| 57f9260 | Thomas B. Mooney | 30 May 2017, 17:29:55 UTC | Merge pull request #1717 from tmooney/use_sys_abspath_in_snapshot_revision Use Genome::Sys->abs_path for DB and snapshot locations. | 30 May 2017, 17:29:55 UTC |
| 5c5d5ec | Thomas B. Mooney | 30 May 2017, 17:00:01 UTC | Merge pull request #1722 from tmooney/move_allocations_doesnt_push_undef Better handling of disk groups in `gmb move-allocations`. | 30 May 2017, 17:00:01 UTC |
| 9e55d49 | Thomas B. Mooney | 30 May 2017, 16:13:22 UTC | Complain if we can't determine a disk group to use. | 30 May 2017, 16:13:22 UTC |
| ef422e3 | Thomas B. Mooney | 30 May 2017, 16:12:42 UTC | Only include the build's allocation if it has one! | 30 May 2017, 16:12:42 UTC |
| 38f39fe | Thomas B. Mooney | 24 May 2017, 20:10:12 UTC | Merge pull request #1716 from tmooney/typo_director_plus_y Typo fix: add "y" to "directory". | 24 May 2017, 20:10:12 UTC |
| 48704b0 | Thomas B. Mooney | 23 May 2017, 15:07:36 UTC | Use Genome::Sys->abs_path for DB and snapshot locations. This is in a further effort to avoid /vol/ paths. | 23 May 2017, 15:07:36 UTC |
| ec5b8a0 | Thomas B. Mooney | 22 May 2017, 22:47:09 UTC | Merge pull request #1709 from tmooney/support_bsmap_in_movecommand Add Bsmap alignment as a possible result class for ReferenceAlignment. | 22 May 2017, 22:47:09 UTC |
| 18d711a | Thomas B. Mooney | 22 May 2017, 22:46:56 UTC | Merge pull request #1711 from tmooney/remove_keggpathway_tool Remove disused "ImportTranscriptFeature" tool tree. | 22 May 2017, 22:46:56 UTC |
| 5bf6d35 | Thomas B. Mooney | 22 May 2017, 22:46:45 UTC | Merge pull request #1712 from tmooney/remove_methylarray_tree Remove disused "MethylArray" tool tree. | 22 May 2017, 22:46:45 UTC |
| 431c0f1 | Thomas B. Mooney | 22 May 2017, 22:46:34 UTC | Merge pull request #1713 from tmooney/remove_simulation_tree Remove disused "Simulation" tool tree. | 22 May 2017, 22:46:34 UTC |
| 43ad7ed | Thomas B. Mooney | 22 May 2017, 22:46:21 UTC | Merge pull request #1714 from tmooney/remove_svsim_tree Remove disused "SvSim" tool tree. | 22 May 2017, 22:46:21 UTC |
| 0752cfc | Thomas B. Mooney | 22 May 2017, 22:46:03 UTC | Merge pull request #1715 from tmooney/only_process_each_sr_once Only process each SR once when purging an AnP. | 22 May 2017, 22:46:03 UTC |
| df49245 | Thomas B. Mooney | 22 May 2017, 21:58:49 UTC | Typo fix: add "y" to "directory". | 22 May 2017, 21:58:49 UTC |
| f0559b7 | Thomas B. Mooney | 18 May 2017, 21:34:28 UTC | Only process each SR once when purging an AnP. | 18 May 2017, 21:34:28 UTC |
| 51e91ba | Thomas B. Mooney | 18 May 2017, 14:38:51 UTC | Remove disused "SvSim" tool tree. | 18 May 2017, 14:46:32 UTC |
| a71620d | Thomas B. Mooney | 18 May 2017, 14:34:38 UTC | Remove disused "Simulation" tool tree. | 18 May 2017, 14:34:38 UTC |
| ccebf22 | Thomas B. Mooney | 18 May 2017, 14:25:43 UTC | Remove disused "MethylArray" tool tree. | 18 May 2017, 14:25:43 UTC |
| 25c7e99 | Thomas B. Mooney | 18 May 2017, 14:16:32 UTC | Remove disused "ImportTranscriptFeature" tool tree. | 18 May 2017, 14:16:32 UTC |
| 2dda798 | Jason Walker | 17 May 2017, 14:36:23 UTC | Merge pull request #1625 from jasonwalker80/unarchive_model_instdata Unarchive Instrument Data | 17 May 2017, 14:36:23 UTC |
| 01091e2 | Thomas B. Mooney | 17 May 2017, 14:03:58 UTC | Add Bsmap alignment as a possible result class for ReferenceAlignment. | 17 May 2017, 14:03:58 UTC |
| e922a6c | Thomas B. Mooney | 16 May 2017, 19:58:11 UTC | Merge pull request #1702 from tmooney/move_allocations_for_build Command to move "all" allocations for a build. | 16 May 2017, 19:58:11 UTC |
| 0672ec5 | Thomas B. Mooney | 16 May 2017, 19:52:46 UTC | Merge pull request #1708 from tmooney/update_speedseq_path Update speedseq path to newer disk array. | 16 May 2017, 19:52:46 UTC |
| 7b46eca | Thomas B. Mooney | 16 May 2017, 19:52:29 UTC | Merge pull request #1700 from tmooney/abs_path_doesnt_return_vol_paths Site: Avoid using `/vol/` paths as canonical. | 16 May 2017, 19:52:29 UTC |
| 574bc09 | Thomas B. Mooney | 16 May 2017, 17:43:27 UTC | Merge pull request #1707 from tmooney/remove_iprscan_predictor Remove `gmt predictor interproscan`. | 16 May 2017, 17:43:27 UTC |
| 30c306d | Thomas B. Mooney | 11 May 2017, 21:24:19 UTC | Update speedseq path to newer disk array. | 11 May 2017, 21:24:19 UTC |
| c2947d0 | Thomas B. Mooney | 10 May 2017, 21:07:30 UTC | Add clarifying parentheses around list-building. | 10 May 2017, 21:07:30 UTC |
| 3e341bc | Thomas B. Mooney | 10 May 2017, 20:24:54 UTC | Use a common list of subclasses for all RunsDV2 build types. | 10 May 2017, 20:24:54 UTC |
| 46522b4 | Thomas B. Mooney | 10 May 2017, 19:21:09 UTC | Only run move command if we have allocations that need moving. | 10 May 2017, 19:21:09 UTC |
| 8cc300a | Thomas B. Mooney | 10 May 2017, 19:17:04 UTC | Add RnaSeq support to the build move command. | 10 May 2017, 19:17:04 UTC |
| 3e85a2e | Thomas B. Mooney | 10 May 2017, 19:16:46 UTC | Need to update to the destination disk group as well! | 10 May 2017, 19:16:46 UTC |
| d0abf56 | Thomas B. Mooney | 10 May 2017, 13:46:47 UTC | Remove `gmt predictor interproscan`. | 10 May 2017, 13:46:47 UTC |
| e170167 | Thomas B. Mooney | 09 May 2017, 21:23:24 UTC | Merge pull request #1703 from tmooney/dont_use_docker_for_archives Don't use docker for archive processes! | 09 May 2017, 21:23:24 UTC |
| 383b7dc | Thomas B. Mooney | 09 May 2017, 21:23:13 UTC | Merge pull request #1697 from tmooney/stop_swallowing_errors_in_model_create Stop swallowing errors in Model create. | 09 May 2017, 21:23:13 UTC |
| 671a570 | Thomas B. Mooney | 08 May 2017, 18:40:58 UTC | Merge pull request #1706 from tmooney/more_tests_with_deleted_data Fixes for more tests due to external changes. | 08 May 2017, 18:40:58 UTC |
| 637067d | Thomas B. Mooney | 04 May 2017, 17:05:59 UTC | Ensure our destroy handler doesn't overwrite the die() message. | 04 May 2017, 17:05:59 UTC |
| 05272d0 | Thomas B. Mooney | 04 May 2017, 14:05:03 UTC | Set an explicit "lsb_sub_additional" config so output is repeatable. We're now testing the "use docker" case instead of the "no docker" case. | 04 May 2017, 14:43:58 UTC |
| a43662c | Thomas B. Mooney | 03 May 2017, 15:20:31 UTC | Remove failing test for detector we no longer support. | 03 May 2017, 15:20:31 UTC |
| 782d625 | Jason Walker | 03 May 2017, 15:05:34 UTC | Merge pull request #1704 from jasonwalker80/fix_set_test_name Remove undefined subroutine call. | 03 May 2017, 15:05:34 UTC |
| a79a20b | Thomas B. Mooney | 02 May 2017, 22:32:05 UTC | Don't notify when we skip object for classes that we do handle. | 02 May 2017, 22:32:05 UTC |
| 6ffff59 | Thomas B. Mooney | 01 May 2017, 17:36:03 UTC | Merge pull request #1705 from tmooney/stop_referencing_ams1158 Remove commented-out code. | 01 May 2017, 17:36:03 UTC |
| 8824cf6 | Thomas B. Mooney | 01 May 2017, 15:03:46 UTC | Remove unused variable. | 01 May 2017, 15:03:46 UTC |
| 4490350 | Thomas B. Mooney | 01 May 2017, 14:59:40 UTC | Remove commented-out code. | 01 May 2017, 14:59:40 UTC |
| eaba001 | Jason Walker | 28 April 2017, 19:40:43 UTC | Remove undefined subroutine call. | 28 April 2017, 19:40:43 UTC |
| 2d49f80 | Thomas B. Mooney | 25 April 2017, 21:12:02 UTC | Don't use docker for archive processes! | 25 April 2017, 21:12:02 UTC |
| 3b9cd69 | Thomas B. Mooney | 25 April 2017, 19:59:42 UTC | Don't include alignment results as belong to SomaticVariation. | 25 April 2017, 19:59:42 UTC |
| e854a3d | Thomas B. Mooney | 25 April 2017, 19:41:23 UTC | Don't try to move allocations that are already in the desired place. | 25 April 2017, 19:49:57 UTC |
| 298aa1c | Thomas B. Mooney | 25 April 2017, 19:29:37 UTC | Merge pull request #1701 from tmooney/disable_dv2_filter_tests_dependent_on_purged_data Disable DV2 filter test cases dependent on purged test data. | 25 April 2017, 19:29:37 UTC |
| 3652e8b | Thomas B. Mooney | 25 April 2017, 19:20:30 UTC | Update the build directory after moving everything. | 25 April 2017, 19:20:30 UTC |
| baa4c48 | Feiyu Du | 25 April 2017, 19:08:31 UTC | Merge pull request #1699 from dufeiyu/fix_GT Fix genotype for pindelRegion vcf | 25 April 2017, 19:08:31 UTC |
| b016224 | Thomas B. Mooney | 25 April 2017, 18:59:18 UTC | New command to move "all" the allocations for a build. Based on genome/genome#1698. | 25 April 2017, 18:59:18 UTC |
| a0315b9 | Jason Walker | 19 April 2017, 20:09:18 UTC | Add a list of known SomVar result class names. | 25 April 2017, 18:55:44 UTC |
| c6f0656 | Jason Walker | 25 April 2017, 18:53:44 UTC | Instead of unarchiving the instrument data, use the unarchive command. | 25 April 2017, 18:53:44 UTC |
| db6f549 | Jason Walker | 25 April 2017, 18:53:36 UTC | Instead of unarchiving the instrument data, use the unarchive command. | 25 April 2017, 18:53:36 UTC |
| c390203 | Jason Walker | 25 April 2017, 18:53:06 UTC | Update class to use the new instrument data command. Also use the configured disk group for allocations. | 25 April 2017, 18:53:06 UTC |
| 12334cb | Jason Walker | 25 April 2017, 18:52:19 UTC | Use the new instrument data command in the observer. | 25 April 2017, 18:52:19 UTC |
| 7437574 | Jason Walker | 25 April 2017, 18:51:55 UTC | initial revision of a command to unarchive one or more instrument data. | 25 April 2017, 18:51:55 UTC |
| 8493482 | Jason Walker | 25 April 2017, 17:45:54 UTC | Remove AnP status subroutine from model command. | 25 April 2017, 17:45:54 UTC |
| 80f231f | Thomas B. Mooney | 24 April 2017, 22:35:46 UTC | Disable test cases dependent on purged test data. | 24 April 2017, 22:35:46 UTC |
| 9c88f4a | Thomas B. Mooney | 24 April 2017, 17:58:48 UTC | Use abs_path wrapper to try to preserve /gscmnt/ paths. | 24 April 2017, 18:44:16 UTC |
| 2817766 | Thomas B. Mooney | 24 April 2017, 17:51:50 UTC | Wrapper for abs_path that preserves /gscmnt/ symlinks. We don't want to use /vol/aggrX/ paths canonically. Outside of the "TGI" site, this should function exactly like Cwd::abs_path. | 24 April 2017, 18:44:16 UTC |
| 62a4c80 | Feiyu Du | 20 April 2017, 21:08:58 UTC | fix genotype for pindelRegion vcf | 20 April 2017, 21:08:58 UTC |
| 3878811 | Thomas B. Mooney | 06 April 2017, 15:52:05 UTC | Merge pull request #1696 from tmooney/discontinue_mailing_list_support Remove support for indexing Mailman mailing lists. | 06 April 2017, 15:52:05 UTC |
| b811be3 | Thomas B. Mooney | 06 April 2017, 15:09:04 UTC | Remove support for indexing Mailman mailing lists. | 06 April 2017, 15:09:04 UTC |
| a9e08ae | Thomas B. Mooney | 06 April 2017, 15:03:27 UTC | Merge pull request #1695 from tmooney/skip_refalign_summary_test Skip test that is dependent on live data. | 06 April 2017, 15:03:27 UTC |
| 6b69752 | Thomas B. Mooney | 05 April 2017, 22:54:51 UTC | Skip test that is dependent on live data. This report is still tested in the model test. | 05 April 2017, 22:54:51 UTC |
| 63da350 | Thomas B. Mooney | 05 April 2017, 15:16:29 UTC | Merge pull request #1692 from tmooney/better_disk_estimates_in_alignment Better disk estimates in alignment | 05 April 2017, 15:16:29 UTC |
| 0a2e0e4 | Jason Walker | 04 April 2017, 18:15:51 UTC | Merge pull request #1693 from jasonwalker80/intermediate_align_disk Intermediate Alignment Disk Check | 04 April 2017, 18:15:51 UTC |
| deb6db9 | Thomas B. Mooney | 04 April 2017, 15:00:28 UTC | Generate estimate based on the instrument data. | 04 April 2017, 17:25:33 UTC |
| 7011b41 | Thomas B. Mooney | 04 April 2017, 15:01:29 UTC | Ensure test data has read lengths and clusters defined. | 04 April 2017, 17:25:33 UTC |
| 938355f | Jason Walker | 04 April 2017, 17:02:32 UTC | decrease alignmenet disk check from 20x to 2x. | 04 April 2017, 17:02:32 UTC |
| 3afacaa | Thomas B. Mooney | 04 April 2017, 15:22:35 UTC | Merge pull request #1665 from tmooney/test_fixes_for_newer_perl Compatibility fixes for running with newer versions of third-party modules. | 04 April 2017, 15:22:35 UTC |
| 10540ba | Thomas B. Mooney | 04 April 2017, 15:21:47 UTC | Merge pull request #1686 from tmooney/remove_ok_files_feature Remove concept of "OK" file marking. | 04 April 2017, 15:21:47 UTC |
| e78e01e | Thomas B. Mooney | 04 April 2017, 15:21:14 UTC | Merge pull request #1688 from tmooney/remove_more_workflow_references_from_genomenv Remove "Workflow" from comments and output for version check. | 04 April 2017, 15:21:14 UTC |
| 258b94d | Thomas B. Mooney | 04 April 2017, 15:19:33 UTC | Merge pull request #1690 from tmooney/move_updates_group_subdirectory Update the group_subdirectory to match our new location. | 04 April 2017, 15:19:33 UTC |
| 7924a0f | Jason Walker | 04 April 2017, 15:14:11 UTC | Merge pull request #1687 from jasonwalker80/ssg_test_names Set SSG Test Names | 04 April 2017, 15:14:11 UTC |
| 1eff96d | Jason Walker | 04 April 2017, 15:12:34 UTC | Merge pull request #1682 from jasonwalker80/alignment_dis Alignment Disk Check | 04 April 2017, 15:12:34 UTC |
| 37f5bdf | Thomas B. Mooney | 29 March 2017, 18:54:33 UTC | Update the group_subdirectory to match our new location. When we moved the allocation into place from the shadow allocation, we adopted its group_subdirectory, so be sure to save it into ourself! | 29 March 2017, 18:54:33 UTC |
| 39e836d | Thomas B. Mooney | 29 March 2017, 13:48:51 UTC | Merge pull request #1683 from tmooney/check_for_available_disk_same_way_as_would_get_it Use the same criteria for checking available disk as would to allocate. | 29 March 2017, 13:48:51 UTC |
| c247cf9 | Thomas B. Mooney | 29 March 2017, 13:48:24 UTC | Merge pull request #1689 from tmooney/update_blessed_clinseq Update blessed ClinSeq test build. | 29 March 2017, 13:48:24 UTC |
| 3458ad0 | Thomas B. Mooney | 28 March 2017, 21:35:01 UTC | Update blessed ClinSeq test build. The old Samstat HTML for the tumor RnaSeq result is no longer available. This updates the expected case to not include it. | 28 March 2017, 21:35:01 UTC |
| bc7e1a8 | Jason Walker | 28 March 2017, 18:18:40 UTC | fix syntax error. | 28 March 2017, 18:18:40 UTC |
| 7eb1741 | Jason Walker | 28 March 2017, 18:07:02 UTC | Remove software result attribute from build abandon message. | 28 March 2017, 18:07:02 UTC |
| abdc70d | Jason Walker | 28 March 2017, 17:17:59 UTC | Use an abstract method to get the list of acceptable results to be returned when evaluating storage or software results that require a test name when invalidating a build. | 28 March 2017, 17:17:59 UTC |
| b86d0f9 | Thomas B. Mooney | 28 March 2017, 15:13:38 UTC | Remove "Workflow" from comments and output for version check. | 28 March 2017, 15:13:38 UTC |
| 2239177 | Jason Walker | 28 March 2017, 14:49:28 UTC | Fix spelling error. | 28 March 2017, 14:49:28 UTC |
| 260ad71 | Jason Walker | 24 March 2017, 17:30:23 UTC | initial revision of a command to simplify the setting of test names for SSG builds. | 24 March 2017, 17:30:23 UTC |
| e75b5fb | Jason Walker | 24 March 2017, 17:29:53 UTC | wait to abandon builds until after we have set all test names. | 24 March 2017, 17:29:53 UTC |
| f3f1725 | Susanna Kiwala | 23 March 2017, 20:35:11 UTC | Merge pull request #1685 from susannasiebert/jenkins Fix failing Genome Perl tests on Jenkins | 23 March 2017, 20:35:11 UTC |
| be92719 | Thomas B. Mooney | 23 March 2017, 16:33:18 UTC | Remove concept of "OK" file marking. | 23 March 2017, 16:33:18 UTC |
| c1725d9 | Susanna Kiwala | 22 March 2017, 20:22:30 UTC | Remove test | 23 March 2017, 14:26:46 UTC |
| ad4fc7b | Susanna Kiwala | 22 March 2017, 20:22:04 UTC | Remove failing subtest | 23 March 2017, 14:26:45 UTC |
| cc18a49 | Jason Walker | 19 March 2017, 20:56:11 UTC | Merge pull request #1681 from jasonwalker80/gc2764 Update internal paths. | 19 March 2017, 20:56:11 UTC |
| 4f3cd7b | Jason Walker | 19 March 2017, 20:54:41 UTC | Merge pull request #1674 from jasonwalker80/lsf_resource_htseq_count LSF Resource for HTSeq Count | 19 March 2017, 20:54:41 UTC |
| 5b28004 | Thomas B. Mooney | 15 March 2017, 14:38:19 UTC | Merge pull request #1684 from tmooney/skip_breakdancer_big_test Skip breakdancer CTX unit test. | 15 March 2017, 14:38:19 UTC |
| 2c8c9c8 | Thomas B. Mooney | 14 March 2017, 17:27:53 UTC | The CTX test data was deleted. Breakdancer still gets tested as part of model tests. | 14 March 2017, 17:27:53 UTC |
| c71a008 | Jason Walker | 01 March 2017, 23:09:34 UTC | Update the expected workflow.xml | 14 March 2017, 15:55:28 UTC |
| 8d51722 | Jason Walker | 28 February 2017, 22:51:52 UTC | Move the has_param up into existing section of class definition. | 14 March 2017, 15:48:33 UTC |
| 45f616d | Jason Walker | 28 February 2017, 20:02:46 UTC | initial revision of lsf_resource_htseq_count environment variable | 14 March 2017, 15:48:32 UTC |
| baaeba1 | Jason Walker | 14 March 2017, 15:42:12 UTC | Merge pull request #1677 from jasonwalker80/abandon_sr_builds SR Test Name : Abandon Builds | 14 March 2017, 15:42:12 UTC |
| e7d882a | Jason Walker | 14 March 2017, 15:16:58 UTC | Remove leading slash. | 14 March 2017, 15:16:58 UTC |
