| 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 |
| ae5b070 | Thomas B. Mooney | 19 July 2021, 15:08:36 UTC | Merge pull request #2021 from tmooney/silence_errors_in_disk_create Avoid warnings about numeric comparisons. | 19 July 2021, 15:08:36 UTC |
| b2b4b20 | Thomas B. Mooney | 19 July 2021, 15:08:16 UTC | Merge pull request #2019 from tmooney/cleanup_succeeded_for_compute1 Handle not having automatic mounts in Cleanup Succeeded | 19 July 2021, 15:08:16 UTC |
| 7911616 | Thomas B. Mooney | 19 July 2021, 15:06:57 UTC | Merge pull request #2022 from tmooney/import_data_for_work_order_lives_up_to_its_promises The help text claims it assigns all data, so let's do it. | 19 July 2021, 15:06:57 UTC |
| 076e0ae | Thomas B. Mooney | 15 July 2021, 20:26:55 UTC | Merge pull request #2024 from tmooney/logger_monkeypatch Monkeypatch to get around longstanding bug in Logger. | 15 July 2021, 20:26:55 UTC |
| 46e8087 | Thomas B. Mooney | 15 July 2021, 20:26:31 UTC | Merge pull request #2025 from tmooney/model_metric_column_names Address errors with metric ghost class [to fix CWL requeueing]. | 15 July 2021, 20:26:31 UTC |
| c1ab162 | Thomas B. Mooney | 12 July 2021, 18:54:58 UTC | Address errors with metric ghost class. When deleting metrics (to replace them), UR was complaining about the column names not matching the database. The capitalized names were held over from before we switched to PostgreSQL, so let's just lowercase them now. | 12 July 2021, 18:54:58 UTC |
| 4dded1f | Thomas B. Mooney | 24 June 2021, 14:38:40 UTC | Fix logic. | 24 June 2021, 14:38:40 UTC |
| a59436e | Thomas B. Mooney | 23 June 2021, 20:29:16 UTC | Monkeypatch to get around longstanding bug in Logger. I think we should switch users of this to use the UR logging methods instead, but this is a quick fix for now. | 23 June 2021, 20:29:16 UTC |
| e498f3c | Thomas B. Mooney | 23 June 2021, 20:06:57 UTC | Merge pull request #2023 from tmooney/confg_file_for_instrument_data Optionally check instrument data against a supplied config file. | 23 June 2021, 20:06:57 UTC |
| df51a53 | Thomas B. Mooney | 23 June 2021, 19:44:09 UTC | Optionally check instrument data against a supplied config file. | 23 June 2021, 19:44:09 UTC |
| d6d5975 | Thomas B. Mooney | 17 June 2021, 20:58:04 UTC | The help text claims it assigns all data, so let's do it. | 17 June 2021, 20:58:04 UTC |
| 7d6f740 | Thomas B. Mooney | 17 June 2021, 20:04:40 UTC | Avoid warnings about numeric comparisons. These UUIDs sure look like numbers to me, anyway :) | 17 June 2021, 20:04:40 UTC |
| 5c05536 | Thomas B. Mooney | 15 June 2021, 22:45:08 UTC | Command to purge allocations for abandoned builds for current user. | 17 June 2021, 16:45:10 UTC |
| 516f985 | Thomas B. Mooney | 16 June 2021, 19:59:29 UTC | Merge pull request #2020 from tmooney/remove_dot Remove accidental double-concatenation. | 16 June 2021, 19:59:29 UTC |
| e9c7f40 | Thomas B. Mooney | 16 June 2021, 19:52:37 UTC | Remove accidental double-concatenation. | 16 June 2021, 19:52:37 UTC |
| 185e790 | Thomas B. Mooney | 15 June 2021, 20:37:49 UTC | Allow for cleaning up via subjob so that mounts can be specified. This is necessary for our new cluster volumes that aren't mounted automatically. | 15 June 2021, 20:37:49 UTC |
| 87ae31b | Thomas B. Mooney | 15 June 2021, 20:34:57 UTC | Add an interactive option to Genome::Sys::LSF::bsub. The main feature of this would be to allow stdout/stderr to be passed through from the job. It does allow for interactivity within the nested job if necessary, too. | 15 June 2021, 20:34:57 UTC |
| 6c32c75 | Thomas B. Mooney | 15 June 2021, 15:09:22 UTC | Pull up possible-volumes logic into AnP class itself. Better testing, too! | 15 June 2021, 15:09:22 UTC |
| 05b88ab | Thomas B. Mooney | 10 June 2021, 16:54:00 UTC | Merge pull request #2018 from tmooney/import_move_option Add option to trusted-data importer to delete the source files. | 10 June 2021, 16:54:00 UTC |
| 11ea45f | Thomas B. Mooney | 09 June 2021, 17:58:57 UTC | Add option to trusted-data importer to delete the source files. | 09 June 2021, 17:58:57 UTC |
| 20f75e9 | Thomas B. Mooney | 02 June 2021, 20:56:24 UTC | Merge pull request #2017 from tmooney/lims_config_is_cake Use a hardcoded lims docker image. | 02 June 2021, 20:56:24 UTC |
| 2b80e56 | Thomas B. Mooney | 01 June 2021, 20:36:31 UTC | Use a hardcoded lims docker image. This purports to look it up in config, but the config is a lie. The latest version of the config is itself stored inside the docker image, so it's not possible to look it up from the outside. Rather than rely on an old version of the config, just put in the current latest value. | 01 June 2021, 20:36:31 UTC |
| da03b55 | Thomas B. Mooney | 01 June 2021, 16:52:18 UTC | Merge pull request #2016 from tmooney/tolerate_disk_volumes_where_groups_belong_in_lims_importer Tolerate the user specifying an explicit volume instead of a group. | 01 June 2021, 16:52:18 UTC |
| 60b9a6c | Thomas B. Mooney | 01 June 2021, 16:51:52 UTC | Merge pull request #2015 from tmooney/synonym_file_converter Add a "synonym file" converter algorithm. | 01 June 2021, 16:51:52 UTC |
| 1e9effd | Thomas B. Mooney | 01 June 2021, 16:50:54 UTC | Merge pull request #2014 from tmooney/refseq_build_uses_anp_config Use AnP config for build creation/running in refseqs. | 01 June 2021, 16:50:54 UTC |
| ad0e800 | Thomas B. Mooney | 27 May 2021, 14:49:37 UTC | Tolerate the user specifying an explicit volume instead of a group. The remote volume support regressed the tolerance added in #1866 in this particular case. It could still be avoided by using the right type of data being requested, though! | 27 May 2021, 14:49:37 UTC |
| 8617aa0 | Thomas B. Mooney | 25 May 2021, 20:14:26 UTC | Add a "synonym file" converter algorithm. The file is a two-column format with the first column being the target chromosome in the destination reference and the second column being the chromosome in the source reference. (This should match the format of synonym files for VEP.) | 25 May 2021, 20:14:26 UTC |
| ab08d16 | Thomas B. Mooney | 25 May 2021, 18:31:38 UTC | Set a basic environment file for the mock "system" AnP. Tests building reference sequences now need an environment file like those building other build types already do. | 25 May 2021, 18:48:23 UTC |
| 0e3c8a3 | Thomas B. Mooney | 25 May 2021, 17:59:34 UTC | Use AnP config for build creation/running in refseqs. | 25 May 2021, 17:59:34 UTC |
| 0f58a00 | Thomas B. Mooney | 25 May 2021, 17:40:14 UTC | Merge pull request #2013 from tmooney/delete_tag_bridges_on_delete Support deleting a config profile item with linked tags. | 25 May 2021, 17:40:14 UTC |
| 5a4abc9 | Thomas B. Mooney | 20 May 2021, 22:12:46 UTC | Support deleting a config profile item with linked tags. This will still fail if the config was ever used for models (which prevents crazy cascading deletes!), but an unused config that happened to have a tag can now be cleaned up. | 20 May 2021, 22:12:46 UTC |
| ae02a8e | John Garza | 13 May 2021, 21:50:51 UTC | Merge pull request #2012 from johnegarza/skip_disk_querying Skip disk querying | 13 May 2021, 21:50:51 UTC |
| 352477d | johnegarza | 13 May 2021, 20:51:55 UTC | More relevant var name | 13 May 2021, 20:51:55 UTC |
| 7b5d91c | johnegarza | 13 May 2021, 20:38:08 UTC | Skip direct disk space queries when allocation path creation is skipped | 13 May 2021, 20:38:08 UTC |
| c2e9669 | John Garza | 11 May 2021, 23:14:19 UTC | Merge pull request #2011 from johnegarza/python3_gsutil_focal Call gsutil with python3 in Ubuntu 20.04 focal based images | 11 May 2021, 23:14:19 UTC |
| 2e4d2db | johnegarza | 11 May 2021, 22:55:56 UTC | Call gsutil with python3 in Ubuntu 20.04 focal based images | 11 May 2021, 22:55:56 UTC |
| 7c49c6d | John Garza | 10 May 2021, 21:45:19 UTC | Merge pull request #2010 from johnegarza/gcp_config_bucket_var Use env variables instead of hardcoding gcp bucket | 10 May 2021, 21:45:19 UTC |
| 47b3277 | johnegarza | 10 May 2021, 21:25:10 UTC | Use env variables instead of hardcoding gcp bucket | 10 May 2021, 21:25:10 UTC |
| 7ace67e | John Garza | 10 May 2021, 20:55:57 UTC | Merge pull request #2009 from johnegarza/update_commands Add an update env file command | 10 May 2021, 20:55:57 UTC |
| 4c04df1 | John Garza | 10 May 2021, 20:55:13 UTC | Merge pull request #2007 from johnegarza/config_skip_allocation_creation Skip allocation path creation for config files | 10 May 2021, 20:55:13 UTC |
| ba32611 | johnegarza | 06 May 2021, 21:39:09 UTC | fix number of tests | 06 May 2021, 21:39:09 UTC |
| 2a6b9b5 | johnegarza | 06 May 2021, 21:33:20 UTC | Add a basic test case | 06 May 2021, 21:33:20 UTC |
| 5361726 | johnegarza | 06 May 2021, 20:01:35 UTC | Keep language consistent | 06 May 2021, 20:01:35 UTC |
| e9b1dde | johnegarza | 05 May 2021, 22:11:20 UTC | Initial work to allow updating AnP environment files | 05 May 2021, 22:11:20 UTC |
| 0ee82ef | johnegarza | 05 May 2021, 21:38:59 UTC | Handle no-commit further upstream | 05 May 2021, 21:38:59 UTC |
| 141c293 | johnegarza | 05 May 2021, 21:14:58 UTC | Use spaces not tabs | 05 May 2021, 21:14:58 UTC |
| 167159c | johnegarza | 04 May 2021, 22:31:53 UTC | Make sure tests can create allocations | 04 May 2021, 22:31:53 UTC |
| 596c145 | johnegarza | 04 May 2021, 21:13:44 UTC | Retain CQID ability to directly write to filesystem | 04 May 2021, 21:13:44 UTC |
| bfe3dc4 | johnegarza | 04 May 2021, 20:50:30 UTC | Better var name and skip path creation for config items too | 04 May 2021, 20:50:30 UTC |
| 0ff0a89 | johnegarza | 03 May 2021, 23:20:34 UTC | Skip creating allocation dirs for env config | 03 May 2021, 23:20:34 UTC |
| 3c5eb40 | John Garza | 03 May 2021, 21:10:59 UTC | Merge pull request #2006 from johnegarza/fix_uploaded_config_name Fix uploaded file name | 03 May 2021, 21:10:59 UTC |
| 00c39e7 | John Garza | 03 May 2021, 20:49:03 UTC | Fix variables Co-authored-by: Thomas B. Mooney <mooney@wustl.edu> | 03 May 2021, 20:49:03 UTC |
| 8e1ce00 | John Garza | 03 May 2021, 20:48:03 UTC | Use join to construct uploaded file name Co-authored-by: Thomas B. Mooney <mooney@wustl.edu> | 03 May 2021, 20:48:03 UTC |
| 6a2f4a3 | johnegarza | 03 May 2021, 20:32:32 UTC | Fix uploaded file name | 03 May 2021, 20:32:32 UTC |
| 13cde6b | John Garza | 30 April 2021, 21:20:36 UTC | Merge pull request #2005 from johnegarza/basic_config_file_changes Basic config file changes | 30 April 2021, 21:20:36 UTC |
| 5b8093e | johnegarza | 29 April 2021, 22:39:08 UTC | Keep terminology consistent | 29 April 2021, 22:39:08 UTC |
| 8b24aea | johnegarza | 29 April 2021, 22:01:25 UTC | Inform the user that the file will not be immediately available | 29 April 2021, 22:01:25 UTC |
| 41dea8b | johnegarza | 29 April 2021, 20:31:30 UTC | Pass original name so update script can use it | 29 April 2021, 20:31:30 UTC |
| 3e2cf8b | Thomas B. Mooney | 28 April 2021, 20:51:31 UTC | Merge pull request #2002 from tmooney/anp_create_wanna_create AnP Create: Now with More Interactivity! | 28 April 2021, 20:51:31 UTC |
| 9dcc085 | Thomas B. Mooney | 28 April 2021, 17:00:57 UTC | Make the interactive menu item adding more interactive. The --no-config option or the --analysis-menu-item options bypass this prompt as per usual, so automated use of this command is still possible. | 28 April 2021, 20:45:52 UTC |
| 14ee58c | Thomas B. Mooney | 28 April 2021, 20:44:01 UTC | Merge pull request #2004 from tmooney/allocation_cleanup_knows_about_certificates Check for certificates for the production database connection. | 28 April 2021, 20:44:01 UTC |
| c35c81f | Thomas B. Mooney | 28 April 2021, 19:46:05 UTC | Check for certificates for the production database connection. | 28 April 2021, 20:14:24 UTC |
| 5a1a89a | Thomas B. Mooney | 28 April 2021, 19:19:51 UTC | Merge pull request #2003 from tmooney/testtracker_certs_in_conf Include certs in test-tracker server config. | 28 April 2021, 19:19:51 UTC |
| 21043d9 | Thomas B. Mooney | 28 April 2021, 18:53:46 UTC | Include certs in test-tracker server config. Once again not a useful file for the world at large, but helpful for us! | 28 April 2021, 18:53:46 UTC |
