| ea2cb07 | apregier | 01 December 2014, 14:54:04 UTC | Merge pull request #242 from apregier/labeled_result_users Labeled result users | 01 December 2014, 14:54:04 UTC |
| b02c8e1 | APipe Tester | 26 November 2014, 21:27:48 UTC | updated jenkins submodule to b914bc4 | 26 November 2014, 21:27:48 UTC |
| 11708e0 | APipe Tester | 26 November 2014, 21:27:25 UTC | updated ur submodule to 595556a | 26 November 2014, 21:27:25 UTC |
| 293ee8d | Nathaniel Nutter | 26 November 2014, 21:19:48 UTC | Merge pull request #248 from nnutter/running_testsuites remove use of running_testsuites | 26 November 2014, 21:19:48 UTC |
| 42ab23d | Dave Larson | 26 November 2014, 20:15:04 UTC | Merge pull request #247 from ernfrid/up_verbosity up the verbosity level for Fgenesh. This will at least give us the comma... | 26 November 2014, 20:15:04 UTC |
| 30ca5f2 | Nathaniel Nutter | 26 November 2014, 19:57:48 UTC | remove use of running_testsuites These tests were unnecessarily using running_testsuites and the volume running_testsuites points to was recently shrunk down to it's current usage so ClinicalData-db.t could no longer write there. | 26 November 2014, 19:57:48 UTC |
| 1d82974 | Eddie Belter | 26 November 2014, 19:50:58 UTC | Merge pull request #243 from ebelter/rdp-training-set RDP | 26 November 2014, 19:50:58 UTC |
| 2b0a555 | David Morton | 26 November 2014, 19:24:52 UTC | Merge pull request #241 from davidlmorton/unique_results Add unique_results method | 26 November 2014, 19:24:52 UTC |
| 0af295a | Dave Larson | 26 November 2014, 15:29:52 UTC | up the verbosity level for Fgenesh. This will at least give us the command line in the log file when it fails. | 26 November 2014, 15:29:52 UTC |
| 55ade62 | APipe Tester | 25 November 2014, 13:22:29 UTC | Updated `gmt` tab completion. | 25 November 2014, 13:22:29 UTC |
| 7827034 | APipe Tester | 25 November 2014, 13:20:52 UTC | Updated `genome` tab completion. | 25 November 2014, 13:20:52 UTC |
| b71ebb3 | Eddie Belter | 25 November 2014, 00:34:19 UTC | RDP: allow cli to take training set name or path; rdp versions require an instantiated training set | 25 November 2014, 00:34:19 UTC |
| e54b4fa | David Morton | 24 November 2014, 22:06:20 UTC | Merge pull request #240 from davidlmorton/wb_constants Add ability to declare constants to WorkflowBuilder Operations | 24 November 2014, 22:06:20 UTC |
| d7de896 | apregier | 24 November 2014, 18:01:35 UTC | DelegateResult accepts a user label | 24 November 2014, 18:13:46 UTC |
| ceac1b4 | apregier | 24 November 2014, 17:50:10 UTC | Pass in actual software result rather than using global variable | 24 November 2014, 17:50:10 UTC |
| 2f044a6 | dmorton | 24 November 2014, 17:18:28 UTC | Add unique_results method This is useful for when there are more than one SoftwareResult::User relationships between the process and the results. | 24 November 2014, 17:18:28 UTC |
| a1df181 | Feiyu Du | 24 November 2014, 16:34:01 UTC | Merge pull request #239 from dufeiyu/extract_rg_bam Modify Genome::Model::Tools::Sam::ExtractReadGroup | 24 November 2014, 16:34:01 UTC |
| 09e33b8 | dmorton | 24 November 2014, 01:26:35 UTC | Automatically add constant_values to execute They can be overridden since @_ comes after them in %inputs. | 24 November 2014, 01:26:35 UTC |
| ee8a5c4 | APipe Tester | 23 November 2014, 13:21:50 UTC | Updated `gmt` tab completion. | 23 November 2014, 13:21:50 UTC |
| 45d56b4 | APipe Tester | 23 November 2014, 13:20:22 UTC | Updated `genome` tab completion. | 23 November 2014, 13:20:22 UTC |
| 61fcc55 | APipe Tester | 23 November 2014, 13:17:02 UTC | Updated class browser cache. | 23 November 2014, 13:17:02 UTC |
| d8ef5df | dmorton | 23 November 2014, 05:20:54 UTC | Add ability to declare constants on Operations Constants cannot be the target of additional links, they automatically connect to the 'input connector'. Constants propagate when the operation is added to a dag via 'add_operation'. | 23 November 2014, 05:31:19 UTC |
| 71afc0d | dmorton | 22 November 2014, 20:48:58 UTC | Replace is_many with ARRAY type properties 1) performance gain (minor) 2) because we want to add some functionality to add_operation. | 22 November 2014, 20:48:58 UTC |
| 193affb | Thomas B. Mooney | 22 November 2014, 18:59:59 UTC | Merge pull request #231 from tmooney/copy_profile_status Copy status when copying the profile items. | 22 November 2014, 18:59:59 UTC |
| e3c14f3 | Thomas B. Mooney | 22 November 2014, 18:59:42 UTC | Merge pull request #228 from tmooney/deduplicate_gcbase Switch over remaining uses of Genome::Command::Base to Command::V2. CHANGELOG: The GENOME_NO_REQUIRE_USER_VERIFY environment variable no longer has any effect and will be removed in a future snapshot. Control of prompting is consolidated into the existing UR_NO_REQUIRE_USER_VERIFY variable. The UR version of the variable should be used in all cases where the GENOME version was previously. | 22 November 2014, 18:59:42 UTC |
| cda7fb3 | APipe Tester | 22 November 2014, 13:21:31 UTC | Updated `gmt` tab completion. | 22 November 2014, 13:21:31 UTC |
| 39da66b | APipe Tester | 22 November 2014, 13:20:08 UTC | Updated `genome` tab completion. | 22 November 2014, 13:20:08 UTC |
| 76ac4df | APipe Tester | 22 November 2014, 13:17:06 UTC | Updated class browser cache. | 22 November 2014, 13:17:06 UTC |
| 11aa168 | jhundal | 21 November 2014, 19:31:41 UTC | Merge pull request #215 from jhundal/master Epitope Prediction : New Module Added | 21 November 2014, 19:31:41 UTC |
| 592d064 | jhundal | 21 November 2014, 19:00:29 UTC | Merge pull request #1 from nnutter/epitope use SeparatedValueReader and SeparatedValueWriter | 21 November 2014, 19:00:29 UTC |
| bd05780 | Nathaniel Nutter | 21 November 2014, 18:03:54 UTC | brackets aren't necessary for single inheritance | 21 November 2014, 18:07:24 UTC |
| 28e9b68 | Nathaniel Nutter | 21 November 2014, 18:03:03 UTC | whitespace | 21 November 2014, 18:05:04 UTC |
| 2e1de32 | Nathaniel Nutter | 21 November 2014, 18:02:02 UTC | specifically import basename | 21 November 2014, 18:02:02 UTC |
| db37004 | Nathaniel Nutter | 21 November 2014, 18:01:14 UTC | whitespace | 21 November 2014, 18:01:14 UTC |
| 00d3496 | Feiyu Du | 21 November 2014, 17:54:14 UTC | remove unnecessary variable | 21 November 2014, 17:54:14 UTC |
| 144d757 | Nathaniel Nutter | 21 November 2014, 17:53:36 UTC | whitespace | 21 November 2014, 17:53:36 UTC |
| 77d793b | Nathaniel Nutter | 21 November 2014, 17:51:52 UTC | refactor to remove duplicate assignments | 21 November 2014, 17:51:52 UTC |
| aa864d5 | Nathaniel Nutter | 21 November 2014, 17:50:42 UTC | refactor to remove duplicated code | 21 November 2014, 17:50:42 UTC |
| 42ae472 | Nathaniel Nutter | 21 November 2014, 17:49:26 UTC | remove double negative | 21 November 2014, 17:49:26 UTC |
| 926f43f | Feiyu Du | 21 November 2014, 17:42:11 UTC | change the naming of temp bam file | 21 November 2014, 17:42:11 UTC |
| bf581fb | apregier | 21 November 2014, 17:32:37 UTC | Merge pull request #234 from apregier/update-docm-in-vr Use updated docm vcfs in variant reporting | 21 November 2014, 17:32:37 UTC |
| 40c7c81 | Eddie Belter | 21 November 2014, 17:29:18 UTC | Merge pull request #227 from ebelter/cg-hub Cg Hub | 21 November 2014, 17:29:18 UTC |
| 9e876e1 | Feiyu Du | 21 November 2014, 17:06:58 UTC | add unit test | 21 November 2014, 17:06:58 UTC |
| 37ff4f3 | Adam Coffman | 21 November 2014, 15:37:01 UTC | Merge pull request #232 from acoffman/add_default_starting_status_for_config_items Add default starting status for config items | 21 November 2014, 15:37:01 UTC |
| ee88209 | APipe Tester | 21 November 2014, 13:20:10 UTC | Updated `genome` tab completion. | 21 November 2014, 13:20:10 UTC |
| 1fdf11e | APipe Tester | 21 November 2014, 13:17:06 UTC | Updated class browser cache. | 21 November 2014, 13:17:06 UTC |
| 2bd9527 | apregier | 21 November 2014, 00:17:37 UTC | Merge pull request #238 from apregier/add_required_experts_docs Add required interpreters and experts section to reporter docs I am merging quickly to try to get this in a snapshot before our presentation tomorrow. | 21 November 2014, 00:17:37 UTC |
| 4b9e01a | David Morton | 21 November 2014, 00:09:20 UTC | Merge pull request #236 from davidlmorton/process_vr Make VariantReporting::Command::CreateReport use Genome::Process | 21 November 2014, 00:09:20 UTC |
| 612ab35 | apregier | 21 November 2014, 00:08:28 UTC | Rename methods requires_interpreters and requires_experts | 21 November 2014, 00:08:28 UTC |
| d98b23b | apregier | 20 November 2014, 23:26:09 UTC | Add required interpreters and experts section to reporter docs | 20 November 2014, 23:26:09 UTC |
| f2f2128 | Adam Coffman | 20 November 2014, 23:23:47 UTC | Merge pull request #237 from acoffman/bless_new_build Bless new test build | 20 November 2014, 23:23:47 UTC |
| f25f3c6 | apregier | 20 November 2014, 23:20:52 UTC | Merge pull request #233 from apregier/no_docs_for_transient Don't display transient properties | 20 November 2014, 23:20:52 UTC |
| 5511601 | Adam Coffman | 20 November 2014, 23:11:20 UTC | bless new test build | 20 November 2014, 23:11:20 UTC |
| d321db5 | Eddie Belter | 20 November 2014, 23:10:25 UTC | CgHub: use env genome-perl in test shebang. | 20 November 2014, 23:10:25 UTC |
| 8000eb7 | apregier | 20 November 2014, 17:47:37 UTC | Don't display transient properties | 20 November 2014, 23:09:20 UTC |
| e35c0dc | dmorton | 20 November 2014, 22:43:02 UTC | Update docs | 20 November 2014, 22:43:02 UTC |
| cead689 | dmorton | 20 November 2014, 22:32:41 UTC | Make transients optional | 20 November 2014, 22:32:41 UTC |
| 60022e6 | Feiyu Du | 20 November 2014, 22:16:59 UTC | Modify ExtractReadGroup.pm | 20 November 2014, 22:16:59 UTC |
| 904de12 | Eddie Belter | 20 November 2014, 21:53:17 UTC | CgHub: move credential file into calculated class property | 20 November 2014, 21:53:17 UTC |
| b8e1cf8 | dmorton | 20 November 2014, 21:40:12 UTC | Merge v3 and v4 into v5 test-data | 20 November 2014, 21:40:12 UTC |
| 083b0cf | dmorton | 20 November 2014, 21:23:46 UTC | Merge branch 'master' of github.com:genome/genome into process_vr Conflicts: lib/perl/Genome/VariantReporting/Suite/Joinx/Homopolymer/Expert.t | 20 November 2014, 21:23:46 UTC |
| fdaaf27 | Eddie Belter | 20 November 2014, 21:17:53 UTC | CgHub: add verify success and correct base class to gene torrent; update tests | 20 November 2014, 21:17:53 UTC |
| becd9d4 | Susanna Siebert | 20 November 2014, 20:27:54 UTC | Merge pull request #222 from susannasiebert/component_descriptions Add documentation (doc lines) to variant reporting components | 20 November 2014, 20:27:54 UTC |
| cf6b506 | dmorton | 20 November 2014, 20:15:17 UTC | Add 'genome process list' command | 20 November 2014, 20:21:47 UTC |
| 18c8862 | dmorton | 20 November 2014, 19:36:30 UTC | CHANGELOG Remove output_directory property from CreateReport The 'genome variant-reporting create-report' command no longer takes an 'ouptut-directory'. The reports will be saved to a disk-allocation instead. To obtain symlinks to the reports run 'genome process symlink-result'. | 20 November 2014, 20:21:47 UTC |
| 6271c54 | dmorton | 20 November 2014, 20:06:28 UTC | Create command to symlink results of a Genome::Process | 20 November 2014, 20:21:47 UTC |
| dab4c0c | dmorton | 19 November 2014, 03:57:28 UTC | Update expected xml to expect process_id | 20 November 2014, 20:17:51 UTC |
| 9486112 | dmorton | 19 November 2014, 01:43:07 UTC | Pass process_id to Commands It will be used to set up appropriate SoftwareResult::User relationships. | 20 November 2014, 20:17:51 UTC |
| fee4328 | dmorton | 18 November 2014, 23:41:34 UTC | Allow Genome::Process to handle log-file location. | 20 November 2014, 20:17:51 UTC |
| b95ba2c | dmorton | 18 November 2014, 22:09:37 UTC | Make VariantReporting::Process::CreateReport | 20 November 2014, 20:17:51 UTC |
| 7322207 | Jim Weible | 20 November 2014, 19:49:57 UTC | Merge pull request #224 from jweible/AUE-305 Analysis Project Status Changes | 20 November 2014, 19:49:57 UTC |
| 330b011 | Susanna Siebert | 20 November 2014, 17:43:58 UTC | update expected lister test data | 20 November 2014, 19:16:57 UTC |
| af32e31 | Susanna Siebert | 20 November 2014, 17:27:50 UTC | documentation for reporters | 20 November 2014, 19:16:39 UTC |
| 87c9c62 | Susanna Siebert | 20 November 2014, 19:16:05 UTC | Merge branch 'master' into component_descriptions Conflicts: lib/perl/Genome/VariantReporting/Suite/BamReadcount/Adaptor.pm | 20 November 2014, 19:16:05 UTC |
| a91ee6e | apregier | 20 November 2014, 19:07:06 UTC | Use updated docm vcfs | 20 November 2014, 19:07:06 UTC |
| 92b122c | David Morton | 20 November 2014, 18:59:29 UTC | Merge pull request #225 from davidlmorton/misc_fixes Some miscellaneous fixes | 20 November 2014, 18:59:29 UTC |
| 2ccc73a | dmorton | 20 November 2014, 18:41:52 UTC | Fix merge mistake (missing },) | 20 November 2014, 18:41:52 UTC |
| d0b49ca | dmorton | 20 November 2014, 18:04:25 UTC | Merge branch 'master' of github.com:genome/genome into misc_fixes Conflicts: lib/perl/Genome/VariantReporting/Framework/ReportResult.pm | 20 November 2014, 18:04:25 UTC |
| 423238b | apregier | 20 November 2014, 17:46:03 UTC | Merge pull request #223 from apregier/improve-showdocs-cli Allow singular versions of component types | 20 November 2014, 17:46:03 UTC |
| 0fdcde8 | Jim Weible | 20 November 2014, 17:00:45 UTC | fix property name | 20 November 2014, 17:00:45 UTC |
| f034a5f | Adam Coffman | 20 November 2014, 16:38:59 UTC | test initial starting state | 20 November 2014, 16:38:59 UTC |
| 7c234d1 | Adam Coffman | 20 November 2014, 16:35:32 UTC | add default value of "active" for config items | 20 November 2014, 16:35:32 UTC |
| 2f4ff1d | Thomas Mooney | 20 November 2014, 16:27:06 UTC | Copy status when copying the profile items. | 20 November 2014, 16:30:31 UTC |
| 0c4c81d | Jim Weible | 20 November 2014, 16:04:19 UTC | remove extra space | 20 November 2014, 16:04:19 UTC |
| ad3d60c | Thomas B. Mooney | 20 November 2014, 15:54:20 UTC | Merge pull request #230 from tmooney/use_test_data Use fake data for this test. (Except the reference...) | 20 November 2014, 15:54:20 UTC |
| 2cd448e | Thomas B. Mooney | 20 November 2014, 15:41:24 UTC | Merge pull request #220 from tmooney/add_menuitem_relations Add accessors to configs and projects using the menu item. | 20 November 2014, 15:41:24 UTC |
| 17d80ec | Jim Weible | 20 November 2014, 15:30:32 UTC | remove the other unnecessary "in" | 20 November 2014, 15:30:32 UTC |
| 8e6a749 | Jim Weible | 20 November 2014, 15:26:02 UTC | remove unnecessary "in" | 20 November 2014, 15:26:02 UTC |
| 6a3ef6d | Jim Weible | 20 November 2014, 15:23:40 UTC | remove references to removed flag and make the test assumptions make sense | 20 November 2014, 15:23:40 UTC |
| 7053ba9 | Thomas Mooney | 20 November 2014, 15:01:22 UTC | Warn if using old GENOME_NO_REQUIRE_USER_VERIFY variable. | 20 November 2014, 15:01:22 UTC |
| 86607d4 | Thomas Mooney | 20 November 2014, 14:44:46 UTC | Use fake data for this test. (Except the reference...) | 20 November 2014, 14:44:46 UTC |
| f844d04 | Susanna Siebert | 20 November 2014, 14:36:38 UTC | bugfixes and other minor improvements | 20 November 2014, 14:36:38 UTC |
| 74942f4 | Susanna Siebert | 20 November 2014, 14:31:06 UTC | bump homopolymer test data version | 20 November 2014, 14:31:06 UTC |
| ddfa76f | Susanna Siebert | 20 November 2014, 14:30:47 UTC | rename homo-polymer to homopolymer | 20 November 2014, 14:30:47 UTC |
| da585ea | Susanna Siebert | 20 November 2014, 14:13:38 UTC | rename HomoPolymer to Homopolymer | 20 November 2014, 14:13:38 UTC |
| b41fa0c | Susanna Siebert | 20 November 2014, 13:59:41 UTC | use q{} instead of escaping ' | 20 November 2014, 13:59:41 UTC |
| c05b79a | APipe Tester | 20 November 2014, 13:20:37 UTC | Updated `genome` tab completion. | 20 November 2014, 13:20:37 UTC |
| 94908d7 | APipe Tester | 20 November 2014, 13:17:09 UTC | Updated class browser cache. | 20 November 2014, 13:17:09 UTC |
| f2c080a | Nathaniel Nutter | 20 November 2014, 01:15:28 UTC | use SeparatedValueWriter to write TSV-based file In order to use SeparatedValueWriter we need/want the keys of the data hash to match the pretty names of the headers. This converts the surrounding code to use the pretty headers adn then uses the SeparatedValueWriter to write the file. | 20 November 2014, 01:21:19 UTC |
| 2a8a6be | Nathaniel Nutter | 20 November 2014, 00:54:22 UTC | use SeparatedValueReader to read the file TSV-based file | 20 November 2014, 01:20:24 UTC |
