24f0ddf | Thomas B. Mooney | 22 September 2020, 21:29:00 UTC | Merge pull request #1986 from tmooney/ssl_for_dgidb Use HTTPS to connect to dgidb. | 22 September 2020, 21:29:00 UTC |
a88cbb1 | Thomas B. Mooney | 22 September 2020, 21:28:51 UTC | Merge pull request #1985 from tmooney/splitpath_typo Fix typo: s/split_path/splitpath/. | 22 September 2020, 21:28:51 UTC |
cfd78bf | Thomas B. Mooney | 22 September 2020, 17:16:11 UTC | Add testcase for updating instrument data bam path on allocation move. | 22 September 2020, 17:16:11 UTC |
54b3b2f | Thomas B. Mooney | 21 September 2020, 20:07:58 UTC | Use HTTPS to connect to dgidb. The new release of dgidb requires SSL. The HTTP version redirects. This code is pretty old and is likely a good candidate for outright removal, but these changes make the tests pass again (albeit mostly in a lame way). | 21 September 2020, 20:07:58 UTC |
2d85d58 | Thomas B. Mooney | 17 September 2020, 22:09:10 UTC | Fix typo: s/split_path/splitpath/. | 17 September 2020, 22:09:10 UTC |
8216cbc | Thomas B. Mooney | 15 September 2020, 21:11:07 UTC | Merge pull request #1981 from tmooney/allocation_transfer New command `genome disk allocation transfer`. | 15 September 2020, 21:11:07 UTC |
b00190a | Thomas B. Mooney | 15 September 2020, 21:10:51 UTC | Merge pull request #1978 from tmooney/file_database_call_caching Cromwell Call Caching support | 15 September 2020, 21:10:51 UTC |
391184c | Thomas B. Mooney | 15 September 2020, 21:10:37 UTC | Merge pull request #1974 from tmooney/remove_extra_subcall Remove extra layer of method calls. | 15 September 2020, 21:10:37 UTC |
819df31 | Thomas B. Mooney | 31 August 2020, 17:24:05 UTC | Switch to xxh64 instead of fingerprint for call-caching. The "fingerprint" method only works with hard-links, but sometimes we have to resort to copying from the original storage to our working volume, which busts the cache since the original file metadata isn't maintained for the copy. | 31 August 2020, 17:24:05 UTC |
24bf893 | Thomas B. Mooney | 10 June 2020, 21:46:58 UTC | Mitigate having multiple workflows per build. The "right" answer here would be to link them to the corresponding Genome::Process. The issue right now is that the process is created *after* the workflow inputs are assigned, so we have no way to accurately determine the correct process for our current run. There are some strategies for trying to figure it out. For example: - look up our current LSF Job ID and check the database for a matching process. - look for the one process that is currently marked as "running" and die if there's a second one. For now this assumes only one process ever "succeeds" for a build and the build view displays all the workflows in an arbitrary order. | 11 August 2020, 15:39:39 UTC |
42b2262 | Thomas B. Mooney | 27 July 2020, 19:41:07 UTC | Merge pull request #1982 from tmooney/no_lsf_tmp_modifications Remove modifications of pre-provided LSF temp directory. | 27 July 2020, 19:41:07 UTC |
365caf9 | Thomas B. Mooney | 24 July 2020, 21:49:23 UTC | Remove modifications of pre-provided LSF temp directory. On the new cluster this directory is locked down so we lack permissions to change it. | 24 July 2020, 21:49:23 UTC |
6cae9c6 | Thomas B. Mooney | 23 July 2020, 19:43:45 UTC | Test execution of the command. We can make sure we updated the database entries, even if testing the rsync portion is impractical! | 23 July 2020, 19:43:45 UTC |
97cff7d | Thomas B. Mooney | 15 July 2020, 21:28:28 UTC | Make sure directory exists before attempting `rsync`. | 15 July 2020, 21:28:28 UTC |
4a5d6db | Thomas B. Mooney | 29 June 2020, 20:26:14 UTC | New `genome disk allocation transfer` for sending to a remote volume. | 15 July 2020, 21:18:12 UTC |
5705880 | Thomas B. Mooney | 29 June 2020, 20:24:20 UTC | Add instrument data to update_owner_for_move. I'm not a big fan of the way this one spot has to be added to for any potential allocation owner to get updated, but it works and it's fairly straightforward! So let's stick with it for now. | 29 June 2020, 20:24:20 UTC |
b363008 | Thomas B. Mooney | 22 June 2020, 19:28:30 UTC | Merge pull request #1979 from tmooney/imported_data_more_tolerant_of_bam_paths Allow imported BAMs with arbitrary filenames | 22 June 2020, 19:28:30 UTC |
80f6afe | Thomas B. Mooney | 22 June 2020, 19:27:49 UTC | Merge pull request #1980 from tmooney/listdockerimages_t_truevalue `test-tracker` in `--track` mode requires tests to return a true value in order to pass. | 22 June 2020, 19:27:49 UTC |
d0023c8 | Thomas B. Mooney | 18 June 2020, 18:14:10 UTC | `test-tracker` requires tests to return a true value in order to pass. But "skip" doesn't do that--it returns undef, so we'll add our own true value! | 18 June 2020, 18:14:10 UTC |
aca76c9 | Thomas B. Mooney | 17 June 2020, 17:03:03 UTC | Try to find any single BAM in the directory if expected path not found. The "trusted data" importer makes it easier to import a BAM with any arbitrary filename. It should be fine to accept this as long as it's the only one. | 17 June 2020, 17:03:03 UTC |
1c5281f | Thomas B. Mooney | 17 June 2020, 17:01:10 UTC | Fix bug in no-allocation error message. See that comma there in the old version? That would eat the second half of the message! | 17 June 2020, 17:02:29 UTC |
c4273f7 | Thomas B. Mooney | 16 June 2020, 19:30:44 UTC | Merge pull request #1976 from tmooney/describe_cwl_pipeline_pps New command to list docker images for a CWL pipeline build. | 16 June 2020, 19:30:44 UTC |
ff6a3f7 | Thomas B. Mooney | 10 June 2020, 19:47:45 UTC | Don't regenerate config and labels on build restart. | 10 June 2020, 21:57:15 UTC |
fddaad0 | Thomas B. Mooney | 10 June 2020, 19:39:48 UTC | Configuration option to enable cromwell call caching. | 10 June 2020, 19:39:48 UTC |
1d679cc | Thomas B. Mooney | 28 May 2020, 20:43:00 UTC | Merge pull request #1977 from tmooney/no_df_of_remote_volumes For now, don't try to `df` remote volumes. | 28 May 2020, 20:43:00 UTC |
3631187 | Thomas B. Mooney | 28 May 2020, 17:59:25 UTC | Merge pull request #1975 from tmooney/skip_copycat_linelength_tests Skip non-deterministic tests. | 28 May 2020, 17:59:25 UTC |
77daed3 | Thomas B. Mooney | 28 May 2020, 15:41:54 UTC | Also use physical path for remote volumes in volume lister. | 28 May 2020, 15:41:54 UTC |
1f5eaba | Thomas B. Mooney | 28 May 2020, 14:32:38 UTC | For now, don't try to `df` remote volumes. For volumes that are mounted via a cache layer, df doesn't work properly (among other non-compliant aspects of the filesystem). In our case we could possibly use SMB to connect to the remote server and find out the canonical used and total KB, but for now let's trust our database to be accurate. | 28 May 2020, 14:32:38 UTC |
45e459a | Thomas B. Mooney | 21 May 2020, 20:47:56 UTC | New command to list docker images for a CWL pipeline build. Someone was asking me what versions of things ran in a given model, and it seemed like there should be an easier way to answer this question! | 21 May 2020, 20:47:56 UTC |
1ceffce | Thomas B. Mooney | 21 May 2020, 17:12:06 UTC | Remove old debug statement. | 21 May 2020, 17:12:06 UTC |
6ec2901 | Thomas B. Mooney | 21 May 2020, 16:47:51 UTC | Merge pull request #1973 from tmooney/uuid_generator_for_disk_tables Use UUID generator for creating disk groups. | 21 May 2020, 16:47:51 UTC |
4ba8b8e | Thomas B. Mooney | 21 May 2020, 16:45:39 UTC | Skip non-deterministic tests. Sometimes they pass. Sometimes they fail. But the code hasn't changed in a long time, so it's clear these tests are not particularly useful. | 21 May 2020, 16:45:39 UTC |
8123730 | Thomas B. Mooney | 21 May 2020, 15:21:31 UTC | Merge pull request #1928 from tmooney/only_count_active_allocations_in_cqid_verification Only consider active allocations when deciding whether to import. | 21 May 2020, 15:21:31 UTC |
6f88458 | Thomas B. Mooney | 21 May 2020, 15:20:51 UTC | Merge pull request #1972 from tmooney/include_docker_volumes_env_when_setting_new Make `docker_volumes` config additive to the existing environment. | 21 May 2020, 15:20:51 UTC |
ed40892 | Thomas B. Mooney | 21 May 2020, 15:16:47 UTC | Remove extra layer of method calls. In 461d694dae993e839e8fee2dd77c7eb6a3b2533a we removed instrumentation, which left the outer call here as a mostly pointless wrapper. So now let's just consolidate them. | 21 May 2020, 15:16:47 UTC |
be544fa | Thomas B. Mooney | 20 May 2020, 21:12:58 UTC | Use UUID generator for creating disk groups. We've heretofore been importing them from an external canonical source that determines their IDs, but now we need to be able to make them directly. | 20 May 2020, 21:12:58 UTC |
4e2e675 | Thomas B. Mooney | 06 April 2020, 21:21:20 UTC | Make `docker_volumes` config additive to the existing environment. The environment will have been set up with necessary mounts to get things started (e.g., via `gsub`). We'll need to keep those along in addition to whatever project-specific mounts someone chooses to add. | 06 April 2020, 21:28:45 UTC |
632d242 | Thomas B. Mooney | 11 March 2020, 14:02:57 UTC | Merge pull request #1971 from tmooney/add_missing_config_spec_lsf_user_group Add missing lsf_user_group config spec file. | 11 March 2020, 14:02:57 UTC |
0c2c931 | Thomas B. Mooney | 10 March 2020, 19:39:11 UTC | Add missing lsf_user_group config spec file. | 10 March 2020, 19:39:11 UTC |
1096ca1 | Thomas B. Mooney | 10 March 2020, 18:03:19 UTC | Merge pull request #1970 from tmooney/fix_workflowbuilder_block Pass the inputs along to the outputs in Block operation. | 10 March 2020, 18:03:19 UTC |
7fbcecd | Thomas B. Mooney | 09 March 2020, 21:00:24 UTC | Pass the inputs along to the outputs in Block operation. | 09 March 2020, 21:00:24 UTC |
f6262bd | Thomas B. Mooney | 05 March 2020, 21:11:52 UTC | Merge pull request #1968 from tmooney/site_ris Have ris.wustl.edu domains use the "TGI" site, too. | 05 March 2020, 21:11:52 UTC |
3dd2f28 | Thomas B. Mooney | 05 March 2020, 21:11:37 UTC | Merge pull request #1967 from tmooney/dont_assume_mount_path_structure Don't assume mount_path structure. | 05 March 2020, 21:11:37 UTC |
98c37c4 | Thomas B. Mooney | 05 March 2020, 21:11:22 UTC | Merge pull request #1966 from tmooney/lsf_compute_group Support setting an LSF user_group. | 05 March 2020, 21:11:22 UTC |
af8841e | Thomas B. Mooney | 04 March 2020, 23:19:59 UTC | Have ris.wustl.edu domains use the "TGI" site, too. Maybe at some point we'll split these up since they represent two different clusters. It might even be a good opportunity to pull things from TGI that really belong in the main classes! But for now, the two clusters are similar enough... | 04 March 2020, 23:19:59 UTC |
71e0a0d | Thomas B. Mooney | 27 February 2020, 20:23:53 UTC | Use standard "get_allocation_for_path" instead of rolling our own. | 27 February 2020, 20:23:53 UTC |
b1e09e4 | Thomas B. Mooney | 27 February 2020, 19:58:07 UTC | Look up the mount path instead of presuming how many parts to remove. | 27 February 2020, 19:58:07 UTC |
3478932 | Thomas B. Mooney | 27 February 2020, 18:52:50 UTC | Merge pull request #1965 from tmooney/hsqldb_cromwell_db Support using file-based database for Cromwell workflows | 27 February 2020, 18:52:50 UTC |
a8bfd94 | Thomas B. Mooney | 27 February 2020, 18:52:17 UTC | Merge pull request #1964 from tmooney/disk_volume_uuids Use UUIDs for new disk volumes. | 27 February 2020, 18:52:17 UTC |
0cdfeb7 | Thomas B. Mooney | 27 February 2020, 18:48:25 UTC | Use new lsf_user_group config for workflow bsubs. | 27 February 2020, 18:48:25 UTC |
537c44c | Thomas B. Mooney | 27 February 2020, 15:40:57 UTC | Support passing the "user group" to bsub. | 27 February 2020, 15:40:57 UTC |
ccdc5c1 | Thomas B. Mooney | 26 February 2020, 20:02:09 UTC | Merge pull request #1963 from tmooney/use_same_interpreter_instead_of_hardcoded_genome_perl Use the current interpreter rather than assuming genome-perl. | 26 February 2020, 20:02:09 UTC |
3d04fa2 | Thomas B. Mooney | 26 February 2020, 15:11:24 UTC | Better messages about skipping WF; only show when requested. | 26 February 2020, 15:11:24 UTC |
c4efdb1 | Thomas B. Mooney | 25 February 2020, 23:03:11 UTC | Don't try to load a local database while the build is running. The running Cromwell process will have a lock on the database, so we can't look. (This view remains primarily useful for looking at failed builds.) | 25 February 2020, 23:03:11 UTC |
6cb38de | Thomas B. Mooney | 25 February 2020, 22:08:29 UTC | Shell out to write the note so it's saved immediately. Hopefully we don't encounter that sudo message, since we can't fix it from here... | 25 February 2020, 22:08:29 UTC |
60d8328 | Thomas B. Mooney | 25 February 2020, 21:43:09 UTC | Save timing report when workflow completes. | 25 February 2020, 21:43:09 UTC |
914a412 | Thomas B. Mooney | 25 February 2020, 21:18:22 UTC | API endpoint to generate a timing report. | 25 February 2020, 21:18:22 UTC |
d3cb71b | Thomas B. Mooney | 18 February 2020, 22:51:21 UTC | Retry server requests up to five times. | 25 February 2020, 20:29:15 UTC |
8b4da7f | Thomas B. Mooney | 18 February 2020, 22:50:52 UTC | Now that we're setting up local servers, can't assume constant here. | 25 February 2020, 20:29:14 UTC |
228db08 | Thomas B. Mooney | 18 February 2020, 20:55:54 UTC | Use local server to get build information when necessary. Maybe this should always do this? | 25 February 2020, 20:29:14 UTC |
31772ac | Thomas B. Mooney | 18 February 2020, 20:55:14 UTC | Use a local server to get the outputs information for Cromwell. | 25 February 2020, 20:29:13 UTC |
f105802 | Thomas B. Mooney | 18 February 2020, 20:53:32 UTC | Use new cmdline generator. | 25 February 2020, 20:29:13 UTC |
e4182d3 | Thomas B. Mooney | 18 February 2020, 20:52:40 UTC | Standardize getting Cromwell path; new method to spawn a local server. | 25 February 2020, 20:29:13 UTC |
8b66ff7 | Thomas B. Mooney | 18 February 2020, 18:03:19 UTC | Support specifying hsqldb server for Cromwell. | 25 February 2020, 20:29:12 UTC |
b143ece | Thomas B. Mooney | 24 February 2020, 18:19:42 UTC | Use UUIDs for new disk volumes. | 24 February 2020, 18:19:42 UTC |
594a51d | Thomas B. Mooney | 20 February 2020, 22:11:27 UTC | Use the current interpreter rather than assuming genome-perl. This usually doesn't matter at all, but if someone is trying to test different perl versions they'll be glad it's here :) | 20 February 2020, 22:11:27 UTC |
4915e2f | Thomas B. Mooney | 18 February 2020, 19:24:59 UTC | Merge pull request #1959 from tmooney/no_more_ptero Remove PTero support. | 18 February 2020, 19:24:59 UTC |
e8d3e88 | Thomas B. Mooney | 18 February 2020, 19:24:16 UTC | Merge pull request #1961 from genome/export Clone of PR#1960 | 18 February 2020, 19:24:16 UTC |
b1dd535 | Thomas B. Mooney | 18 February 2020, 15:57:25 UTC | A little bonus delineation between our error message and $! | 18 February 2020, 15:57:25 UTC |
6bd1626 | Chris Miller | 18 February 2020, 15:41:57 UTC | verifying output | 18 February 2020, 15:41:57 UTC |
f00b0a9 | Chris Miller | 18 February 2020, 03:36:22 UTC | update sys wrapper, rm debugging | 18 February 2020, 03:36:22 UTC |
8823b74 | Thomas B. Mooney | 17 February 2020, 21:44:28 UTC | Merge pull request #1957 from tmooney/manual_input_support_for_cwlpipeline Support supplying input classes directly in CwlPipeline commands | 17 February 2020, 21:44:28 UTC |
9c9665c | Thomas B. Mooney | 13 February 2020, 22:03:10 UTC | Remove PTero support. | 17 February 2020, 21:06:17 UTC |
4074550 | Chris Miller | 14 February 2020, 22:09:18 UTC | adding tarball option | 14 February 2020, 22:09:18 UTC |
cd160fd | Chris Miller | 12 February 2020, 20:20:19 UTC | Merge pull request #1958 from chrisamiller/instdata add useful message about AnP hold state | 12 February 2020, 20:20:19 UTC |
0f36532 | Chris Miller | 12 February 2020, 16:12:51 UTC | revised cmd | 12 February 2020, 16:12:51 UTC |
d55b53a | Chris Miller | 12 February 2020, 04:05:13 UTC | rewording | 12 February 2020, 04:05:13 UTC |
8f14a26 | Chris Miller | 12 February 2020, 04:02:24 UTC | add message about AnP being on hold | 12 February 2020, 04:02:24 UTC |
a9f51d1 | Chris Miller | 11 February 2020, 17:01:04 UTC | Merge pull request #1956 from genome/chrisamiller-patch-1 preserve "build" prefix on build directory name | 11 February 2020, 17:01:04 UTC |
7d13b58 | Thomas B. Mooney | 11 February 2020, 16:23:51 UTC | Merge pull request #1955 from tmooney/support_more_configurations CWLPipeline: Accept WDL and custom mount paths | 11 February 2020, 16:23:51 UTC |
26c9846 | Thomas B. Mooney | 11 February 2020, 16:22:29 UTC | Merge pull request #1952 from apaul7/is_10x_barcoded Adding is_10x_barcoded | 11 February 2020, 16:22:29 UTC |
faf951a | Thomas B. Mooney | 11 February 2020, 16:21:02 UTC | Merge pull request #1953 from tmooney/update_missing_perlane_alignment_error Offer a self-service option in error, remove old queue reference. | 11 February 2020, 16:21:02 UTC |
13ff5eb | Thomas B. Mooney | 11 February 2020, 16:07:27 UTC | Allow specifying input classes directly. This will bypass the normal CWLPipeline input resolution process. | 11 February 2020, 16:11:27 UTC |
082500c | Thomas B. Mooney | 11 February 2020, 16:06:13 UTC | Add use strict, etc. No loosey-goosey modules here! | 11 February 2020, 16:06:13 UTC |
82d230a | Chris Miller | 07 February 2020, 18:49:32 UTC | preserve "build" prefix on build directory name the rest of gms uses a "build" prefix, this should too, for consistency (especially during storage1 migration) | 07 February 2020, 18:49:32 UTC |
b15a79b | Thomas B. Mooney | 05 February 2020, 20:43:37 UTC | Support specifying additional docker mount paths in CWL runner. | 05 February 2020, 20:56:06 UTC |
74cb902 | Thomas B. Mooney | 05 February 2020, 20:38:16 UTC | New config for specifying volumes that should be mounted in Docker jobs. | 05 February 2020, 20:42:46 UTC |
8bfe399 | Thomas B. Mooney | 05 February 2020, 20:37:57 UTC | Whitespace. | 05 February 2020, 20:37:57 UTC |
aee2fae | Thomas B. Mooney | 05 February 2020, 20:37:28 UTC | Allow for the possibility of WDL workflows sneaking in. | 05 February 2020, 20:37:28 UTC |
7a41637 | Thomas B. Mooney | 05 February 2020, 19:27:34 UTC | Not always cwltoil, so be more generic. | 05 February 2020, 19:27:34 UTC |
cc84bf6 | Chris Miller | 22 January 2020, 20:15:06 UTC | Merge pull request #1954 from chrisamiller/export_alloc allow build exports to use the same disk group | 22 January 2020, 20:15:06 UTC |
590a18f | Chris Miller | 22 January 2020, 20:14:40 UTC | Update lib/perl/Genome/Disk/Detail/Allocation/Copier.pm Co-Authored-By: Thomas B. Mooney <mooney@wustl.edu> | 22 January 2020, 20:14:40 UTC |
ba72491 | Chris Miller | 22 January 2020, 19:54:22 UTC | allow build exports to use the same disk group | 22 January 2020, 19:54:22 UTC |
3419c72 | Thomas B. Mooney | 14 January 2020, 18:22:56 UTC | Offer a self-service option in error, remove old queue reference. | 14 January 2020, 18:22:56 UTC |
1dfd7fc | apaul7 | 17 December 2019, 19:55:11 UTC | add is_10x_barcoded tests | 17 December 2019, 19:55:11 UTC |
c19ab45 | apaul7 | 17 December 2019, 19:54:08 UTC | add is_10x_barcoded | 17 December 2019, 19:54:08 UTC |
cba84bf | Thomas B. Mooney | 16 December 2019, 18:04:05 UTC | Merge pull request #1951 from tmooney/10x_gex_regex Convert protocol lists to regexes to account for lack of LIMS normalization. | 16 December 2019, 18:04:05 UTC |
b0fd5f8 | Thomas B. Mooney | 16 December 2019, 18:03:41 UTC | Merge pull request #1950 from tmooney/remove_limsy_flowcell_class Remove Genome::InstrumentData::FlowCell. | 16 December 2019, 18:03:41 UTC |
ab75aca | Thomas B. Mooney | 11 December 2019, 21:45:18 UTC | Remove Genome::InstrumentData::FlowCell. It doesn't represent a real entity in the system and has mostly been lingering a long while. | 12 December 2019, 23:17:05 UTC |
366a1f0 | Thomas B. Mooney | 12 December 2019, 23:10:05 UTC | Convert lists to regexes to account for lack of LIMS normalization. | 12 December 2019, 23:10:05 UTC |