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 |
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 |
17d245b | Thomas B. Mooney | 14 March 2017, 15:06:47 UTC | Use the same criteria for checking available disk as would to allocate. The check for avaialble disk was finding volumes that were not available to be used for allocations later. To prevent this, use the same method that creating an allocation uses. | 14 March 2017, 15:06:47 UTC |
68848c2 | Jason Walker | 14 March 2017, 14:41:45 UTC | Reduce the check for available disk from 20x the allocation to 2x | 14 March 2017, 14:41:45 UTC |
073e8fb | Thomas B. Mooney | 14 March 2017, 13:16:57 UTC | Merge pull request #1679 from tmooney/refalign_coverage_tests_use_test_data Remove old ReferenceCoverage modules; update current one to use test data | 14 March 2017, 13:16:57 UTC |
f45b320 | Jason Walker | 13 March 2017, 20:10:01 UTC | Update manta path to gc2764. | 13 March 2017, 20:10:01 UTC |
1dba419 | Jason Walker | 13 March 2017, 20:06:48 UTC | update paths to ERCC. | 13 March 2017, 20:06:48 UTC |
7620ab8 | Jason Walker | 13 March 2017, 20:00:28 UTC | Update the example value to RepeatMasker output file. | 13 March 2017, 20:00:28 UTC |
9c0156b | Thomas B. Mooney | 09 March 2017, 15:42:45 UTC | Remove disused ReferenceCoverage report. | 09 March 2017, 15:42:45 UTC |