thomas B. Mooney | 03 August 2015, 21:01:08 UTC | Merge pull request #896 from tmooney/indices_set_archivable_false Primary References and Indices Default to Not Archivable | 03 August 2015, 21:01:08 UTC |
| b96e431 | Thomas Mooney | 03 August 2015, 20:06:15 UTC | Account for the existences of other non-disabled statuses. | 03 August 2015, 20:06:15 UTC |
| bbf3093 | Indraniel Das | 03 August 2015, 19:32:45 UTC | + aregier's 2nd recommendation - refactoring 'get_library_name_labels'. Putting a method common across all three report types into a new abstract base class. - Once the UR Roles (https://github.com/genome/UR/pull/63) are released, the base class (Genome::VariantReporting::Command::Wrappers::Utils) can be converted into a proper role. | 03 August 2015, 19:32:45 UTC |
| e3f9c4c | Indraniel Das | 03 August 2015, 19:05:22 UTC | + add a test for the ModelReport module | 03 August 2015, 19:05:22 UTC |
| acfd7f4 | Indraniel Das | 03 August 2015, 19:04:37 UTC | + apply aregier's first suggestion - remove unneeded 'get_common_translations' method | 03 August 2015, 19:04:37 UTC |
