| be76916 | Thomas Mooney | 24 June 2014, 15:39:18 UTC | New command to show config (mis)matches for an instrument-data | 24 June 2014, 15:39:18 UTC |
| 9114971 | APipe Tester | 24 June 2014, 12:17:02 UTC | Updated `genome` tab completion. | 24 June 2014, 12:17:02 UTC |
| baccbc0 | Nathaniel Nutter | 23 June 2014, 22:24:24 UTC | delegate permission changes to allocation | 23 June 2014, 22:27:40 UTC |
| 82175ba | Nathaniel Nutter | 23 June 2014, 22:19:17 UTC | add set_files_read_only (as opposed to files and directories) | 23 June 2014, 22:27:39 UTC |
| 71e5381 | Nathaniel Nutter | 23 June 2014, 22:18:55 UTC | add alias for function | 23 June 2014, 22:27:38 UTC |
| dc9fda7 | Thomas Mooney | 23 June 2014, 20:46:51 UTC | Update ClinSeq to account for DGIdb changes. | 23 June 2014, 20:46:51 UTC |
| 1a890a9 | Nathaniel Nutter | 23 June 2014, 20:12:22 UTC | add --unstartable-ok option In BQM unstartable "failures" do not need to result in an error since they are monitored downstream. Using this option will keep BQM from turning red when there are unstartable builds. | 23 June 2014, 20:12:22 UTC |
| 3cca138 | Thomas Mooney | 23 June 2014, 18:14:32 UTC | Merge the keys of the response hash instead of overwriting them | 23 June 2014, 18:14:32 UTC |
| 7a6de6e | Jim Weible | 23 June 2014, 15:22:59 UTC | allow 0 sized output files | 23 June 2014, 15:22:59 UTC |
| fe60d05 | Steve Wilkerson | 20 June 2014, 21:41:41 UTC | Added additional fields for report | 20 June 2014, 21:42:48 UTC |
| 57953aa | Nathaniel Nutter | 20 June 2014, 14:25:11 UTC | fix not telling Perl that string was an octal number | 20 June 2014, 14:25:39 UTC |
| a7791f6 | APipe Tester | 20 June 2014, 12:17:59 UTC | Updated `gmt` tab completion. | 20 June 2014, 12:17:59 UTC |
| fc3889e | APipe Tester | 20 June 2014, 12:17:16 UTC | Updated `genome` tab completion. | 20 June 2014, 12:17:16 UTC |
| 3b57be9 | APipe Tester | 20 June 2014, 12:15:42 UTC | Updated class browser cache. | 20 June 2014, 12:15:42 UTC |
| 04e44d4 | Thomas Mooney | 20 June 2014, 03:27:15 UTC | Allow output_dir to be specified as input. The command already offers output_dir as a command-line option, but any supplied value was ignored. Now it will be used if provided. | 20 June 2014, 03:27:15 UTC |
| 3b0b768 | Thomas Mooney | 20 June 2014, 03:23:38 UTC | Fix test--fill in param to get_response. | 20 June 2014, 03:23:38 UTC |
| c7a9112 | Thomas Mooney | 20 June 2014, 03:16:15 UTC | whitespace | 20 June 2014, 03:16:15 UTC |
| e43a0f1 | Thomas Mooney | 20 June 2014, 03:13:43 UTC | Set batch query size to avoid server timeout. | 20 June 2014, 03:13:43 UTC |
| e37491a | Thomas Mooney | 20 June 2014, 03:12:59 UTC | Include server error in error message on failure. | 20 June 2014, 03:12:59 UTC |
| 5cba95d | dmorton | 19 June 2014, 23:25:54 UTC | Only clean up locks that you create Locks created before a fork/exec had the potential to be cleaned up after the fork but before the exec if the forked child died. Now we just store the pid of the process when the lock is created and ensure that it is the same process that cleans up the lock. | 20 June 2014, 00:29:44 UTC |
| 8ab464e | Nathaniel Nutter | 19 June 2014, 22:41:08 UTC | remove development environment option from local web-app According to `plackup` docs the 'development' environment just enables three middleware. One of those is AccessLog and since we are adding our own custom version of AccessLog we need to disable the original. The production server also enabled the 'development' environment and will need the same change. | 19 June 2014, 22:44:06 UTC |
| c91b092 | Nathaniel Nutter | 19 June 2014, 22:37:57 UTC | add custom logging middleware This adds to Plack::Middleware to our web app: - GenomeAccessLog is a copy of AccessLog with the PID added. This will allow us to connect a response to a worker PID. - GenomePreAccessLog is a fork of AccessLog to log requests before running the PSGI app. This will allow us to know what a worker is doing before the request completes. | 19 June 2014, 22:44:05 UTC |
| 9a46a8f | APipe Tester | 19 June 2014, 21:35:24 UTC | updated jenkins submodule to 5b180ee | 19 June 2014, 21:35:29 UTC |
| b6ad270 | APipe Tester | 19 June 2014, 21:35:08 UTC | updated ur submodule to 95c1411 | 19 June 2014, 21:35:28 UTC |
| 5434c41 | apregier | 19 June 2014, 21:35:18 UTC | Merge branch 'updated' into gb_master | 19 June 2014, 21:35:18 UTC |
| 37eaec3 | apregier | 19 June 2014, 21:34:06 UTC | Remove unneeded sub::install | 19 June 2014, 21:34:06 UTC |
| 563417c | Feiyu Du | 19 June 2014, 21:14:05 UTC | make G::VR::E::BamReadcout::RunResult produce the correct region list to feed to bam-readcount | 19 June 2014, 21:14:05 UTC |
| 1867c35 | Nathaniel Nutter | 19 June 2014, 19:02:56 UTC | use is_near_soft_limit instead of is_over_soft_limit To avoid allocations "flapping", i.e. create and rollback, when volumes are approaching soft limit we will disable them when they get "close enough". | 19 June 2014, 19:53:22 UTC |
| 40e7c61 | Nathaniel Nutter | 19 June 2014, 19:01:54 UTC | add method to dynamically define proximity to soft limit | 19 June 2014, 19:53:22 UTC |
| b634b4e | Nathaniel Nutter | 19 June 2014, 19:00:24 UTC | update allocated_kb to also return allocation count in list context | 19 June 2014, 19:53:21 UTC |
| be83206 | Nathaniel Nutter | 18 June 2014, 19:26:58 UTC | add cached_unallocated_kb and use instead of unallocated_kb | 19 June 2014, 19:53:21 UTC |
| b6bf8d3 | Nathaniel Nutter | 18 June 2014, 19:17:02 UTC | add metric to record the number of attempted volumes | 19 June 2014, 19:53:20 UTC |
| a0d9d92 | Nathaniel Nutter | 18 June 2014, 19:08:48 UTC | convert debug_message to Genome::Logger Convert debug_message to Genome::Logger so that they go to logstash. | 19 June 2014, 19:53:19 UTC |
| 58f2914 | Nathaniel Nutter | 18 June 2014, 19:05:32 UTC | make has_space also check used_kb to reduce rollbacks due to over_used | 19 June 2014, 19:53:19 UTC |
| 0ad0e36 | Nathaniel Nutter | 18 June 2014, 19:03:04 UTC | add some convience methods to check proximity of soft/hard limits | 19 June 2014, 19:53:18 UTC |
| 3ad40be | Ian Ferguson | 19 June 2014, 18:48:53 UTC | Modify Picard and Bwamem memory handling | 19 June 2014, 18:49:31 UTC |
| 4134083 | Jason Walker | 19 June 2014, 18:48:21 UTC | Add a common model_identifier param so results are consistent for SummarizeAnalysisProject | 19 June 2014, 18:48:21 UTC |
| a8ca55a | Jason Walker | 19 June 2014, 18:46:40 UTC | Add support for either paired-end or fragment data | 19 June 2014, 18:46:40 UTC |
| 9500510 | Jason Walker | 19 June 2014, 18:45:00 UTC | Add command to list per instrument data alignment BAM files | 19 June 2014, 18:45:00 UTC |
| d54e27d | Jason Walker | 19 June 2014, 18:44:13 UTC | Add methods to retrive per-instrument data BAM files from merged alignment result. | 19 June 2014, 18:44:13 UTC |
| 4a17ecc | apregier | 19 June 2014, 16:22:29 UTC | Merge branch 'updated' into gb_master | 19 June 2014, 16:22:29 UTC |
| 7b0ba1b | apregier | 16 June 2014, 22:11:22 UTC | Add debug message | 19 June 2014, 16:18:51 UTC |
| c499d7b | apregier | 16 June 2014, 18:45:53 UTC | No filter value should pass | 19 June 2014, 16:18:50 UTC |
| 3fae48e | Thomas Mooney | 19 June 2014, 15:36:29 UTC | Limit genotypes processed in a single run. When too many are backlogged the process times out. | 19 June 2014, 15:36:29 UTC |
| 6a10067 | Thomas Mooney | 19 June 2014, 15:35:51 UTC | Add LSF resource request to SNV-Indel Report | 19 June 2014, 15:35:51 UTC |
| c129595 | Susanna Siebert | 19 June 2014, 15:01:36 UTC | Merge branch 'epitope_prediction' | 19 June 2014, 15:01:36 UTC |
| 11e286a | Susanna Siebert | 19 June 2014, 14:14:23 UTC | pull annotation db name and version from the somatic variation build, if provided | 19 June 2014, 14:14:23 UTC |
| 8247f51 | Thomas Mooney | 19 June 2014, 13:37:03 UTC | Remove stray ' after table name. | 19 June 2014, 13:37:03 UTC |
| 235c50b | APipe Tester | 19 June 2014, 12:17:39 UTC | Updated `genome` tab completion. | 19 June 2014, 12:17:39 UTC |
| a3dec5c | APipe Tester | 19 June 2014, 12:15:53 UTC | Updated class browser cache. | 19 June 2014, 12:15:53 UTC |
| 8b623b3 | Adam Coffman | 18 June 2014, 22:52:21 UTC | add columns to show config command | 18 June 2014, 22:52:21 UTC |
| 13e597a | Eddie Belter | 18 June 2014, 22:04:34 UTC | InstData: isa object with allocations! | 18 June 2014, 22:04:34 UTC |
| 5e8176d | Eddie Belter | 18 June 2014, 21:45:12 UTC | InstData: remove really old dacc command | 18 June 2014, 21:45:12 UTC |
| c2e6bf2 | Feiyu Du | 18 June 2014, 21:03:08 UTC | add bam-readcount indel case handling to Vcf::AnnotateWithReadcounts | 18 June 2014, 21:03:08 UTC |
| 341be76 | Mark Burnett | 18 June 2014, 19:20:06 UTC | g a-p view: add --disabled-configs option | 18 June 2014, 19:20:06 UTC |
| 9bb8b94 | Mark Burnett | 18 June 2014, 19:15:32 UTC | only display active config_items in terse mode | 18 June 2014, 19:15:55 UTC |
| 312a806 | Eddie Belter | 17 June 2014, 21:07:32 UTC | Build subclasses use reallocate_disk_allocations | 18 June 2014, 18:55:32 UTC |
| 98c2ece | Eddie Belter | 17 June 2014, 20:43:58 UTC | Build: isa object w/ allocations | 18 June 2014, 18:55:31 UTC |
| 870b8fd | Eddie Belter | 17 June 2014, 20:22:10 UTC | Obj w/ Allocations: test uses disk allocation test factory | 18 June 2014, 18:55:30 UTC |
| 5d96154 | Eddie Belter | 17 June 2014, 20:21:29 UTC | Test Factory: disk allocation overwrites archive/unarchive methods in disk allocation | 18 June 2014, 18:55:30 UTC |
| 6495fce | Eddie Belter | 17 June 2014, 16:21:24 UTC | Test Factory: add disk allocation | 18 June 2014, 18:55:29 UTC |
| a92a770 | Eddie Belter | 17 June 2014, 16:15:33 UTC | obj w/ Allocations: fix deallocate/delete | 18 June 2014, 18:55:29 UTC |
| e19bba5 | Eddie Belter | 16 June 2014, 23:23:19 UTC | Obj w/ Allocations: rename methods to indicate they are working with allocations | 18 June 2014, 18:55:28 UTC |
| fef40a8 | Eddie Belter | 16 June 2014, 21:33:19 UTC | Objects w/ Allocations: cleanup and Coffman suggestions | 18 June 2014, 18:55:27 UTC |
| 48fd9e4 | Eddie Belter | 16 June 2014, 17:46:21 UTC | Add utility obects with allocations for shared methods | 18 June 2014, 18:55:27 UTC |
| 8a20bb4 | Thomas Mooney | 18 June 2014, 18:53:33 UTC | Blithely update test data. | 18 June 2014, 18:53:33 UTC |
| 83ece68 | Mark Burnett | 18 June 2014, 18:12:57 UTC | sort displayed config_items by created_at | 18 June 2014, 18:13:22 UTC |
| 0cc09d5 | Thomas Mooney | 18 June 2014, 17:56:56 UTC | Cleanly exit when skipping diagram generation due to too many variants. | 18 June 2014, 17:56:56 UTC |
| f83f6e3 | Mark Burnett | 18 June 2014, 15:49:34 UTC | bugfix: `genome analysis-project view` config item status was wrong | 18 June 2014, 15:49:34 UTC |
| 680d0e2 | Mark Burnett | 18 June 2014, 14:34:48 UTC | add `genome analysis-project view` command | 18 June 2014, 15:31:56 UTC |
| 3cbc486 | Gabriel Sanderson | 17 June 2014, 22:29:31 UTC | Use factory to get_class for all reporter tests | 17 June 2014, 22:29:31 UTC |
| 5b150cd | Gabriel Sanderson | 17 June 2014, 22:19:26 UTC | use factory to get_class for all run tests. | 17 June 2014, 22:19:26 UTC |
| 72b9dbc | Gabriel Sanderson | 17 June 2014, 22:10:32 UTC | Use factory to get_class for all expert tests. | 17 June 2014, 22:10:32 UTC |
| f043dd1 | Gabriel Sanderson | 17 June 2014, 21:49:18 UTC | change lives_ok to isa_ok | 17 June 2014, 21:49:18 UTC |
| 1d9d05d | Gabriel Sanderson | 17 June 2014, 21:27:53 UTC | Use factory to get_class for all interpreter tests. | 17 June 2014, 21:32:05 UTC |
| 5174934 | Gabriel Sanderson | 17 June 2014, 20:54:28 UTC | Renamed filters to contain 'Filter' in the name. | 17 June 2014, 20:56:11 UTC |
| 162e626 | Gabriel Sanderson | 17 June 2014, 20:49:25 UTC | In every filter test, use the factory to get the class. This catches the case where the filter is not valid because of not being named *Filter.pm, or potentially other things. | 17 June 2014, 20:55:56 UTC |
| e4c1fe4 | Nathaniel Nutter | 17 June 2014, 20:21:01 UTC | fix mismatched quotes | 17 June 2014, 20:30:46 UTC |
| bcc635e | Nathaniel Nutter | 17 June 2014, 19:33:31 UTC | replace lchown We don't want to manage symlink permissions. | 17 June 2014, 19:33:31 UTC |
| 10fc09a | Thomas Mooney | 17 June 2014, 16:59:32 UTC | Use lchown to change the owner of the symlink. Perl's chown() would try to modify the file it points to, which we often lack permission to change. | 17 June 2014, 16:59:32 UTC |
| 3fecc26 | Michael J. Kiwala | 17 June 2014, 16:55:09 UTC | Point allpaths tests to new example output dir | 17 June 2014, 16:55:09 UTC |
| 6909164 | Susanna Siebert | 17 June 2014, 15:35:40 UTC | use whole_rmdup_bam_file instead of bam_path. set alignment result to be a correct AlignmentResult::Merged object | 17 June 2014, 15:36:29 UTC |
| 5d70c6d | Michael J. Kiwala | 17 June 2014, 15:30:51 UTC | Update allpaths pattern matching of sxresults file names | 17 June 2014, 15:32:02 UTC |
| 57e6270 | Thomas Mooney | 17 June 2014, 13:43:56 UTC | Print the username, not the user object. | 17 June 2014, 13:43:56 UTC |
| 7a0a793 | Nathaniel Nutter | 16 June 2014, 23:18:47 UTC | towards making permissions work correctly in CLE and Research | 16 June 2014, 23:18:47 UTC |
| 205189d | Nathaniel Nutter | 13 June 2014, 20:45:35 UTC | restore exceptions removed when Genome::Sys->rename threw exceptions | 16 June 2014, 23:18:40 UTC |
| 38dc46d | Nathaniel Nutter | 13 June 2014, 19:35:40 UTC | mimic CORE::rename better Since CORE::rename doesn't throw exception change this to not either. Which means some existing uses need to throw exceptions again to match previous CORE::rename usage. Check known error conditions CORE::rename produces and mimic by setting $! and returning false. | 16 June 2014, 23:18:39 UTC |
| ce189bb | Nathaniel Nutter | 13 June 2014, 19:35:27 UTC | return instead of die | 16 June 2014, 23:18:38 UTC |
| f25dd02 | Nathaniel Nutter | 12 June 2014, 22:02:48 UTC | use Genome::Sys->rename instead of CORE::rename Genome::Sys->rename does not preserve permissions, user, and group so respects setgid which is usually desired. | 16 June 2014, 23:18:38 UTC |
| 6cc285d | Nathaniel Nutter | 09 June 2014, 16:51:40 UTC | remove code that is trying to restore "default permissions" It is believed these were trying to work around issues with umask and setgid "not working" but instead we should try to fix the problem. | 16 June 2014, 23:18:37 UTC |
| bfcd094 | Nathaniel Nutter | 10 June 2014, 22:20:50 UTC | set umask when Genome is loaded This seems bold but I don't know how else to deal with user's custom umask's that restrict results. | 16 June 2014, 23:18:36 UTC |
| b4fa242 | Nathaniel Nutter | 16 June 2014, 20:42:09 UTC | restore space between options and values Options and values were squished together because it made it easier to secure now-deprecated 'run_as' behavior and because it appeared to work. However, if a user's email started with a lowercase 'L' then the '-u' option would get interpreted as an '-ul' option and fail. | 16 June 2014, 20:42:09 UTC |
| f0256c4 | Thomas Mooney | 16 June 2014, 19:25:47 UTC | Don't assume the genotype file is in the top-level of the allocation. | 16 June 2014, 19:25:47 UTC |
| d1915cb | APipe Tester | 16 June 2014, 18:41:47 UTC | updated ur submodule to 1bbd8d9 | 16 June 2014, 19:14:19 UTC |
| 776da49 | Malachi Griffith | 16 June 2014, 19:01:54 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 16 June 2014, 19:01:54 UTC |
| cc889f7 | Malachi Griffith | 16 June 2014, 19:01:45 UTC | add timeline plots to snv-indel-reports | 16 June 2014, 19:01:45 UTC |
| 9076fd2 | Mark Burnett | 16 June 2014, 15:33:24 UTC | build view: display associated analysis projects | 16 June 2014, 15:35:50 UTC |
| d3a1649 | Mark Burnett | 16 June 2014, 15:32:58 UTC | don't right-pad "Build" heading | 16 June 2014, 15:35:49 UTC |
| d603f1c | Thomas Mooney | 16 June 2014, 15:19:30 UTC | Delete needs to cascade to mappings containing that subject. | 16 June 2014, 15:26:11 UTC |
| aac6387 | apregier | 13 June 2014, 21:11:21 UTC | Merge branch 'updated' into gb_master | 13 June 2014, 21:11:21 UTC |
