| 2393868 | Thomas B. Mooney | 21 February 2022, 21:40:24 UTC | Merge pull request #2056 from tmooney/requeue_command_enumerates_options Fix enumeration of valid values for --action parameter. | 21 February 2022, 21:40:24 UTC |
| 49e361e | Thomas B. Mooney | 16 February 2022, 21:19:24 UTC | Fix enumeration of valid values for --action parameter. They're actually defined on the model class and not the derived build class. Also, a little explanation for "0" seems helpful! | 16 February 2022, 21:19:24 UTC |
| f2a49d3 | Thomas B. Mooney | 03 February 2022, 21:23:16 UTC | Merge pull request #2055 from tmooney/update_tab_completion_and_class_browser_cache Update repo version of class browser cache and tab-completion spec. | 03 February 2022, 21:23:16 UTC |
| 7faeec2 | Thomas B. Mooney | 03 February 2022, 20:22:05 UTC | Update repo version of class browser cache and tab-completion spec. We already update these routinely as part of the snapshot process, but the job that was keeping the repo updated has been disabled for awhile. This is just prep for turning it back on. | 03 February 2022, 20:22:05 UTC |
| 152a147 | Thomas B. Mooney | 02 February 2022, 23:14:23 UTC | Merge pull request #2054 from tmooney/different_name_for_prodbuilder Rename "prod-builder" env option to "automated". | 02 February 2022, 23:14:23 UTC |
| 24ca45e | Thomas B. Mooney | 26 January 2022, 22:06:39 UTC | Rename "prod-builder" env option to "automated". Since "prod-builder" isn't really descriptive and is also the name of the default runner user, it was suggested we use a neutral term instead, especially for those circumstances where a different runner is being used. | 26 January 2022, 22:06:39 UTC |
| ec3edd5 | Thomas B. Mooney | 26 January 2022, 22:02:15 UTC | Merge pull request #2053 from tmooney/make_abandonpriorstatus_test_consistent_with_command Don't use "last_complete_build" in this test. | 26 January 2022, 22:02:15 UTC |
| ff09e31 | Thomas B. Mooney | 26 January 2022, 21:18:30 UTC | Don't use "last_complete_build" in this test. Our command uses the creation date to determine which build is most recent for purposes of abandoning prior attempts. However if an older build completed after a later build, then our test would be grabbing the wrong one for being "saved". (Instead let's keep tabs on the last one we made, since it should be the most-recently-created and thus the one to be saved. | 26 January 2022, 21:39:43 UTC |
| f654dc0 | Thomas B. Mooney | 26 January 2022, 19:12:37 UTC | Merge pull request #2052 from tmooney/tolerate_multiple_succeeded_cromwell_workflows If there are multiple Cromwell workflows, use the most recent. | 26 January 2022, 19:12:37 UTC |
| 97c6d99 | Thomas B. Mooney | 26 January 2022, 18:01:51 UTC | If there are multiple Cromwell workflows, use the most recent. If a build fails after the Cromwell workflow has succeeded, then a build `restart` may create a new workflow in which case there may be multiple succeeded workflows. Instead of crashing, we'll trust that the most recent one is the one we care about. | 26 January 2022, 18:01:51 UTC |
| 7066a6a | Thomas B. Mooney | 25 January 2022, 21:41:22 UTC | Merge pull request #2051 from tmooney/abandon_prior_builds_test_unique_timestamps For test stability, have each build created at a different time. | 25 January 2022, 21:41:22 UTC |
| 99681a6 | Thomas B. Mooney | 25 January 2022, 20:25:46 UTC | For test stability, have each build created at a different time. It is true that some of our commands will fail if multiple builds were created within the same second. There's locking in place that prevents that from happening in practice, so this test was failing for an edge condition we don't normall encounter. (If we truly have multiple simultaneous builds in the same status, picking one arbitrarily to execute is the "right" behavior here, anyway.) | 25 January 2022, 20:25:46 UTC |
| dc4c22f | John Maruska | 25 January 2022, 17:47:01 UTC | Merge pull request #2048 from johnmaruska/gcp-separate-buckets GCP subnet | 25 January 2022, 17:47:01 UTC |
| 70c0680 | Thomas B. Mooney | 24 January 2022, 22:43:31 UTC | Merge pull request #2050 from tmooney/dont_worry_about_allocation_size_for_cwl_run_test Don't worry about if we have space for allocations in this test. | 24 January 2022, 22:43:31 UTC |
| 063c375 | Thomas B. Mooney | 24 January 2022, 22:24:39 UTC | Don't worry about if we have space for allocations in this test. Currently CWL scratch directories reserve 50GB, but the test uses local temp and doesn't require nigh that much space anyway! | 24 January 2022, 22:26:30 UTC |
| b09344e | Thomas B. Mooney | 24 January 2022, 20:49:29 UTC | Merge pull request #2049 from tmooney/tiebreaker_for_model_input_sort Add a tiebreaker in the sorting algorithm. | 24 January 2022, 20:49:29 UTC |
| cadad49 | Thomas B. Mooney | 24 January 2022, 20:25:37 UTC | Add a tiebreaker in the sorting algorithm. If perchance both items have identical timestamps, use ID as a tiebreaker so the ordering is still consistent between them. | 24 January 2022, 20:25:37 UTC |
| dfa677e | Maruska | 21 January 2022, 17:43:43 UTC | Bump tag version to reverted cloud-workflows | 21 January 2022, 17:43:43 UTC |
| 8910335 | Maruska | 21 January 2022, 17:28:35 UTC | How'd this get here? | 21 January 2022, 17:28:35 UTC |
| b15735b | Maruska | 21 January 2022, 17:27:11 UTC | Revert separate buckets, we decided against this | 21 January 2022, 17:27:11 UTC |
| cb115b2 | Thomas B. Mooney | 20 January 2022, 21:45:39 UTC | Merge pull request #2047 from tmooney/straggling_test_fixes Some straggling test fixes | 20 January 2022, 21:45:39 UTC |
| e550e63 | Thomas B. Mooney | 20 January 2022, 18:13:23 UTC | Disable MethRatio test. Version 2.6 was in someone's homedir and we don't really use this any more, so it has been decided to disable this test rather than switch it to the other version. | 20 January 2022, 18:13:23 UTC |
| 0f9d48e | John Maruska | 20 January 2022, 16:32:55 UTC | Merge branch 'master' of https://github.com/genome/genome into gcp-separate-buckets | 20 January 2022, 16:32:55 UTC |
| cee852a | John Maruska | 20 January 2022, 16:31:23 UTC | Bump cloudize-workflow tag | 20 January 2022, 16:31:23 UTC |
| ee9d5a9 | John Maruska | 20 January 2022, 16:21:43 UTC | Merge branch 'gcp-specify-subnet' into gcp-separate-buckets | 20 January 2022, 16:21:43 UTC |
| a1b7570 | Thomas B. Mooney | 20 January 2022, 05:01:09 UTC | Check the directory we really plan to write to. No need to have write access to the input directory if they gave us an output one. | 20 January 2022, 05:01:09 UTC |
| b245bae | John Maruska | 19 January 2022, 23:07:39 UTC | Split cromwell_gcp_bucket into inputs and executions buckets This is related to work in griffith-lab/cloud-workflows repo. The intention behind splitting buckets is to apply separate lifecycle rules so input files stick around but execution files are deleted after 30 days | 19 January 2022, 23:07:39 UTC |
| 2319304 | Thomas B. Mooney | 18 January 2022, 23:14:43 UTC | Merge pull request #2046 from tmooney/bam_size_for_perlane_tests Claim that .t test per-lane BAMs are all 1024KB. | 18 January 2022, 23:14:43 UTC |
| 217eed7 | Thomas B. Mooney | 18 January 2022, 21:41:50 UTC | Claim that .t test per-lane BAMs are all 1024KB. The tests try to allocate space when revivifying the per-lane BAMs. When the bam size is unknown, the default size request is 100,000,000KB. When temp on the host running the test has less than this amount of space free, the test can fail. (If temp has less than 1024KB free, we're probably going to have other trouble, anyway!) | 18 January 2022, 21:41:50 UTC |
| 85c6150 | Thomas B. Mooney | 18 January 2022, 20:04:47 UTC | Merge pull request #2045 from tmooney/no_hardcoding_java Use the Genome::Sys method to get the java executable path. | 18 January 2022, 20:04:47 UTC |
| a85d7c7 | Thomas B. Mooney | 18 January 2022, 18:33:45 UTC | Use the Genome::Sys method to get the java executable path. There is no `/gapp` on the new cluster, so use our config instead. | 18 January 2022, 18:33:45 UTC |
| 8e0e55c | Thomas B. Mooney | 18 January 2022, 15:24:58 UTC | Merge pull request #2043 from tmooney/filetest_fixes Consistently use Genome::Sys to test readability of files. | 18 January 2022, 15:24:58 UTC |
| a5255b6 | Thomas B. Mooney | 18 January 2022, 15:24:34 UTC | Merge pull request #2044 from tmooney/no_blade_name Revise check for matching hosts. | 18 January 2022, 15:24:34 UTC |
| 1324826 | Thomas B. Mooney | 13 January 2022, 20:49:47 UTC | Revise check for matching hosts. We don't care if they're "blades". In fact, we only care that the command tries to return any results at all, so check for the header row! When there aren't any hosts, it'll return this instead: Not enough host(s) currently eligible So looking for the line to start with HOST is good enough. | 13 January 2022, 20:49:47 UTC |
| d227aee | Thomas B. Mooney | 13 January 2022, 20:14:27 UTC | Consistently use Genome::Sys to test readability of files. To handle non-POSIX permissions we need to not rely on the default behavior of -r. | 13 January 2022, 20:14:27 UTC |
| 247509a | Thomas B. Mooney | 12 January 2022, 22:49:59 UTC | Merge pull request #2042 from tmooney/absolute_url_for_db_server Use fully qualified domain name for database server. | 12 January 2022, 22:49:59 UTC |
| 3c3ad2c | Thomas B. Mooney | 12 January 2022, 20:11:09 UTC | Use fully qualified domain name for database server. Some hosts don't have a friendly search path configured, so this is a little more certain to work as expected. | 12 January 2022, 20:11:09 UTC |
| c355ce5 | Thomas B. Mooney | 11 January 2022, 22:23:04 UTC | Merge pull request #2041 from tmooney/only_set_tmp_basedir_if_writable Only modify tmp basedir if new location is writable. | 11 January 2022, 22:23:04 UTC |
| 7127671 | Thomas B. Mooney | 11 January 2022, 20:03:51 UTC | Only modify tmp basedir if new location is writable. For some reason, some servers we're using create a doubly-nested LSF tmpdir structure, and the inner one is r/w only by root. In this case they're already giving us the first level as $ENV{TMPDIR} so we can just trust it anyway. This code is still useful on our older cluster, though, so not just removing it outright yet. | 11 January 2022, 20:03:51 UTC |
| 1dee886 | John Maruska | 10 January 2022, 22:57:51 UTC | Use docker image that allows subnet specification | 10 January 2022, 22:57:51 UTC |
| 8960a82 | John Maruska | 10 January 2022, 19:32:39 UTC | Add cromwell_gcp_subnet which propagates to gms/start.sh | 10 January 2022, 19:32:39 UTC |
| a94fc2a | John Maruska | 06 January 2022, 22:04:27 UTC | Merge pull request #2040 from johnmaruska/incorrect-quoting-in-workflow-options Misplaced quote in workflow_options heredoc, fails json parse | 06 January 2022, 22:04:27 UTC |
| 1dfd431 | John Maruska | 06 January 2022, 21:13:36 UTC | Misplaced quote in workflow_options heredoc, fails json parse | 06 January 2022, 21:13:36 UTC |
| 9651bb1 | John Maruska | 06 January 2022, 17:09:46 UTC | Merge pull request #2039 from johnmaruska/gcp-project-passed-to-start Propagate cromwell_gcp_project setting to gms/start.sh script | 06 January 2022, 17:09:46 UTC |
| 7eabe68 | John Maruska | 06 January 2022, 16:44:23 UTC | Propagate cromwell_gcp_project setting to gms/start.sh script | 06 January 2022, 16:44:23 UTC |
| f63af58 | Thomas B. Mooney | 22 December 2021, 21:57:26 UTC | Merge pull request #2038 from tmooney/build_queued_models Commands to back BQM and RQB on the new CI server | 22 December 2021, 21:57:26 UTC |
| 197b09d | Thomas B. Mooney | 22 December 2021, 20:42:16 UTC | Merge pull request #2037 from tmooney/interactive_queue_config Add config for specifying the queue for interactive jobs. | 22 December 2021, 20:42:16 UTC |
| 9e96fb4 | Thomas B. Mooney | 21 December 2021, 22:16:05 UTC | Don't propagate LSF_DOCKER_NETWORK to builds. If a process needs to expose a port it can still do so via other means, but in general we don't want to have collisions of local processes when more than one lands on the same execution host. | 21 December 2021, 22:16:05 UTC |
| 62ab163 | Thomas B. Mooney | 21 December 2021, 18:58:36 UTC | Add config for specifying the queue for interactive jobs. | 21 December 2021, 18:58:36 UTC |
| 6544230 | Thomas B. Mooney | 20 December 2021, 20:40:50 UTC | Merge pull request #2036 from tmooney/toil_take_two Updates to support per-job containers when running with toil. | 20 December 2021, 20:40:50 UTC |
| 2690b17 | Thomas B. Mooney | 20 December 2021, 18:36:12 UTC | Add rebuild-queued-builds command for automated restarts. | 20 December 2021, 18:39:14 UTC |
| 682306d | Thomas B. Mooney | 03 November 2021, 14:29:29 UTC | Updates to support per-job containers when running with toil. The container must be capable of running python3 with glibc version of at least 2.16. | 14 December 2021, 19:09:33 UTC |
| d47074a | John Maruska | 14 December 2021, 17:26:29 UTC | Merge pull request #2035 from johnmaruska/run-cromwell-gcp-fully-cloud Switch cromwell_gcp workflow runner from central Cromwell server to per-run Cromwell VM | 14 December 2021, 17:26:29 UTC |
| de420d9 | Maruska | 13 December 2021, 17:19:56 UTC | Use status message instead of debug | 13 December 2021, 17:19:56 UTC |
| 5377214 | Maruska | 10 December 2021, 16:57:25 UTC | Download outputs using nested structure that's cromwell's default | 10 December 2021, 16:57:25 UTC |
| 310e7ad | Maruska | 10 December 2021, 16:53:34 UTC | not sure how these happened | 10 December 2021, 16:53:34 UTC |
| 1561267 | Maruska | 10 December 2021, 16:50:23 UTC | Add cleanup() call to remove tmp cromwell.service file | 10 December 2021, 16:50:23 UTC |
| e4de584 | Maruska | 10 December 2021, 16:39:05 UTC | Remove extraneous changes, less bloat in PR | 10 December 2021, 16:39:05 UTC |
| c5c8ee5 | Maruska | 10 December 2021, 16:31:57 UTC | Remove shared_config, they don't actually share anything | 10 December 2021, 16:31:57 UTC |
| 572c367 | Maruska | 09 December 2021, 20:46:25 UTC | Verified full run using full cloud | 09 December 2021, 20:46:25 UTC |
| 01d22fb | Maruska | 29 November 2021, 19:49:16 UTC | Switch to using cloud instance for managing Cromwell JAR etc Have to pull files back instead of writing them locally. Secures endpoints from unauthorized workflow kickoffs. | 29 November 2021, 19:49:16 UTC |
| 6034f39 | Maruska | 23 November 2021, 16:23:23 UTC | First pass at local run command, cloud task execution WIP have not solved service account scope error | 23 November 2021, 16:23:23 UTC |
| 66e4572 | Thomas B. Mooney | 16 November 2021, 22:53:02 UTC | New command for processing BQM for current user. This faciliates migrating to the Submittable role so that AnP environment can be easily respected. | 18 November 2021, 18:43:01 UTC |
| f3fed97 | Thomas B. Mooney | 16 November 2021, 21:24:44 UTC | Remove disused subtree. | 16 November 2021, 21:24:44 UTC |
| 0397678 | Thomas B. Mooney | 09 November 2021, 16:06:56 UTC | Merge pull request #2034 from johnmaruska/run-cromwell-gcp Enable GCP workflows via environment configuration options | 09 November 2021, 16:06:56 UTC |
| 3fb1007 | Thomas B. Mooney | 04 November 2021, 21:16:59 UTC | Merge pull request #2031 from tmooney/archiving_v2 A simpler archive system. | 04 November 2021, 21:16:59 UTC |
| 0795303 | Maruska | 04 November 2021, 20:56:01 UTC | more File::Spec->join() | 04 November 2021, 20:56:01 UTC |
| 6f7f9eb | Maruska | 04 November 2021, 20:43:45 UTC | Use File::Spec->join and File::Spec->splitpath | 04 November 2021, 20:43:45 UTC |
| 8c300c4 | Thomas B. Mooney | 04 November 2021, 18:29:11 UTC | Remove requirement to link an AnP when unarchiving an allocation. An optional reason can still be given. | 04 November 2021, 20:24:38 UTC |
| 49a8e22 | Thomas B. Mooney | 03 November 2021, 19:41:35 UTC | By popular request, add allocation status to instrument data listers. | 04 November 2021, 20:24:38 UTC |
| 7ed1371 | Thomas B. Mooney | 03 November 2021, 15:28:04 UTC | Don't try to link the allocations to AnPs. This was part of a transition where things may have originally been created without an AnP. These days you need one from the beginning (and users have more control over their own disk space) so this won't accomplish anything except generating support requests. | 04 November 2021, 20:24:38 UTC |
| aa0c55f | Thomas B. Mooney | 03 November 2021, 15:26:38 UTC | Don't worry about getting user object if not set. We just want to record the username of who did it, anyway. | 04 November 2021, 20:24:38 UTC |
| 12f0c43 | Thomas B. Mooney | 10 August 2021, 20:41:31 UTC | A new much simpler archive system. As long as both classes of storage can be mounted on the host, this is a lot less cumbersome to deal with than using a special queue and tarring files! | 04 November 2021, 20:24:37 UTC |
| 2ad1876 | Maruska | 04 November 2021, 19:25:36 UTC | Automatically zip workflow deps on Run | 04 November 2021, 19:25:36 UTC |
| 78cde1c | Maruska | 02 November 2021, 22:23:22 UTC | Bracket looked better before | 02 November 2021, 22:23:22 UTC |
| cfb9425 | Maruska | 02 November 2021, 20:36:56 UTC | Resolve legacy compilation errors | 02 November 2021, 20:36:56 UTC |
| cd1b93b | Maruska | 02 November 2021, 20:27:36 UTC | Move fetch_cromwell_log before fatal_message for safety | 02 November 2021, 20:27:36 UTC |
| bdadf2d | Maruska | 02 November 2021, 20:25:29 UTC | Remove redundant Scope::Guard reset | 02 November 2021, 20:25:29 UTC |
| 3fa1126 | Maruska | 02 November 2021, 20:23:53 UTC | Use debug and status methods instead of print | 02 November 2021, 20:23:53 UTC |
| 11b86d6 | Maruska | 02 November 2021, 20:21:35 UTC | Pin cloudize-workflow docker image to version 1.0.0 | 02 November 2021, 20:21:35 UTC |
| 1781379 | Maruska | 02 November 2021, 20:17:11 UTC | Re-indent request ATTEMPT | 02 November 2021, 20:17:11 UTC |
| f0c7706 | Maruska | 02 November 2021, 19:28:57 UTC | Add spec for cromwell_gcp_bucket setting | 02 November 2021, 19:28:57 UTC |
| 9f37675 | Maruska | 02 November 2021, 19:11:32 UTC | Bring bucket in from env, not hard-code Also flip lsb_sub_additional less, relocated scripts | 02 November 2021, 19:11:32 UTC |
| 56b3457 | Maruska | 28 October 2021, 20:10:06 UTC | Enable running workflows via a central GCP Cromwell server | 28 October 2021, 20:10:06 UTC |
| b10cc48 | Thomas B. Mooney | 15 September 2021, 17:11:20 UTC | Merge pull request #2032 from tmooney/dont_use_logger_in_listbuildqueue Stop using Genome::Logger in list-build-queue. | 15 September 2021, 17:11:20 UTC |
| be515ec | Thomas B. Mooney | 15 September 2021, 17:10:29 UTC | Merge pull request #2033 from tmooney/stop_and_abandon_queue A queue for requesting stop/abandon for production builds. | 15 September 2021, 17:10:29 UTC |
| 68dfe72 | Thomas B. Mooney | 01 September 2021, 17:00:09 UTC | Remove breakpoint. | 01 September 2021, 17:00:09 UTC |
| a0e80c4 | Thomas B. Mooney | 01 September 2021, 16:53:33 UTC | Add missing role. | 01 September 2021, 16:53:33 UTC |
| 8dcc55f | Thomas B. Mooney | 31 August 2021, 20:30:30 UTC | Command for processing the new actions queued for builds. Restart will still be handled by a separate process for now--it has stricter requirements for only happening once, whereas these actions might be triggered even if someone has already manually stopped/abandoned the relevant builds. It's harmless to try stopping/abandoning a second time generally. This queue processor only tries each build once, even if the stop/abandon fails. | 01 September 2021, 16:35:03 UTC |
| 47bf351 | Thomas B. Mooney | 18 August 2021, 17:34:31 UTC | More general action queue for CwlPipeline builds. Users can't take direct action on "production" builds, so this provides a mechanism for self-service interaction when needed. | 01 September 2021, 16:35:02 UTC |
| 3f0d379 | Thomas B. Mooney | 18 August 2021, 17:37:40 UTC | Extract common elements of job submission. This is becoming a fairly common pattern to use, so let's make it a bit easier to add to new places. | 30 August 2021, 20:43:59 UTC |
| 9e5a10e | Thomas B. Mooney | 23 August 2021, 21:34:48 UTC | Merge pull request #2029 from tmooney/docker-kill-docker I believe this should be kill-docker like it's submit-docker. | 23 August 2021, 21:34:48 UTC |
| a22e18b | Thomas B. Mooney | 16 August 2021, 15:20:58 UTC | Stop using Genome::Logger in list-build-queue. I'm inclined to say we shouldn't be using it anywhere--UR has built-in logging already that meets our needs. This makes progress towards that goal! | 16 August 2021, 15:20:58 UTC |
| f848347 | Thomas B. Mooney | 16 August 2021, 15:13:34 UTC | Merge pull request #2030 from tmooney/list_build_queue_infof_fix Some fixes to a log message. | 16 August 2021, 15:13:34 UTC |
| dc72908 | Thomas B. Mooney | 09 August 2021, 17:14:08 UTC | Some fixes to a log message. The `::` in place of `->` was preventing this from proceeding if any given AnP was at its cap. | 09 August 2021, 17:14:08 UTC |
| ddce3f1 | Thomas B. Mooney | 29 July 2021, 18:21:44 UTC | I believe this should be kill-docker like it's submit-docker. | 29 July 2021, 18:21:44 UTC |
| df99eae | Thomas B. Mooney | 21 July 2021, 17:27:18 UTC | Merge pull request #2027 from tmooney/list_build_queue_knows_about_anps Add a per-AnP limit for scheduled builds. | 21 July 2021, 17:27:18 UTC |
| 6e25052 | Thomas B. Mooney | 21 July 2021, 15:31:39 UTC | Add a per-AnP limit for scheduled builds. This way a single project won't monopolize the queues when it has a job group configured that causes its builds to PEND even when slots are available for other builds to run. | 21 July 2021, 16:10:22 UTC |
| 40d32f1 | Thomas B. Mooney | 19 July 2021, 19:39:26 UTC | Merge pull request #2026 from tmooney/only_assign_when_data_to_assign Only try to assign existing data when there is some. | 19 July 2021, 19:39:26 UTC |
| 72ce27d | Thomas B. Mooney | 19 July 2021, 15:32:42 UTC | Only try to assign existing data when there is some! | 19 July 2021, 15:32:42 UTC |
