| 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 |
| d0551d8 | Thomas B. Mooney | 09 March 2017, 15:42:10 UTC | Remove unfinished experimental view from 2010. | 09 March 2017, 15:42:10 UTC |
| 90f9f4c | Thomas B. Mooney | 09 March 2017, 15:32:58 UTC | Use test data instead of a live build in test. | 09 March 2017, 15:32:58 UTC |
| c306c1a | Susanna Kiwala | 08 March 2017, 16:05:49 UTC | Merge pull request #1678 from susannasiebert/rt112130 Add "GMAF=" before value when parsing CAFs | 08 March 2017, 16:05:49 UTC |
| d5e069e | Susanna Kiwala | 07 March 2017, 16:04:27 UTC | Some code cleanup | 07 March 2017, 16:04:27 UTC |
| 7b944d3 | Susanna Kiwala | 07 March 2017, 16:04:07 UTC | Add GMAF= string before the value when adding CAF values | 07 March 2017, 16:04:07 UTC |
| 86d61c6 | Susanna Kiwala | 07 March 2017, 15:09:44 UTC | Set $GMAF to empty if we don't have a CAF value | 07 March 2017, 15:09:44 UTC |
| 39efb55 | APipe Tester | 06 March 2017, 17:04:54 UTC | updated graphite submodule to 705afc6 | 06 March 2017, 17:04:54 UTC |
| 664f781 | APipe Tester | 06 March 2017, 17:04:37 UTC | updated jenkins submodule to 80b7ba2 | 06 March 2017, 17:04:37 UTC |
| ab82550 | Thomas B. Mooney | 06 March 2017, 16:13:05 UTC | Merge pull request #1663 from tmooney/guiven_given Spelling: s/guiven/given/. | 06 March 2017, 16:13:05 UTC |
| bc5c589 | Thomas B. Mooney | 06 March 2017, 16:12:47 UTC | Merge pull request #1675 from tmooney/fs_local_cache_should_be_a_directory For the local cache to be usable, it must be a directory. | 06 March 2017, 16:12:47 UTC |
| d481e9c | Thomas B. Mooney | 06 March 2017, 14:29:08 UTC | Merge pull request #1666 from tmooney/workflow_builder_sorts_xml_attribute_keys Sort attribute keys for Operation XML. | 06 March 2017, 14:29:08 UTC |
| 81d567e | Jason Walker | 03 March 2017, 15:29:00 UTC | Option to abandon builds when setting software result test name. | 03 March 2017, 15:29:00 UTC |
| 3aa42a2 | Thomas B. Mooney | 01 March 2017, 19:20:08 UTC | For the local cache to be usable, it must be a directory. | 01 March 2017, 19:20:08 UTC |
| e04e1f7 | Kilannin Krysiak | 01 March 2017, 06:30:20 UTC | Merge pull request #1661 from kkrysiak/master Fixing problems with rsID annotation code | 01 March 2017, 06:30:20 UTC |
| 2b1594d | Feiyu Du | 28 February 2017, 19:04:21 UTC | Merge pull request #1671 from dufeiyu/error_rate_bug Fix an error_rate bug | 28 February 2017, 19:04:21 UTC |
| 65b8448 | Thomas B. Mooney | 28 February 2017, 18:09:42 UTC | Merge pull request #1664 from tmooney/fix_perl522_compile_errors Fix perl 5.22 compile errors | 28 February 2017, 18:09:42 UTC |
| 0987ab9 | Thomas B. Mooney | 28 February 2017, 18:08:29 UTC | Merge pull request #1672 from tmooney/simpler_queue_validation_in_sys_lsf_bsub Use simpler means of validating LSF queue. | 28 February 2017, 18:08:29 UTC |
| a3b039e | Jason Walker | 28 February 2017, 17:22:25 UTC | Merge pull request #1633 from jasonwalker80/sambamba_tool_interface Base Tool Class and Sambamba sort | 28 February 2017, 17:22:25 UTC |
| 169b278 | Thomas B. Mooney | 28 February 2017, 16:51:50 UTC | Use simpler means of validating LSF queue. Idea borrowed from Genome::ConfigValidator::LSFQueue. That module cannot "use Genome;" so can't be changed to refer to this version instead. | 28 February 2017, 16:51:50 UTC |
| b15a6fc | Thomas B. Mooney | 28 February 2017, 13:51:38 UTC | Merge pull request #1670 from tmooney/disable_tests_without_test_data Disable tests that relied on now-deleted production data. | 28 February 2017, 13:51:38 UTC |
| bb730b5 | Thomas B. Mooney | 28 February 2017, 13:51:29 UTC | Merge pull request #1669 from tmooney/small_rna_test_files_move Use files in test data directory. | 28 February 2017, 13:51:29 UTC |
| 1d94521 | Thomas B. Mooney | 23 February 2017, 20:45:28 UTC | Disable tests that relied on now-deleted production data. | 23 February 2017, 22:22:48 UTC |
| b36624e | Feiyu Du | 23 February 2017, 20:58:04 UTC | update the unit test | 23 February 2017, 20:58:04 UTC |
| 82eac40 | Feiyu Du | 23 February 2017, 20:44:24 UTC | is rate, not percentage | 23 February 2017, 20:44:24 UTC |
| 98a46af | Feiyu Du | 23 February 2017, 20:41:35 UTC | correct the variable names | 23 February 2017, 20:41:35 UTC |
| 956ddb1 | Thomas B. Mooney | 23 February 2017, 20:29:19 UTC | Use files in test data directory. | 23 February 2017, 20:29:19 UTC |
| 4bb277b | Thomas B. Mooney | 23 February 2017, 17:47:31 UTC | Merge pull request #1667 from tmooney/remove_wublast_tree Remove GMT WuBlast tree and dependent tools. | 23 February 2017, 17:47:31 UTC |
| 23ba70d | Jason Walker | 23 February 2017, 17:46:41 UTC | Merge pull request #1668 from jasonwalker80/disk_usage AnP Disk Usage | 23 February 2017, 17:46:41 UTC |
| 0b00556 | Jason Walker | 23 February 2017, 16:48:32 UTC | spellcheck | 23 February 2017, 16:48:32 UTC |
| d7ae7a3 | Jason Walker | 23 February 2017, 14:54:01 UTC | note about running builds in docs. | 23 February 2017, 14:54:01 UTC |
| 27be859 | Jason Walker | 23 February 2017, 14:51:54 UTC | Improve documentation and stipulations. | 23 February 2017, 14:51:54 UTC |
| 9ae0821 | Jason Walker | 23 February 2017, 14:46:21 UTC | Remove commented lines. | 23 February 2017, 14:46:21 UTC |
| f6efe41 | Jason Walker | 22 February 2017, 22:31:44 UTC | Remove status messages. loop all builds. hash ref syntax fix. | 22 February 2017, 22:31:44 UTC |
| 85b0089 | Jason Walker | 22 February 2017, 18:10:31 UTC | hash typo: curly for square brackets. | 22 February 2017, 18:10:31 UTC |
| 6ab01e4 | Jason Walker | 22 February 2017, 17:50:38 UTC | Only look at last succeeded build. Avoid divide my zero errors. Status messages. | 22 February 2017, 17:50:38 UTC |
| 830696c | Jason Walker | 20 February 2017, 22:09:43 UTC | Remove unnecessary import. | 20 February 2017, 22:09:43 UTC |
| 1fb3550 | Jason Walker | 20 February 2017, 22:02:52 UTC | Use separated value writer. | 20 February 2017, 22:02:52 UTC |
| f395285 | Jason Walker | 20 February 2017, 21:51:20 UTC | improve docs. | 20 February 2017, 21:51:20 UTC |
| d935bfa | Jason Walker | 20 February 2017, 21:36:59 UTC | Initial revision of command to report disk usage. WIP. | 20 February 2017, 21:36:59 UTC |
| b125b13 | Thomas B. Mooney | 20 February 2017, 17:53:30 UTC | Remove GMT WuBlast tree and dependent tools. The installation of WUBLAST is changing, so stop supporting it here. | 20 February 2017, 17:53:30 UTC |
| b1aaf6b | Thomas B. Mooney | 16 February 2017, 23:34:20 UTC | Sort attribute keys for Operation XML. Otherwise the order may vary, making the tests subject to failure depending on the environment. | 20 February 2017, 16:03:43 UTC |
| fb946ef | Thomas B. Mooney | 16 February 2017, 23:13:05 UTC | Bug: tempdir is not a method. | 16 February 2017, 23:13:05 UTC |
| 923b528 | Thomas B. Mooney | 16 February 2017, 23:05:27 UTC | Fix useless use of string in void context. This one's an issue in older Perls, too :) | 16 February 2017, 23:05:27 UTC |
| a362c52 | Thomas B. Mooney | 16 February 2017, 19:35:07 UTC | Ensure no-commit is set in tests to avoid creating production locks. | 16 February 2017, 19:35:07 UTC |
| 246052b | Thomas B. Mooney | 16 February 2017, 19:27:49 UTC | Tests should "use above". | 16 February 2017, 19:27:49 UTC |
| 8e57964 | Thomas B. Mooney | 16 February 2017, 19:16:48 UTC | Log::Dispatch moved list of levels in version 2.54. | 16 February 2017, 19:21:29 UTC |
| 31968b6 | Thomas B. Mooney | 16 February 2017, 18:23:56 UTC | Merge pull request #1662 from tmooney/stop_validating_disk_groups Stop Validating Disk Groups | 16 February 2017, 18:23:56 UTC |
| f62bcd2 | Thomas B. Mooney | 16 February 2017, 16:57:29 UTC | Only check if Scalar::Util::looks_like_number returned true or false. Different versions return 0 or '', so don't worry which it is. | 16 February 2017, 16:57:29 UTC |
| 5de605a | Thomas B. Mooney | 16 February 2017, 16:38:12 UTC | The order of the help text is not guaranteed. | 16 February 2017, 16:38:12 UTC |
| d0429d9 | Thomas B. Mooney | 16 February 2017, 16:37:48 UTC | Newer Carp::croak includes the ".". | 16 February 2017, 16:37:48 UTC |
| a412463 | Thomas B. Mooney | 15 February 2017, 20:27:06 UTC | In newer Perls, defined(@array) is disallowed. | 15 February 2017, 20:27:06 UTC |
| acfded9 | Thomas B. Mooney | 15 February 2017, 20:25:52 UTC | In newer Perls qw() doesn't make something a list. | 15 February 2017, 20:25:52 UTC |
| 0a5a716 | Thomas B. Mooney | 15 February 2017, 18:21:12 UTC | Spelling: s/guiven/given/. | 15 February 2017, 18:21:12 UTC |
| bd41e55 | Thomas B. Mooney | 14 February 2017, 21:48:40 UTC | Merge pull request #1660 from tmooney/remove_gsc_var Remove remaining references to `/gsc/var/`. | 14 February 2017, 21:48:40 UTC |
| 0e5b674 | Thomas B. Mooney | 14 February 2017, 21:39:03 UTC | Don't fail if a particular disk group configuration isn't set. | 14 February 2017, 21:39:03 UTC |
| 4805019 | Thomas B. Mooney | 14 February 2017, 21:38:36 UTC | Don't validate disk groups on get/create. | 14 February 2017, 21:38:36 UTC |
| 7e3e415 | Kilannin Krysiak | 13 February 2017, 23:38:22 UTC | Fixing header bug that led to repeat headers being printed | 13 February 2017, 23:38:22 UTC |
| a053d9c | Kilannin Krysiak | 09 February 2017, 00:10:56 UTC | Added code to disallow the annotation of indels since this code was not designed to handle them | 09 February 2017, 00:10:56 UTC |
