166fca5 | Thomas Mooney | 12 August 2015, 20:36:06 UTC | Remove unused includes. | 12 August 2015, 20:36:06 UTC |
2571a4b | Jason Walker | 12 August 2015, 18:25:50 UTC | Merge pull request #919 from jasonwalker80/inactivate_config_file Inactivate AnP Config Files | 12 August 2015, 18:25:50 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 |
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 |
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 |
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 |
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 |
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 |
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 |
9bc8f03 | Eddie Belter | 03 August 2015, 18:47:43 UTC | Utility Test: spell check | 03 August 2015, 18:47:43 UTC |
fbe4599 | Eddie Belter | 03 August 2015, 18:46:07 UTC | Picard: spellcheck | 03 August 2015, 18:46:07 UTC |
683652a | Thomas Mooney | 03 August 2015, 18:20:38 UTC | Don't disconnect if we're not going to wait on the lock. | 03 August 2015, 18:20:38 UTC |
029abd6 | Thomas B. Mooney | 03 August 2015, 15:36:22 UTC | Merge pull request #891 from tmooney/tolerate_unused_annotation_input Only schedule annotation if we have variants to annotate. | 03 August 2015, 15:36:22 UTC |
1c9330c | Thomas Mooney | 30 July 2015, 20:11:10 UTC | Prevent archiving of basic data. Typically these allocations are too small to archive, anyway! | 03 August 2015, 15:30:22 UTC |
2bb803e | Thomas Mooney | 30 July 2015, 19:56:00 UTC | Don't allow archiving of main indices. (Indices for "rederivable" references are not widely used and so can generally still be archived.) | 03 August 2015, 15:30:22 UTC |
ce51605 | Allison Penner Regier | 03 August 2015, 15:20:10 UTC | Merge pull request #897 from apregier/build_diff_change Don't require builds to be from the same model to diff | 03 August 2015, 15:20:10 UTC |
7bb901c | Eddie Belter | 31 July 2015, 23:16:40 UTC | RefAlign GC: use Picard GC versions as valid values | 31 July 2015, 23:16:40 UTC |
9cd1bd9 | Eddie Belter | 31 July 2015, 23:06:05 UTC | Picard: restrict by min version when returning available versions | 31 July 2015, 23:15:09 UTC |
43a7eee | Eddie Belter | 29 July 2015, 01:24:28 UTC | Picard: add test names to GC | 31 July 2015, 23:15:08 UTC |
2ed91ac | Eddie Belter | 29 July 2015, 01:21:23 UTC | Picard: remove unused ignore_state function from genotype concordance | 31 July 2015, 23:15:07 UTC |
da5d610 | Eddie Belter | 29 July 2015, 01:19:56 UTC | Picard: make genotype concordance inherit from base | 31 July 2015, 23:15:06 UTC |
52473d4 | Eddie Belter | 29 July 2015, 01:07:12 UTC | Picard: have enforce min version use version set on class and verify during execute | 31 July 2015, 23:15:06 UTC |
7550f72 | Eddie Belter | 28 July 2015, 22:23:03 UTC | Picard: add minimum_version_required method | 31 July 2015, 23:15:04 UTC |
e98239b | Eddie Belter | 31 July 2015, 22:18:14 UTC | Utility Test: use validate_pos for data_dir | 31 July 2015, 22:22:53 UTC |
d00a4bb | Eddie Belter | 31 July 2015, 22:17:15 UTC | Utility Test: add data_dir perldoc | 31 July 2015, 22:17:47 UTC |
8291dee | apregier | 31 July 2015, 17:10:57 UTC | Don't require builds to be from the same model to diff We have a use case for CLE regression testing where we are making new models in a testdb and want to diff the resulting builds with builds from old models. They should be equivalent, but not the same model. I don't see any reason why this check adds to the integrity of the diff | 31 July 2015, 17:13:27 UTC |
f941263 | Thomas B. Mooney | 30 July 2015, 18:50:54 UTC | Merge pull request #893 from tmooney/somvar_loh_requires_normal_snv_detection Don't try to run LOH without a normal to compare to. | 30 July 2015, 18:50:54 UTC |
21ac56c | APipe Tester | 30 July 2015, 12:19:39 UTC | Updated `gmt` tab completion. | 30 July 2015, 12:19:39 UTC |
f9d4e66 | APipe Tester | 30 July 2015, 12:18:46 UTC | Updated `genome` tab completion. | 30 July 2015, 12:18:46 UTC |
b479d64 | Eddie Belter | 29 July 2015, 23:46:25 UTC | DV2 Novo Realign: replace _run_cmd with sys shellcmd | 29 July 2015, 23:46:25 UTC |