| 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 |
| 720482b | Thomas B. Mooney | 04 December 2019, 20:49:45 UTC | Merge pull request #1949 from tmooney/increase_cromwell_timeout Increase connection timeout in Cromwell config to 30s. | 04 December 2019, 20:49:45 UTC |
| 5e2a541 | Thomas B. Mooney | 04 December 2019, 16:37:49 UTC | Increase connection timeout in Cromwell config to 30s. | 04 December 2019, 16:37:49 UTC |
| 1bac4ad | Thomas B. Mooney | 19 November 2019, 21:45:25 UTC | Merge pull request #1948 from tmooney/handle_scratch_dirs_in_build_allocations Handle builds with multiple allocations. | 19 November 2019, 21:45:25 UTC |
| 7f47344 | Thomas B. Mooney | 19 November 2019, 19:08:40 UTC | A build might have more than one allocation. * Use the plural accessor. * Avoid triggering UR's "multiple results in scalar context" error. | 19 November 2019, 19:08:40 UTC |
| d5eb9f3 | Thomas B. Mooney | 18 November 2019, 21:56:15 UTC | Merge pull request #1947 from tmooney/cromwell_config_job_group Use job group for Cromwell workers. | 18 November 2019, 21:56:15 UTC |
| 6a11f3f | Thomas B. Mooney | 18 November 2019, 16:48:52 UTC | Add a job group for Cromwell workers. | 18 November 2019, 16:48:52 UTC |
| e292172 | Thomas B. Mooney | 18 November 2019, 16:48:16 UTC | Distinguish ptero workers from process job groups. | 18 November 2019, 16:48:16 UTC |
| 583b793 | Thomas B. Mooney | 21 October 2019, 17:42:56 UTC | Merge pull request #1946 from tmooney/allow_chains_in_instrument_data_properties Allow chains in instrument data properties for model inputs. | 21 October 2019, 17:42:56 UTC |
| 1e29add | Thomas B. Mooney | 17 October 2019, 15:53:29 UTC | Allow chains in instrument data properties for model inputs. This does require each step in the chain to only return a single object, so no crazy multiplicative effects! (Like the listers and the rules, putting "delete" in would be amusing, so don't do that either!) | 17 October 2019, 15:53:29 UTC |
| ffcc067 | Thomas B. Mooney | 18 September 2019, 18:08:43 UTC | Merge pull request #1945 from tmooney/cleanup_scratch_command Command to clean up Scratch Directory for a Build | 18 September 2019, 18:08:43 UTC |
| d747746 | Thomas B. Mooney | 17 September 2019, 18:02:17 UTC | Don't try to clean up running builds! Maybe this should be more picky about what statuses it accepts? But this is the only status where the scratch allocation should be in active use. | 17 September 2019, 18:02:17 UTC |
| 5d3bbd5 | Thomas B. Mooney | 17 September 2019, 17:59:45 UTC | New command to cleanup scratch allocations for builds. Pretty bare-bones. Trusts that you picked the right builds! | 17 September 2019, 17:59:45 UTC |
| be2f5ba | Thomas B. Mooney | 27 August 2019, 19:37:10 UTC | Merge pull request #1941 from apaul7/add_is_10x Add is_10x_ support | 27 August 2019, 19:37:10 UTC |
| dc86987 | Thomas B. Mooney | 27 August 2019, 19:36:50 UTC | Merge pull request #1943 from tmooney/fix_invalid_perl_in_music_survival Don't use defined on an array. | 27 August 2019, 19:36:50 UTC |
| ff306e8 | Thomas B. Mooney | 27 August 2019, 19:36:41 UTC | Merge pull request #1938 from tmooney/better_error_message_when_wf_not_found Include the data in the error message, not the memory reference! | 27 August 2019, 19:36:41 UTC |
| 9f6d75e | Thomas B. Mooney | 13 August 2019, 14:19:09 UTC | Don't use defined on an array. It used to be a warning back when this was written. Now it's an error. Either way, it doesn't make sense, so I borrowed the conditional from a different line of the file to replace this one. I make no guarantees of the ongoing usefulness of this tool, but it compiles now :) | 13 August 2019, 14:19:09 UTC |
| 50c0d7c | apaul7 | 05 August 2019, 16:21:13 UTC | fix typo, 5'->3' | 05 August 2019, 16:21:13 UTC |
| 8dcf39f | apaul7 | 02 August 2019, 17:33:24 UTC | update test count | 02 August 2019, 17:33:24 UTC |
| 4ffc4ee | apaul7 | 02 August 2019, 16:39:26 UTC | add is_10x tests | 02 August 2019, 16:39:26 UTC |
| 1a24855 | apaul7 | 02 August 2019, 16:37:57 UTC | add is_10x lib support | 02 August 2019, 16:37:57 UTC |
| 6abac49 | Thomas B. Mooney | 23 July 2019, 03:45:39 UTC | Merge pull request #1940 from tmooney/better_symlink_prefix_handling_in_cwlpipeline Better symlink handling in CWL output staging. | 23 July 2019, 03:45:39 UTC |
| a3eb5e3 | Thomas B. Mooney | 22 July 2019, 18:13:02 UTC | Also use File::Copy::Recursive for directories. Similar story to symlinks, but different solution :) | 22 July 2019, 18:13:02 UTC |
| 468fa0c | Thomas B. Mooney | 22 July 2019, 15:58:21 UTC | Better symlink handling in CWL output staging. | 22 July 2019, 15:58:21 UTC |
| 897ad9b | Thomas B. Mooney | 18 July 2019, 15:35:48 UTC | Merge pull request #1937 from tmooney/scratch_storage Create a separate allocation for scratch space for CWL builds. | 18 July 2019, 15:35:48 UTC |
| 8096f76 | Thomas B. Mooney | 10 July 2019, 22:28:31 UTC | Merge pull request #1939 from tmooney/exclude_abandon_from_priors Exclude "Abandoned" status from choices for builds to abandon. | 10 July 2019, 22:28:31 UTC |
| ce4209b | Thomas B. Mooney | 19 June 2019, 18:36:30 UTC | Create a separate allocation for scratch space for CWL builds. This way we can have a pool of scratch space and final project disk groups can be sized to only hold the final data products. | 10 July 2019, 21:09:11 UTC |
| ff96558 | Thomas B. Mooney | 10 July 2019, 21:08:35 UTC | Add new config for defining a scratch disk group. | 10 July 2019, 21:09:10 UTC |
| 09e618e | Thomas B. Mooney | 09 July 2019, 20:30:36 UTC | Exclude "Abandoned" status from choices for builds to abandon. They're already taken care of ;) | 09 July 2019, 20:30:36 UTC |
| 6264751 | Thomas B. Mooney | 19 June 2019, 19:43:09 UTC | Include the data in the error message, not the memory reference! This should hopefully make this error a little more useful. | 19 June 2019, 19:43:09 UTC |
| b3cebfe | Thomas B. Mooney | 05 June 2019, 16:34:00 UTC | Merge pull request #1934 from tmooney/skip_abandon_when_no_matching_builds Skip running the abandon command when no builds match. | 05 June 2019, 16:34:00 UTC |
| 11f74c6 | Thomas B. Mooney | 30 May 2019, 18:52:39 UTC | Merge pull request #1936 from tmooney/import_lims_data_in_subprocess Use a subprocess to import LIMS instrument data. | 30 May 2019, 18:52:39 UTC |
| 5e90d5f | Thomas B. Mooney | 30 May 2019, 18:34:58 UTC | Use a subprocess to import LIMS instrument data. The command wants to commit() for each instrument data, which causes some nasty side-effects to CQID. We'd still like this to commit immediately--importing can take a long time and CQID timeouts might otherwise prevent it from making progress is certain situations. | 30 May 2019, 18:34:58 UTC |
| 3ee799d | Thomas B. Mooney | 30 May 2019, 14:35:44 UTC | Merge pull request #1935 from tmooney/validate_disk_groups_when_volume_specified Check that we got exactly one disk group and explicitly die if not. | 30 May 2019, 14:35:44 UTC |
| 5dd5ef8 | Thomas B. Mooney | 29 May 2019, 21:02:18 UTC | Check that we got exactly one disk group and explicitly die if not. This should help make more plain errors if a volume belongs to multiple disk groups (or...none, if such a thing ever were to happen!). | 29 May 2019, 21:02:18 UTC |
| 59f5daf | Thomas B. Mooney | 29 May 2019, 19:58:30 UTC | Skip running the abandon command when no builds match. | 29 May 2019, 19:58:30 UTC |
| c262cc1 | Thomas B. Mooney | 22 May 2019, 17:25:03 UTC | Merge pull request #1933 from tmooney/tool_to_abandon_prior_builds Tool to abandon prior builds for a model. | 22 May 2019, 17:25:03 UTC |
| 15aa350 | Thomas B. Mooney | 22 May 2019, 17:24:42 UTC | Merge pull request #1932 from tmooney/fix_disk_group_fix Make sure we're in the AnP environment when looking up the disk group. | 22 May 2019, 17:24:42 UTC |
| 78ea58b | Thomas B. Mooney | 13 May 2019, 18:15:24 UTC | Tool to abandon prior builds for a model. If a model has many builds, sometimes we only want to keep the recent ones. This facilitates abandoning the others for a large project. | 13 May 2019, 18:22:48 UTC |
| 9fe2000 | Thomas B. Mooney | 23 April 2019, 22:19:36 UTC | Make sure we're in the AnP environment when looking up the disk group. | 23 April 2019, 22:19:36 UTC |
| 3c31477 | Thomas B. Mooney | 22 April 2019, 15:02:26 UTC | Merge pull request #1931 from tmooney/trusted_importer New command to import a directory of instrument data. | 22 April 2019, 15:02:26 UTC |
| 626fe46 | Thomas Mooney | 19 April 2019, 21:41:28 UTC | Make read_count into a required property. | 19 April 2019, 21:41:28 UTC |
| b4e740f | Thomas B. Mooney | 19 April 2019, 20:05:13 UTC | Only pass the description along if we have one. No setting of descriptions to `0` or the empty string ;) | 19 April 2019, 20:05:13 UTC |
| 62ca245 | Thomas B. Mooney | 16 April 2019, 21:53:02 UTC | Skip the `rsync` test on protocol version 30. Probably older versions don't work either, but we don't currently have to deal with those :) | 16 April 2019, 21:53:02 UTC |
| 74af554 | Thomas B. Mooney | 16 April 2019, 21:02:26 UTC | New command to import a directory of instrument data. No validation is performed whatsoever... it trusts you and the data! If it happens to conform to an expected standard, it'll work with existing tools. If it doesn't, it won't! But in the age of CWL pipelines, someone could make one that handles it. | 16 April 2019, 21:02:26 UTC |
| 283a878 | Thomas B. Mooney | 02 April 2019, 18:02:54 UTC | Merge pull request #1930 from tmooney/dont_load_disk_group_in_lims_importer Don't bother loading up the disk group. | 02 April 2019, 18:02:54 UTC |
| 465b342 | Thomas B. Mooney | 02 April 2019, 15:28:23 UTC | Don't bother loading up the disk group. The allocation system will handle that! Also... sometimes the config specifies a specific volume instead of a group, in which case this extra code would crash. | 02 April 2019, 15:28:23 UTC |
| b5f96f0 | Thomas B. Mooney | 25 March 2019, 18:35:38 UTC | Only consider active allocations when deciding whether to import. A previous import might have been purged, in which case new analysis would require reimporting the data. (Users can then also use `genome analysis-project reprocess` if they need to pull back the data to build again later.) | 25 March 2019, 18:35:38 UTC |
| 7c89f25 | Thomas B. Mooney | 19 March 2019, 14:34:46 UTC | Merge pull request #1924 from tmooney/cqid_imports_data Site Feature: Import instrument data from LIMS in CQID. | 19 March 2019, 14:34:46 UTC |
| 02c6795 | Thomas B. Mooney | 07 March 2019, 16:05:59 UTC | Fixup CQID test so that instrument data already looks "imported". | 11 March 2019, 22:41:20 UTC |
| bcc19c1 | Thomas B. Mooney | 11 March 2019, 17:59:07 UTC | Merge pull request #1926 from tmooney/note_only_the_lsf_job_id Ensure only the LSF Job ID gets into the process note. | 11 March 2019, 17:59:07 UTC |
| 994a93d | Thomas B. Mooney | 11 March 2019, 17:58:42 UTC | Merge pull request #1925 from tmooney/dont_mail_build_reports Stop e-mailing build reports. | 11 March 2019, 17:58:42 UTC |
| 9875147 | Thomas B. Mooney | 11 March 2019, 17:58:10 UTC | Merge pull request #1923 from tmooney/cromwell_in_workflow_view Display Cromwell workflows in `genome model build view`. | 11 March 2019, 17:58:10 UTC |
| 6dce239 | Thomas B. Mooney | 11 March 2019, 17:56:22 UTC | Merge pull request #1922 from tmooney/simple_backend_fixes A few fixes for the "simple" backend. | 11 March 2019, 17:56:22 UTC |
| b32d835 | Thomas B. Mooney | 11 March 2019, 17:56:01 UTC | Merge pull request #1916 from johnegarza/import_basic_picard_fix Using updated picard version to fix a bug in the old version | 11 March 2019, 17:56:01 UTC |
| f5f810f | Thomas B. Mooney | 11 March 2019, 14:24:40 UTC | Ensure only the LSF Job ID gets into the process note. There's logic to prepend any notes with a sudo message when running as another user, but that's not helpful here. (Really, storing this as a note is not great--it should just be a column on the table.) | 11 March 2019, 14:24:40 UTC |
| 902e058 | Thomas B. Mooney | 07 March 2019, 21:04:39 UTC | Stop e-mailing build reports. We'd already turned these off for production users as they're noisy. | 07 March 2019, 21:04:39 UTC |
| cc589ec | Thomas B. Mooney | 05 March 2019, 23:01:59 UTC | Site Feature: Import instrument data from LIMS in CQID. This will cause CQID failures when the data could not be imported. But that's probably fine, since the builds would themselves fail later! There is an additional complication in that this would need to be run as a user with access to import the data. | 05 March 2019, 23:01:59 UTC |
| dd3f895 | Alex Paul | 04 March 2019, 15:25:01 UTC | Typo fix: s/thsi/this. Co-Authored-By: tmooney <mooney@wustl.edu> | 04 March 2019, 15:25:01 UTC |
| 298f3b5 | Thomas B. Mooney | 28 February 2019, 20:07:17 UTC | Implement the summary threshold. | 28 February 2019, 20:07:17 UTC |
| 3bf04c1 | Thomas B. Mooney | 28 February 2019, 19:59:12 UTC | Display Cromwell workflows in `genome model build view`. For CWL, this will be a lot more informative than the Ptero workflow (if one even exists)! | 28 February 2019, 19:59:12 UTC |
| 1d2fce3 | Thomas B. Mooney | 28 February 2019, 16:56:33 UTC | A few fixes for the "simple" backend. * The bsub module expects "log_dir" not "out_dir". * The DAG should process a simple workflow like an inline one. | 28 February 2019, 16:56:33 UTC |
| 385fe08 | Thomas B. Mooney | 27 February 2019, 17:46:32 UTC | Merge pull request #1921 from tmooney/cromwell_set_default_memory_request Set default memory request of 4096MB. | 27 February 2019, 17:46:32 UTC |
| daff014 | Thomas B. Mooney | 27 February 2019, 17:21:50 UTC | Merge pull request #1920 from tmooney/cromwell_config_span Add "span[hosts=1]" to our LSF requests. | 27 February 2019, 17:21:50 UTC |
| 5e5cc79 | Thomas B. Mooney | 27 February 2019, 16:28:30 UTC | Merge pull request #1919 from tmooney/everything_old_is_new_again-simple_backend New WorkflowBuilder Backend: `simple` | 27 February 2019, 16:28:30 UTC |
| 7a4e2f3 | Thomas B. Mooney | 26 February 2019, 19:22:33 UTC | Set default memory request of 4096MB. | 26 February 2019, 19:22:33 UTC |
| 09a575f | Thomas B. Mooney | 26 February 2019, 15:33:47 UTC | Add "span[hosts=1]" to our LSF requests. When requesting multiple cores, we'd really like them to be on the same host! | 26 February 2019, 15:33:47 UTC |
| ae590b1 | Thomas B. Mooney | 20 February 2019, 23:37:27 UTC | More and better error messages. | 20 February 2019, 23:37:27 UTC |
| 32f70e8 | Thomas B. Mooney | 20 February 2019, 23:28:01 UTC | New WorkflowBuilder backend: "simple". This `bsub`s a single job which then runs the workflow inline. For one-step workflows (like CwlPipeline or ReferenceSequence) this is approximately the same as launching with Ptero, but without the overhead! For more complicated workflows (like SomaticValidation) this would almost certainly be a poor choice. This is pretty much equivalent to this combo of options from "Workflow": --server-dispatch lsf --job-dispatch inline | 20 February 2019, 23:32:45 UTC |
