| d2c2aa1 | apregier | 08 December 2014, 18:02:25 UTC | Merge pull request #281 from davidlmorton/sr-simple Remove extra / from begining of allocation_path | 08 December 2014, 18:02:25 UTC |
| 282adcc | Dave Larson | 08 December 2014, 17:01:29 UTC | Merge pull request #285 from ernfrid/joinx_version_check Refactor version checking in Joinx. This fixes VcfAnnotate for | 08 December 2014, 17:01:29 UTC |
| 4f0558f | Dave Larson | 08 December 2014, 15:33:35 UTC | use version module in Joinx.pm | 08 December 2014, 15:33:35 UTC |
| 66a17a0 | Dave Larson | 08 December 2014, 05:27:54 UTC | accept minimum version as argument and drop version module from VcfAnnotate | 08 December 2014, 05:27:54 UTC |
| 671e2c0 | Dave Larson | 08 December 2014, 03:35:16 UTC | Refactor version checking in Joinx. This fixes VcfAnnotate for v1.10 and provides a basis for centralizing Joinx version checking as there are other modules that will fail with v1.10 as well. | 08 December 2014, 03:35:16 UTC |
| e12b17e | APipe Tester | 08 December 2014, 01:47:50 UTC | Merge pull request #282 from apregier/update_joinx_version | 08 December 2014, 01:47:50 UTC |
| e900908 | apregier | 07 December 2014, 03:30:33 UTC | Use joinx1.10 for vcf-annotate This will give a very large performance improvement | 07 December 2014, 03:46:04 UTC |
| af5d265 | APipe Tester | 06 December 2014, 20:12:00 UTC | updated ur submodule to 6324bbd | 06 December 2014, 20:12:00 UTC |
| 7b28f87 | dmorton | 06 December 2014, 19:52:23 UTC | Remove extra / from begining of allocation_path | 06 December 2014, 19:52:23 UTC |
| 32f71e6 | Nathaniel Nutter | 06 December 2014, 17:37:59 UTC | Merge pull request #273 from nnutter/RT/102920 update tests to not write to GENOME_TEST_INPUTS | 06 December 2014, 17:37:59 UTC |
| 851082e | Nathaniel Nutter | 06 December 2014, 17:10:56 UTC | Merge pull request #269 from iferguson90/mode-fix Fix bitwise bug in G::Utility::File::Mode | 06 December 2014, 17:10:56 UTC |
| c280f69 | APipe Tester | 06 December 2014, 13:16:53 UTC | Updated `genome` tab completion. | 06 December 2014, 13:16:53 UTC |
| fe6e515 | APipe Tester | 06 December 2014, 13:15:06 UTC | Updated class browser cache. | 06 December 2014, 13:15:06 UTC |
| 43a50ee | Nathaniel Nutter | 06 December 2014, 11:01:26 UTC | Merge pull request #280 from nnutter/genome_test_inputs make tests more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 11:01:26 UTC |
| a24f44a | Nathaniel Nutter | 06 December 2014, 09:59:32 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 10:04:07 UTC |
| da7fcb2 | Nathaniel Nutter | 06 December 2014, 09:57:27 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 10:04:05 UTC |
| a900853 | Nathaniel Nutter | 06 December 2014, 09:55:03 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 10:04:02 UTC |
| 728e3a8 | Nathaniel Nutter | 06 December 2014, 09:55:19 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 10:03:56 UTC |
| f26902f | Nathaniel Nutter | 06 December 2014, 09:45:31 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 10:02:10 UTC |
| 3c1b1b9 | Nathaniel Nutter | 06 December 2014, 09:38:16 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 10:02:08 UTC |
| 2ffa3e3 | Nathaniel Nutter | 06 December 2014, 09:29:45 UTC | make test more resilient to GENOME_TEST_INPUTS changes This makes use of the new `compare_dirs` test function and updated test inputs to make this test more resilient to GENOME_TEST_INPUTS changes. | 06 December 2014, 10:02:06 UTC |
| 18646f2 | Nathaniel Nutter | 06 December 2014, 09:28:40 UTC | add compare_dirs Adds a compare_dirs test function for comparing the files in two directories. | 06 December 2014, 10:02:04 UTC |
| a3faf3b | Nathaniel Nutter | 06 December 2014, 02:40:18 UTC | remove commented out debug code | 06 December 2014, 10:02:02 UTC |
| a149b94 | Nathaniel Nutter | 06 December 2014, 02:39:48 UTC | make test more resilient to GENOME_TEST_INPUTS changes | 06 December 2014, 10:02:00 UTC |
| 2157afe | David Morton | 06 December 2014, 04:45:50 UTC | Merge pull request #276 from davidlmorton/trio Trio | 06 December 2014, 04:45:50 UTC |
| ed62145 | dmorton | 06 December 2014, 03:41:57 UTC | Merge branch 'master' of github.com:genome/genome into trio Conflicts: lib/perl/Genome/Model/SomaticValidation/Command/CoverageStatsSummary.pm | 06 December 2014, 03:41:57 UTC |
| dac6531 | dmorton | 06 December 2014, 03:34:14 UTC | Add plan_yaml to expected directories | 06 December 2014, 03:39:09 UTC |
| 6f01097 | dmorton | 06 December 2014, 03:32:57 UTC | Allow transient properties in show-docs | 06 December 2014, 03:39:09 UTC |
| c7d7ef8 | dmorton | 06 December 2014, 03:31:37 UTC | Make compare_directories work more intuitivly is and is_deeply use (got, expected) so we changed the order. | 06 December 2014, 03:39:09 UTC |
| 0f67826 | dmorton | 06 December 2014, 03:30:36 UTC | Remove overly sensitive test | 06 December 2014, 03:39:08 UTC |
| cbc72d7 | dmorton | 06 December 2014, 01:54:59 UTC | Allowing withManySampleNames to live on DB backed objects. | 06 December 2014, 03:39:08 UTC |
| 10eee49 | dmorton | 06 December 2014, 01:54:34 UTC | Fix extra \t in full-reporter | 06 December 2014, 03:39:08 UTC |
| 9ecd767 | dmorton | 06 December 2014, 01:53:44 UTC | Fixed compare_directories in TestHelper | 06 December 2014, 03:39:07 UTC |
| e57c7d2 | dmorton | 06 December 2014, 00:39:52 UTC | Eliminate redundant definition | 06 December 2014, 03:39:07 UTC |
| 72224b9 | dmorton | 06 December 2014, 00:38:46 UTC | Disable Report Object validation during Plan validation | 06 December 2014, 03:39:07 UTC |
| 6f14d1c | dmorton | 06 December 2014, 00:35:38 UTC | Report::WithHeader validates during initialize It was being validated when the Report Plan was validated, but now that it isn't we validate at runtime. At least this way we still see the nice error messages, albiet later than we used to. | 06 December 2014, 02:08:34 UTC |
| e506d33 | dmorton | 05 December 2014, 23:56:27 UTC | Remove combination_label from test data | 06 December 2014, 02:08:34 UTC |
| 527719c | dmorton | 05 December 2014, 23:55:40 UTC | Make CreateMergedReports dag name generic | 06 December 2014, 02:08:33 UTC |
| d93177e | dmorton | 05 December 2014, 23:19:26 UTC | Delete transient after Results are got/created The transients sometimes contain values that Flow cannot serialize/deserialize. It shouldn't affect anything since they were transient (i.e. not persisted to the db). | 06 December 2014, 02:08:33 UTC |
| 19b52f4 | dmorton | 05 December 2014, 22:42:00 UTC | Fix required/requires oversight | 06 December 2014, 02:08:33 UTC |
| 1bb098c | dmorton | 05 December 2014, 21:08:42 UTC | Add resassuring message | 06 December 2014, 02:02:14 UTC |
| 794fa45 | Nathaniel Nutter | 06 December 2014, 01:43:30 UTC | Merge pull request #267 from nnutter/apipe_ci add apipe_ci as valid disk group | 06 December 2014, 01:43:30 UTC |
| 1ddeaac | Nathaniel Nutter | 06 December 2014, 01:25:44 UTC | Merge pull request #278 from nnutter/cross_sample_test replace test_dir with TEST_INPUTS_DIR | 06 December 2014, 01:25:44 UTC |
| 3a3ec87 | Nathaniel Nutter | 06 December 2014, 00:56:03 UTC | replace test_dir with TEST_INPUTS_DIR | 06 December 2014, 01:10:18 UTC |
| 5fc1292 | Nathaniel Nutter | 06 December 2014, 00:53:14 UTC | whitespace | 06 December 2014, 00:55:49 UTC |
| 54d358b | Nathaniel Nutter | 05 December 2014, 23:06:37 UTC | Merge remote-tracking branch 'origin/master' into apipe_ci | 05 December 2014, 23:06:37 UTC |
| e0e47fd | Eddie Belter | 05 December 2014, 23:04:32 UTC | Merge pull request #257 from ebelter/instdata-helpers-flagstat InstData Import flagstat and metrics modifications. | 05 December 2014, 23:04:32 UTC |
| 2cc1808 | apregier | 05 December 2014, 21:44:14 UTC | Merge pull request #259 from jasonwalker80/somatic_validation_coverage_stats Single-Sample SomaticValidation CoverageStatsSummary | 05 December 2014, 21:44:14 UTC |
| 60cec88 | dmorton | 05 December 2014, 20:41:42 UTC | Make CreateReport less noisy | 05 December 2014, 20:59:03 UTC |
| 1682f35 | dmorton | 05 December 2014, 20:29:36 UTC | Trio Process objects can symlink their results | 05 December 2014, 20:59:03 UTC |
| 9a0e8bc | dmorton | 05 December 2014, 20:28:28 UTC | All Reports save their plans in their allocation | 05 December 2014, 20:59:02 UTC |
| 4d9fb14 | dmorton | 05 December 2014, 20:27:16 UTC | Remove unused combination_label | 05 December 2014, 20:59:02 UTC |
| 355bc97 | dmorton | 05 December 2014, 20:05:05 UTC | Test xml produced by trio wrapper | 05 December 2014, 20:59:02 UTC |
| b1745f4 | dmorton | 05 December 2014, 20:03:21 UTC | Make Command less noisy | 05 December 2014, 20:59:01 UTC |
| 114587b | dmorton | 05 December 2014, 19:58:28 UTC | Use json to encode metadata into SR labels | 05 December 2014, 20:59:01 UTC |
| b428f15 | dmorton | 05 December 2014, 19:56:09 UTC | Pass process_id to StatsSummary commands | 05 December 2014, 20:59:01 UTC |
| 3f5fb39 | dmorton | 05 December 2014, 06:36:41 UTC | Support Merging MergedReports This commit also moves the Result class into Component::Report | 05 December 2014, 20:59:00 UTC |
| dfbd58b | dmorton | 05 December 2014, 05:32:51 UTC | Work on Process::Trio | 05 December 2014, 20:59:00 UTC |
| 474a444 | dmorton | 05 December 2014, 05:29:36 UTC | Allow UR objects as workflow_inputs | 05 December 2014, 20:59:00 UTC |
| f2e0f30 | dmorton | 05 December 2014, 05:28:42 UTC | Ensure is_many property is passed an array_ref | 05 December 2014, 20:58:59 UTC |
| 73d0e42 | dmorton | 05 December 2014, 00:22:16 UTC | Get Trio Wrapper DAG produced properly | 05 December 2014, 20:58:59 UTC |
| 0b812cf | dmorton | 05 December 2014, 00:20:14 UTC | Use TestHelper to test dag xml | 05 December 2014, 20:58:59 UTC |
| f02e525 | dmorton | 05 December 2014, 00:19:26 UTC | Remove output_dir as input from Trio | 05 December 2014, 20:58:58 UTC |
| 453e194 | dmorton | 05 December 2014, 00:15:14 UTC | Extract get_models_for_roi method | 05 December 2014, 20:58:58 UTC |
| b7b5078 | dmorton | 05 December 2014, 00:08:24 UTC | Use TestHelper to check dag xml | 05 December 2014, 20:58:58 UTC |
| da780d9 | dmorton | 05 December 2014, 00:02:41 UTC | Cache dag and eliminate is_valid check Turns out that __errors__ gets the values of transient_optional properties and this leads to premature caching. | 05 December 2014, 20:58:57 UTC |
| de8ee06 | dmorton | 05 December 2014, 00:02:10 UTC | Let ModelPair generate combination_label | 05 December 2014, 20:58:57 UTC |
| 9587ec7 | dmorton | 04 December 2014, 23:59:28 UTC | Eliminate calculated property | 05 December 2014, 20:50:58 UTC |
| 459aaf2 | dmorton | 04 December 2014, 23:55:39 UTC | Add missing import | 05 December 2014, 20:50:58 UTC |
| 4105ccf | apregier | 04 December 2014, 17:49:58 UTC | Enable test for dag comparison | 05 December 2014, 20:50:58 UTC |
| 2e1d199 | apregier | 04 December 2014, 16:56:31 UTC | ModelPair params_for_dag returns a hashref rather than a hash | 05 December 2014, 20:50:58 UTC |
| b86bf11 | apregier | 04 December 2014, 16:50:40 UTC | Small change to how translated is-many properties can be specified in the plan This happened in commit 811a2f4 but we failed to update the full complement of production plan files | 05 December 2014, 20:50:57 UTC |
| e98bd7f | apregier | 04 December 2014, 16:44:44 UTC | Model pair factory no longer takes output_dir as input | 05 December 2014, 20:50:57 UTC |
| 8138d9e | apregier | 04 December 2014, 16:40:37 UTC | Reenable basic trio test | 05 December 2014, 20:50:57 UTC |
| ed35b6c | apregier | 04 December 2014, 16:38:54 UTC | Writer properties need to be transient | 05 December 2014, 20:50:57 UTC |
| 626c956 | apregier | 04 December 2014, 16:26:26 UTC | Add interface to trio wrapper to get the dag Useful for testing, and follows a similar pattern to other process-command pairs we have made | 05 December 2014, 20:50:57 UTC |
| 7213eba | apregier | 04 December 2014, 16:24:29 UTC | Use roi_name instead of roi directory Still need to figure out how to get the list of roi names other than through the directory structure | 05 December 2014, 20:50:57 UTC |
| 5e0d435 | apregier | 04 December 2014, 16:09:30 UTC | No longer need counter | 05 December 2014, 20:50:57 UTC |
| 9b6dc85 | apregier | 04 December 2014, 15:54:41 UTC | Add merge discovery and followup reports to workflow This is not functional yet, just getting the preliminary idea of how it will work. | 05 December 2014, 20:50:57 UTC |
| c20ea58 | apregier | 04 December 2014, 02:12:47 UTC | Add operations to dag rather than execute them on their own This is still an incomplete commit (see TODOs) Also need to add a test that looks at the final DAG given a set of models | 05 December 2014, 20:50:56 UTC |
| 3321a61 | apregier | 04 December 2014, 01:34:43 UTC | Add expected xml file | 05 December 2014, 20:50:56 UTC |
| 44d1ebd | apregier | 04 December 2014, 00:01:51 UTC | Move CreateMergedReport dag creation to model pair | 05 December 2014, 20:50:56 UTC |
| ebbe2d5 | apregier | 03 December 2014, 23:59:14 UTC | Remove output directory from ModelPair and factory Replace with the idea of a "label" to distinguish the results | 05 December 2014, 20:50:56 UTC |
| 362d326 | apregier | 03 December 2014, 20:52:37 UTC | Command-sr pair for creating igv sessions | 05 December 2014, 20:50:56 UTC |
| b11bf5d | apregier | 03 December 2014, 17:41:44 UTC | Change AlignmentStatsSummary to a command-sr pair Change coverage stats summary to cmd-sr pair | 05 December 2014, 20:50:56 UTC |
| 292d405 | apregier | 03 December 2014, 17:35:09 UTC | Command can still use model interface | 05 December 2014, 20:50:56 UTC |
| 77543cf | apregier | 03 December 2014, 17:05:09 UTC | Change model input to build input for summary commands | 05 December 2014, 20:50:56 UTC |
| 16ae122 | dmorton | 03 December 2014, 19:18:32 UTC | Add Test::MergedReport | 05 December 2014, 20:50:55 UTC |
| c007f43 | dmorton | 03 December 2014, 19:10:02 UTC | Move MergeReports into Framework | 05 December 2014, 20:50:55 UTC |
| a66d3f5 | dmorton | 03 December 2014, 17:43:56 UTC | Rename MergedReportsResult to MergedReport | 05 December 2014, 20:50:55 UTC |
| 02b8d29 | dmorton | 03 December 2014, 17:37:31 UTC | Rename Combine to Merge | 05 December 2014, 20:50:55 UTC |
| e2f2bec | dmorton | 03 December 2014, 02:21:25 UTC | Rename Reporter to Report everywhere | 05 December 2014, 20:50:55 UTC |
| b4bf116 | dmorton | 02 December 2014, 22:38:20 UTC | Redeclare labels This will make it possible to look up any specific SR we create. | 05 December 2014, 20:50:55 UTC |
| e7fd661 | dmorton | 02 December 2014, 22:24:12 UTC | Relax restriction on declaring constants again | 05 December 2014, 20:50:54 UTC |
| 384a391 | dmorton | 02 December 2014, 22:17:46 UTC | Add CreateCombinedReports Command | 05 December 2014, 20:50:54 UTC |
| f521ae2 | dmorton | 02 December 2014, 22:01:03 UTC | Add interface to determine combine parameters This will be used by CreateCombinedReports to determine if we should try to combine reports or not and with what parameters. | 05 December 2014, 20:50:54 UTC |
| 21c25db | dmorton | 02 December 2014, 22:00:17 UTC | Make inputs into constants This makes it easier to compose these dags later. | 05 December 2014, 20:50:54 UTC |
| e4dbbae | dmorton | 02 December 2014, 21:59:37 UTC | Add user and process_id inputs to CombineReports | 05 December 2014, 20:50:54 UTC |
| 1ef93c7 | dmorton | 02 December 2014, 21:57:04 UTC | Add explicit is_optional to input property Some places in our codebase accept that is_optional is implied by default declarations, but not all places do. Perhaps this should be set for us by UR if we supply a default declaration. | 05 December 2014, 20:50:54 UTC |
| 48df037 | dmorton | 02 December 2014, 21:55:58 UTC | Make call signature more specific | 05 December 2014, 20:50:54 UTC |
