| 22f8aea | Chris Miller | 29 May 2015, 21:25:46 UTC | adding option to omit the quality/depth columns | 29 May 2015, 21:25:46 UTC |
| 31127e0 | Nathaniel Nutter | 29 May 2015, 19:44:09 UTC | Merge pull request #778 from nnutter/lsf allow calculated_default to be used for special lsf properties | 29 May 2015, 19:44:09 UTC |
| df43f83 | Nathaniel Nutter | 29 May 2015, 19:44:03 UTC | Merge pull request #781 from nnutter/logger don't need to use Genome here | 29 May 2015, 19:44:03 UTC |
| 95447e1 | Nathaniel Nutter | 29 May 2015, 19:43:46 UTC | Merge pull request #782 from nnutter/sam misc cleanup in `gmt sam` | 29 May 2015, 19:43:46 UTC |
| 7eed81b | Nathaniel Nutter | 29 May 2015, 19:43:38 UTC | Merge pull request #783 from nnutter/less-perms remove execute permissions from several types of files | 29 May 2015, 19:43:38 UTC |
| edf37a3 | David Morton | 29 May 2015, 17:25:11 UTC | Merge pull request #784 from davidlmorton/workflowbuilder_fixes Workflowbuilder fixes | 29 May 2015, 17:25:11 UTC |
| 072cc83 | dmorton | 28 May 2015, 23:01:10 UTC | Add support for Events to WorkflowBuilder | 28 May 2015, 23:01:10 UTC |
| dbdc090 | dmorton | 28 May 2015, 22:32:28 UTC | Get operationtype attributes from the xml These attributes: - lsf_project - lsf_queue - lsf_resource were only being found (if they existed) on the Command class itself. Therefore when you read in a workflow, and it had specified any of these values, they were ignored. The hash EXPECTED_ATTRIBUTES was changed to a method so we could move the functionality for finding these attributes in the xml up into the base class. | 28 May 2015, 22:32:28 UTC |
| d3a75d2 | Nathaniel Nutter | 28 May 2015, 21:46:28 UTC | remove execute permissions from several types of files Permissions were removed with the following commands: ``` $ find * -name '*.pm' -perm /a+x -exec chmod a-x {} \; $ find * -name '*.png' -perm /a+x -exec chmod a-x {} \; $ find * -name '*.psd' -perm /a+x -exec chmod a-x {} \; $ find * -name '*.js' -perm /a+x -exec chmod a-x {} \; $ find * -name '*.css' -perm /a+x -exec chmod a-x {} \; $ find * -name '*.html' -perm /a+x -exec chmod a-x {} \; $ chmod a-x java/edu/wustl/genome/samtools/GCSamToFastq.java $ find * -name '*.Rnw' -perm /a+x -exec chmod a-x {} \; ``` | 28 May 2015, 21:46:28 UTC |
| 8a3dce3 | Nathaniel Nutter | 28 May 2015, 20:16:37 UTC | default is displayed by UR so no need to add it to doc string | 28 May 2015, 20:16:37 UTC |
| 8120b17 | Nathaniel Nutter | 28 May 2015, 20:16:20 UTC | remove out-of-date comment | 28 May 2015, 20:16:20 UTC |
| ba82d33 | Nathaniel Nutter | 28 May 2015, 20:15:12 UTC | whitespace | 28 May 2015, 20:15:12 UTC |
| 3ff2ba9 | Nathaniel Nutter | 28 May 2015, 20:07:26 UTC | don't need to use Genome here I'm trying to avoid just blindly using Genome which can trigger accidental circular dependencies if packages such as this are used by any of the packages that are loading during `use Genome`. | 28 May 2015, 20:07:26 UTC |
| df14787 | Nathaniel Nutter | 28 May 2015, 19:21:07 UTC | only make class/package in memory | 28 May 2015, 19:21:07 UTC |
| f29ca99 | Nathaniel Nutter | 28 May 2015, 15:52:25 UTC | allow calculated_default to be used for special lsf properties | 28 May 2015, 16:41:26 UTC |
| 849cc9f | David Morton | 28 May 2015, 15:33:28 UTC | Merge pull request #760 from davidlmorton/builds_use_processes Builds use processes | 28 May 2015, 15:33:28 UTC |
| f40fbdf | Nathaniel Nutter | 27 May 2015, 16:49:09 UTC | Merge pull request #770 from nnutter/config-misc convert a couple more values to configuration | 27 May 2015, 16:49:09 UTC |
| c7b165f | Nathaniel Nutter | 27 May 2015, 16:49:00 UTC | Merge pull request #772 from nnutter/master minor changes to `Genome::Sys::make_path()` | 27 May 2015, 16:49:00 UTC |
| e7e509f | Eddie Belter | 27 May 2015, 15:14:11 UTC | Merge pull request #766 from ebelter/inputs-import-pp Utility Inputs: import pp; add test | 27 May 2015, 15:14:11 UTC |
| ec97ba5 | Thomas B. Mooney | 27 May 2015, 13:14:27 UTC | Merge pull request #773 from tmooney/sync_unloads_after_transaction Unload LIMS entities outside of the transaction. | 27 May 2015, 13:14:27 UTC |
| 7b7adce | APipe Tester | 27 May 2015, 13:00:11 UTC | Updated `gmt` tab completion. | 27 May 2015, 13:00:11 UTC |
| cbdebbc | APipe Tester | 27 May 2015, 12:58:12 UTC | Updated `genome` tab completion. | 27 May 2015, 12:58:12 UTC |
| 983911b | APipe Tester | 27 May 2015, 12:51:10 UTC | Updated class browser cache. | 27 May 2015, 12:51:10 UTC |
| f1501da | Nathaniel Nutter | 26 May 2015, 21:23:00 UTC | remove `next` There is nothing wrong with the `next` but I felt I should either add one in the `$rv` condition or remove this one. | 26 May 2015, 21:23:00 UTC |
| 64e5a0b | Nathaniel Nutter | 26 May 2015, 21:15:05 UTC | use `$mkdir_errno`, i.e. the preserved value of `$!` | 26 May 2015, 21:15:05 UTC |
| f3f69b3 | Thomas Mooney | 26 May 2015, 20:42:54 UTC | Unload LIMS entities outside of the transaction. We don't need to bother registering 100s of thousands of "unload" records as changes inside the transaction. Now that transactions only verify changed objects, this will save tons of unnecessary work. | 26 May 2015, 20:42:54 UTC |
| 7805953 | Jason Walker | 26 May 2015, 15:45:49 UTC | Merge pull request #758 from jasonwalker80/speedseq_align_tools Initial implementation of Speedseq alignment tools. | 26 May 2015, 15:45:49 UTC |
| 3261cfb | APipe Tester | 23 May 2015, 12:23:56 UTC | Updated `genome` tab completion. | 23 May 2015, 12:23:56 UTC |
| 9e27f48 | APipe Tester | 23 May 2015, 12:21:24 UTC | Updated class browser cache. | 23 May 2015, 12:21:24 UTC |
| 42f312f | APipe Tester | 22 May 2015, 21:20:32 UTC | updated jenkins submodule to 32f3b54 | 22 May 2015, 21:20:32 UTC |
| dff2e36 | APipe Tester | 22 May 2015, 21:20:04 UTC | updated ur submodule to aa0b831 | 22 May 2015, 21:20:04 UTC |
| 9297e37 | Nathaniel Nutter | 22 May 2015, 21:15:20 UTC | Merge pull request #763 from nnutter/logger remove duplication in Genome::Role::Logger | 22 May 2015, 21:15:20 UTC |
| 19ad18f | Nathaniel Nutter | 22 May 2015, 21:14:46 UTC | Merge pull request #771 from nnutter/perm update broken test | 22 May 2015, 21:14:46 UTC |
| 0bec48f | Nathaniel Nutter | 22 May 2015, 18:20:23 UTC | update broken test Test was broken due to 'sys_umask' configuration value changing from '0002' to '0007'. Test is updated to test that write permissions are removed not to test specific mode. | 22 May 2015, 18:20:23 UTC |
| 8d96fa5 | Nathaniel Nutter | 21 May 2015, 15:52:37 UTC | add usage_log_db_username and usage_log_db_password to config | 22 May 2015, 17:37:40 UTC |
| d3426e1 | Nathaniel Nutter | 20 May 2015, 18:40:07 UTC | convert MAX_SYSLOG_MSG_LEN to Genome::Config | 22 May 2015, 17:13:39 UTC |
| 3af6367 | Nathaniel Nutter | 22 May 2015, 16:25:34 UTC | empty commit to add changelog CHANGELOG: Almost all environment variables used to configure Genome have been changed. If you have any scripts, etc. outside of the Genome Git repo then you'll need to update them to use the new Config API. In addition to the documentation in the source code I've also started a [Confluence page](https://confluence.gsc.wustl.edu/display/APIPE/Configuration+Recipes). | 22 May 2015, 16:25:34 UTC |
| 4cb4a3c | Nathaniel Nutter | 22 May 2015, 16:23:50 UTC | Merge pull request #755 from nnutter/config change `env` prefixes to XGENOME_ | 22 May 2015, 16:23:50 UTC |
| 9e7ce4e | Nathaniel Nutter | 22 May 2015, 16:16:27 UTC | Merge pull request #769 from nnutter/master delete allocation rollback test | 22 May 2015, 16:16:27 UTC |
| ee3da30 | APipe Tester | 22 May 2015, 12:25:56 UTC | Updated `gmt` tab completion. | 22 May 2015, 12:25:56 UTC |
| dedf2d9 | APipe Tester | 22 May 2015, 12:24:49 UTC | Updated `genome` tab completion. | 22 May 2015, 12:24:49 UTC |
| 8856ff4 | APipe Tester | 22 May 2015, 12:21:58 UTC | Updated class browser cache. | 22 May 2015, 12:21:58 UTC |
| 4cf32f2 | APipe Tester | 22 May 2015, 03:50:36 UTC | updated jenkins submodule to b8de860 | 22 May 2015, 03:50:36 UTC |
| 32f0aca | APipe Tester | 22 May 2015, 03:50:23 UTC | updated ur submodule to cd43acc | 22 May 2015, 03:50:23 UTC |
| f7c3536 | Thomas B. Mooney | 21 May 2015, 20:44:00 UTC | Merge pull request #768 from tmooney/remove_gmt_gatk_germlinesnv Remove old `gmt gatk germline-snv` tool. | 21 May 2015, 20:44:00 UTC |
| cd2b76e | Thomas B. Mooney | 21 May 2015, 19:55:55 UTC | Merge pull request #764 from tmooney/model_summary_max_fail_count Model Summary: Allow specification of max fail count | 21 May 2015, 19:55:55 UTC |
| 0d2263f | dmorton | 21 May 2015, 19:53:57 UTC | Save 'workflow lsf job_id' as not on Processes This allows build->stop to look up the lsf job_id of the workflow job in order to stop it. | 21 May 2015, 19:53:57 UTC |
| bec90fa | Nathaniel Nutter | 21 May 2015, 19:37:43 UTC | Merge remote-tracking branch 'origin/master' into config Not a conflict but due to merge I moved `etc/genome/gmt_gene_predictor_snap_lsf.yaml` to `etc/genome/spec/`. | 21 May 2015, 19:38:31 UTC |
| fa4bc69 | Nathaniel Nutter | 21 May 2015, 19:30:29 UTC | delete allocation rollback test This test isn't very clear about what it's testing and I feel like making it clearly would too strongly couple it to implementation details and UR tests the actual underlying cause of this problem so I think it's fair to just delete this test. The motivation to delete it is that getting an iterator for all allocations against the production database is extremely expensive. | 21 May 2015, 19:30:29 UTC |
| 0e138ef | Thomas Mooney | 21 May 2015, 18:59:46 UTC | Remove old `gmt gatk germline-snv` tool. | 21 May 2015, 18:59:46 UTC |
| 6fbfb8b | Allison Penner Regier | 21 May 2015, 18:18:13 UTC | Merge pull request #767 from apregier/bedpe Expose gmt bedpe on the command line | 21 May 2015, 18:18:13 UTC |
| e19d894 | Nathaniel Nutter | 21 May 2015, 15:42:40 UTC | Merge pull request #762 from nnutter/genomex convert GENOMEX_GMT_GENE_PREDICTOR_SNAP_LSF to Genome::Config | 21 May 2015, 15:42:40 UTC |
| 4cdf36b | Thomas B. Mooney | 21 May 2015, 15:39:48 UTC | Merge pull request #757 from tmooney/remove_alert_from_disk_group_available_space_report Remove alert from `genome disk group available-space` report | 21 May 2015, 15:39:48 UTC |
| 39b49d4 | apregier | 21 May 2015, 15:02:34 UTC | Remove unneeded self | 21 May 2015, 15:02:34 UTC |
| a871ae1 | apregier | 21 May 2015, 15:02:06 UTC | Use modern base class for command | 21 May 2015, 15:02:06 UTC |
| f9d6f66 | apregier | 20 May 2015, 21:09:20 UTC | Expose gmt bedpe on the command line | 20 May 2015, 21:09:20 UTC |
| 2566fbd | dmorton | 20 May 2015, 20:37:27 UTC | Mock GMB::start so test can pass This test was relying on some sketchy behavior where GMB::start would pretend to succeed if UR_DBI_NO_COMMIT was turned on. The start command now returns undef if NO_COMMIT is turned on, which is more reasonable, but made this test fail. | 20 May 2015, 20:37:27 UTC |
| f7004d1 | Eddie Belter | 20 May 2015, 20:26:55 UTC | Utility Inputs: import pp; add test | 20 May 2015, 20:26:55 UTC |
| c8d47a7 | APipe Tester | 20 May 2015, 18:54:48 UTC | updated ur submodule to 94c616c | 20 May 2015, 18:54:48 UTC |
| 500a9e8 | Thomas Mooney | 20 May 2015, 15:01:54 UTC | Don't bother to reverse now that we look at all builds. | 20 May 2015, 18:13:25 UTC |
| 1a7bfa3 | Thomas Mooney | 20 May 2015, 15:01:07 UTC | Allow undef to mean "any amount is okay". | 20 May 2015, 18:13:24 UTC |
| 6d80efe | Thomas Mooney | 20 May 2015, 14:57:10 UTC | Make max_fail_count a command-line option. | 20 May 2015, 18:13:24 UTC |
| ccd797e | Thomas Mooney | 20 May 2015, 14:56:21 UTC | Count all failures for the model, not just the most recent. | 20 May 2015, 18:13:23 UTC |
| 568eb53 | Thomas Mooney | 20 May 2015, 14:44:40 UTC | "too many" instead of "to many". | 20 May 2015, 18:13:23 UTC |
| 6fd8117 | dmorton | 20 May 2015, 17:58:48 UTC | Do not launch process if NO_COMMIT is turned on. CHANGELOG Flow will now be used when doing 'genome model build start' unless it is explicitly turned off (WF_USE_FLOW=0). Also, with this change, $build->the_master_event->lsf_job_id is no longer filled in, so scripts that rely on it will need to be updated. | 20 May 2015, 17:58:48 UTC |
| d29e76a | Thomas Mooney | 20 May 2015, 17:52:46 UTC | Exit non-zero if there are disk groups low on space. | 20 May 2015, 17:57:41 UTC |
| 641d2e3 | Eddie Belter | 20 May 2015, 16:30:21 UTC | Merge pull request #761 from ebelter/site-tgi Sync: LIMS organism classes names are optional | 20 May 2015, 16:30:21 UTC |
| 1db0ab2 | Gue Su Chang | 20 May 2015, 14:51:07 UTC | Merge pull request #756 from gschang/master Minor bug fixation in R | 20 May 2015, 14:51:07 UTC |
| 1486ed8 | Anthony Brummett | 20 May 2015, 14:32:46 UTC | Merge pull request #747 from brummett/create_symlink Make Genome::Sys->create_symlink() idempotent | 20 May 2015, 14:32:46 UTC |
| b245abb | APipe Tester | 20 May 2015, 12:23:42 UTC | Updated `genome` tab completion. | 20 May 2015, 12:23:42 UTC |
| 2005883 | APipe Tester | 20 May 2015, 12:21:21 UTC | Updated class browser cache. | 20 May 2015, 12:21:21 UTC |
| 9a7b89d | Nathaniel Nutter | 19 May 2015, 23:50:04 UTC | make Genome::Role::Logger inherit from Genome::Logger | 20 May 2015, 05:38:46 UTC |
| 28267ce | Nathaniel Nutter | 19 May 2015, 23:48:55 UTC | reorder class properties | 20 May 2015, 05:38:45 UTC |
| d2ba7aa | Nathaniel Nutter | 19 May 2015, 23:42:48 UTC | convert package into a class while mimicking the package API | 20 May 2015, 05:38:44 UTC |
| b40a7ad | Eddie Belter | 19 May 2015, 23:38:42 UTC | Merge pull request #759 from ebelter/sync-usage Update the disk volume sync usage command | 19 May 2015, 23:38:42 UTC |
| af0129a | Nathaniel Nutter | 19 May 2015, 23:24:43 UTC | memoize by hand | 19 May 2015, 23:29:14 UTC |
| 4d608ff | Nathaniel Nutter | 19 May 2015, 23:20:07 UTC | add color screen support byt reusing Genome::Logger->screen_to_add() | 19 May 2015, 23:29:12 UTC |
| c2e1aac | Nathaniel Nutter | 19 May 2015, 23:17:00 UTC | extract method: screen_to_add | 19 May 2015, 23:29:11 UTC |
| fdb4a23 | Nathaniel Nutter | 19 May 2015, 23:12:47 UTC | bring Genome::Role::Logger into parity with Genome::Logger Genome::Role::Logger was missing the `*f`, `croak`, `fatal`, and `fatalf` methods. | 19 May 2015, 23:29:09 UTC |
| 7e8476d | Nathaniel Nutter | 19 May 2015, 23:01:04 UTC | get log_levels from Log::Dispatch | 19 May 2015, 23:29:08 UTC |
| 0133dcf | Nathaniel Nutter | 19 May 2015, 23:00:51 UTC | enable strict/warnings | 19 May 2015, 23:29:07 UTC |
| 5a186e5 | Eddie Belter | 19 May 2015, 23:16:53 UTC | Merge pull request #754 from ebelter/instdata-import-process InstData Import: make the batch importer [formerly known as Manager, now called launch] a genome process. | 19 May 2015, 23:16:53 UTC |
| fb32104 | Nathaniel Nutter | 19 May 2015, 22:53:29 UTC | convert GENOMEX_GMT_GENE_PREDICTOR_SNAP_LSF to Genome::Config | 19 May 2015, 22:53:29 UTC |
| e9b35bf | dmorton | 19 May 2015, 22:50:35 UTC | Ensure transaction commit was successful | 19 May 2015, 22:52:33 UTC |
| 2c22745 | dmorton | 19 May 2015, 22:48:54 UTC | Return value of build->start instead of dying This allows the build to be created as 'unstartable' with a note telling why it was unstartable. | 19 May 2015, 22:48:54 UTC |
| 682f285 | Eddie Belter | 19 May 2015, 21:24:55 UTC | Sync: LIMS organism classes names are optional | 19 May 2015, 21:24:55 UTC |
| 32af909 | Eddie Belter | 19 May 2015, 20:47:23 UTC | PR suggestions | 19 May 2015, 20:47:23 UTC |
| f201ea0 | Nathaniel Nutter | 19 May 2015, 20:47:07 UTC | Merge pull request #752 from nnutter/user validate values to hash | 19 May 2015, 20:47:07 UTC |
| 0bf9acb | Nathaniel Nutter | 19 May 2015, 20:46:52 UTC | Merge pull request #751 from nnutter/archivable avoid side effects if an allocation is rolled back | 19 May 2015, 20:46:52 UTC |
| 3ee2c46 | Nathaniel Nutter | 19 May 2015, 20:46:41 UTC | Merge pull request #750 from nnutter/start acquire build_requested lock before creating builds to start | 19 May 2015, 20:46:41 UTC |
| bcca514 | Eddie Belter | 19 May 2015, 20:15:50 UTC | Update the disk volume sync usage command | 19 May 2015, 20:15:50 UTC |
| c6d50a9 | dmorton | 19 May 2015, 18:22:07 UTC | Fix typo in debug message | 19 May 2015, 18:22:07 UTC |
| ddfad42 | dmorton | 19 May 2015, 15:23:23 UTC | Make Builds use a Genome::Process when run This should be invisible to users, except for a few debug lines that get emitted when you run 'genome model build start'. * Logs still go in the usual place (build's data directory). * Workflow job has same lsf_project name. * Workflow has the same name (meaning genome model build view works as expected). * Emails are still sent when the build starts, fails or succeeds. Command 'genome model services build run' is left only because job_dispatch=inline is used in various tests. Since PTero will not support this, we will eventually have to update all places that utilize that feature. | 19 May 2015, 18:21:59 UTC |
| 4836a35 | APipe Tester | 19 May 2015, 18:02:52 UTC | updated workflow submodule to 701271d | 19 May 2015, 18:02:52 UTC |
| b802725 | Jason Walker | 19 May 2015, 16:40:59 UTC | Initial implementation of Speedseq alignment tools. | 19 May 2015, 16:40:59 UTC |
| 2f35b41 | dmorton | 19 May 2015, 14:53:50 UTC | Die if build->start returns undef This makes sure you don't display to the user that the build was successfully started when it wasn't. This showed up when there was a compilation error in something that was used first inside build->start somewhere. | 19 May 2015, 14:53:50 UTC |
| d7baccc | dmorton | 19 May 2015, 02:27:25 UTC | Allow lsf_project to be different from workflow_name This is going to be used when we have a Genome::Model::Build::Process that overrides lsf_project_name to be 'build12345' | 19 May 2015, 02:27:25 UTC |
| 4445ba3 | dmorton | 19 May 2015, 02:25:28 UTC | Only add analysis_project param if not undef Without this, models that are not part of an analysis project end up emitting warnings about an odd number of arguments to a boolean expression. | 19 May 2015, 02:25:28 UTC |
| 12cd9cf | Thomas Mooney | 18 May 2015, 22:35:53 UTC | Remove "send_alert" and "alert_recipients" options. Sending an e-mail will be the responsibility of the system running this report. | 18 May 2015, 22:35:53 UTC |
| 5580649 | Thomas Mooney | 18 May 2015, 22:34:31 UTC | Whitespace. | 18 May 2015, 22:34:31 UTC |
