https://github.com/genome/genome

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Revision Author Date Message Commit Date
696b1e7 Merge pull request #2077 from tmooney/retry_connections Retry postgres connections for up to 90 seconds. 13 March 2024, 13:58:29 UTC
dd19bb8 Retry postgres connections for up to 90 seconds. We sometimes get our TCP connection failing trying to connect, so let's try harder to successfully connect. (This depends on genome/docker_genome_perl_environment#39 to work on our cluster.) 12 March 2024, 18:22:29 UTC
84b1df4 Merge pull request #2076 from tmooney/smaller_allocation_request_in_somvar_tests Use a smaller allocation size for testing. 21 November 2023, 18:53:22 UTC
2f5bfbf Use a smaller allocation size for testing. The test data is about 50MB so a 100MB allocation provides plenty of room. This prevents failures when running tests on a blade with <32GB of free temp space, since we defintiely don't need that much! 21 November 2023, 18:28:51 UTC
2a4735d Merge pull request #2074 from tmooney/custom_per_job_queue_in_wdl Define a "queue" runtime attribute for WDL tasks. 21 November 2023, 17:44:54 UTC
4aea4ff Merge pull request #2075 from tmooney/avoid_loading_oltp Avoid attempting to connect to OLTP database 21 November 2023, 17:44:38 UTC
27d097e Skip tests that require an OLTP connection to function. 20 November 2023, 22:04:27 UTC
9303a5e Only consider disconnecting datasources that we've loaded. This is a check at an even deeper level than whether the default handle exists--we don't need to worry if the database could be connected to here if we haven't connected to it yet. (With the shutdown of our OLTP server this become relevant--we'll have a backup database we could connect to sometimes but not always.) 20 November 2023, 22:01:58 UTC
b59277f Define a "queue" runtime attribute for WDL tasks. This will let certain jobs be dispatched to different queues. 20 November 2023, 20:32:46 UTC
595c5ee Merge pull request #2073 from tmooney/deprecate_legacy_lims Remove LIMS-specific extensions. 14 November 2023, 20:39:03 UTC
9101534 Remove LIMS-sepcific extensions. With the retirement of the legacy LIMS system these are no longer functional. (Many of the classes under Genome/Site/TGI/Synchronize are also likely candidates for removal, but there will be a final database snapshot we could theoretically query for a time as needed.) 13 November 2023, 22:23:32 UTC
4755ca7 Merge pull request #1987 from tmooney/lsf10_memory_units Use explicit units for memory reservations (LSF10 feature). 26 October 2023, 20:01:57 UTC
2ded320 Merge pull request #2072 from tmooney/only_delete_archive_location_if_we_created_it Only cleanup if we started to try to do work. 26 October 2023, 20:01:48 UTC
d4ed2ec Only try to cleanup the archive if we started to try to do work. We shouldn't try to clean up if we're erroring out before attempting the archive-especially if the data was already archived! Also Switch to Try::Tiny for better error handling--instead of lamenting the lack of finally blocks, use one! 26 October 2023, 16:40:48 UTC
11154ea Merge pull request #2071 from tmooney/read_only_tie Only tie read-only since we don't need to write this file. 18 October 2023, 16:18:14 UTC
44b0fb9 Only tie read-only since we don't need to write this file. Also, actually report the error when the tie fails instead of mysteriously failing to parse the header later. 18 October 2023, 15:21:04 UTC
2662511 Merge pull request #2065 from tmooney/restart_cloud Support restarting if our local build fails but the cloud VM is still running. 17 October 2023, 16:30:04 UTC
2baebf8 Merge pull request #2070 from tmooney/unstartable_on_bsub_failure Don't crash if `bsub` for inner job fails. 17 October 2023, 16:29:38 UTC
ccc6ae4 Merge pull request #2067 from tmooney/lsf_parsing_hosts Centralize checking for the existence of eligible LSF hosts. 17 October 2023, 16:29:18 UTC
9eefa3e Centralize checking for the existence of eligible LSF hosts. There were a few competing implementations around for this; better that we have one that we can fix up when/if issues arise. 06 October 2023, 01:41:30 UTC
ea6c3ae Don't crash if `bsub` for inner job fails. A misconfigured AnP could result in the bsub failing for various reasons. Better to skip it and move on than to prevent any other queue processing. 11 September 2023, 17:38:14 UTC
721185c Merge pull request #2069 from tmooney/skip_memcache_test Add done_testing so that test-tracker handles skip properly. 11 April 2023, 22:19:00 UTC
d208ec0 Add done_testing so that test-tracker handles skip properly. As also seen in #1980. 11 April 2023, 21:07:44 UTC
7756dc6 Merge pull request #2068 from tmooney/skip_memcache_test Skip Memcache.t that depends on production memcache. 11 April 2023, 20:35:26 UTC
c93f871 Skip Memcache.t that depends on production memcache. It's also not really safe for concurrent test runs! 11 April 2023, 17:18:35 UTC
51e4e50 Merge pull request #2066 from johnegarza/cache_hashing_typo Fix typo 27 March 2023, 21:23:41 UTC
3db4c5c Fix typo 27 March 2023, 19:22:15 UTC
6ce0e71 Merge pull request #2064 from johnegarza/better_pp_installation Add multithreading and suppress output 12 August 2022, 17:29:14 UTC
0382498 If we detect an existing VM for our build, then use it. 04 August 2022, 20:32:44 UTC
5551784 Extract subroutine to check if cloud instance is running. 04 August 2022, 20:14:53 UTC
263122c Updated `gmt` tab completion. 12 July 2022, 14:44:42 UTC
97c8dc9 Updated `genome` tab completion. 12 July 2022, 14:44:13 UTC
d425286 Updated class browser cache. 12 July 2022, 14:43:10 UTC
9ed6def Add multithreading and suppress output 30 May 2022, 07:01:25 UTC
e97262e Merge pull request #2059 from johnegarza/proc_prof_queueing Changes to allow adding PPs from compute1 30 April 2022, 23:20:41 UTC
f021a29 Merge pull request #2062 from genome/chrisamiller-patch-3 fixing pull_outputs command for cloud workflows 27 April 2022, 21:04:12 UTC
44acf63 Merge pull request #2061 from genome/chrisamiller-patch-2 updating cloudize-workflow image 27 April 2022, 21:03:55 UTC
3bb6c5d fixing pull_outputs command for cloud workflows Removing deep option, as it no longer exists in the pull output script 16 April 2022, 02:59:46 UTC
53350ae updating cloudize-workflow image updating to 1.2.2 16 April 2022, 02:51:36 UTC
2ad5bb2 Send user uploaded pp to cloud queue instead of installing direct to filesystem 13 April 2022, 19:08:25 UTC
ad02fb6 Merge pull request #2058 from johnmaruska/cromwell-gcp-uses-mgibio-image Use mgibio image for cloudize-workflows in cromwell_gcp workflows 05 April 2022, 16:49:53 UTC
a6613fc Use mgibio image for cloudize-workflows in cromwell_gcp workflows 05 April 2022, 16:00:06 UTC
11f99b6 Merge pull request #2057 from tmooney/import_data_from_lims_return_code Only return true if we succeeded to process all instrument data. 09 March 2022, 14:58:52 UTC
a7ec2e0 Only return true if we succeeded to process all instrument data. 08 March 2022, 20:35:51 UTC
2393868 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 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 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 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 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 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 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 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 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 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 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 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 Merge pull request #2048 from johnmaruska/gcp-separate-buckets GCP subnet 25 January 2022, 17:47:01 UTC
70c0680 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 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 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 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 Bump tag version to reverted cloud-workflows 21 January 2022, 17:43:43 UTC
8910335 How'd this get here? 21 January 2022, 17:28:35 UTC
b15735b Revert separate buckets, we decided against this 21 January 2022, 17:27:11 UTC
cb115b2 Merge pull request #2047 from tmooney/straggling_test_fixes Some straggling test fixes 20 January 2022, 21:45:39 UTC
e550e63 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 Merge branch 'master' of https://github.com/genome/genome into gcp-separate-buckets 20 January 2022, 16:32:55 UTC
cee852a Bump cloudize-workflow tag 20 January 2022, 16:31:23 UTC
ee9d5a9 Merge branch 'gcp-specify-subnet' into gcp-separate-buckets 20 January 2022, 16:21:43 UTC
a1b7570 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 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 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 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 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 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 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 Merge pull request #2044 from tmooney/no_blade_name Revise check for matching hosts. 18 January 2022, 15:24:34 UTC
1324826 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 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 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 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 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 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 Use docker image that allows subnet specification 10 January 2022, 22:57:51 UTC
8960a82 Add cromwell_gcp_subnet which propagates to gms/start.sh 10 January 2022, 19:32:39 UTC
a94fc2a 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 Misplaced quote in workflow_options heredoc, fails json parse 06 January 2022, 21:13:36 UTC
9651bb1 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 Propagate cromwell_gcp_project setting to gms/start.sh script 06 January 2022, 16:44:23 UTC
f63af58 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 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 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 Add config for specifying the queue for interactive jobs. 21 December 2021, 18:58:36 UTC
6544230 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 Add rebuild-queued-builds command for automated restarts. 20 December 2021, 18:39:14 UTC
682306d 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 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 Use status message instead of debug 13 December 2021, 17:19:56 UTC
5377214 Download outputs using nested structure that's cromwell's default 10 December 2021, 16:57:25 UTC
310e7ad not sure how these happened 10 December 2021, 16:53:34 UTC
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