| 5365b6d | Feiyu Du | 19 May 2014, 22:11:44 UTC | run SpliceJunctionSummary specifically on tophat alignment | 19 May 2014, 22:11:44 UTC |
| eaafd94 | Nathaniel Nutter | 19 May 2014, 21:28:12 UTC | remove unused line | 19 May 2014, 21:28:32 UTC |
| b024645 | Nathaniel Nutter | 19 May 2014, 21:27:11 UTC | it seems like default implies optional but it doesn't so make explicit This fixes what looks like an invalid workflow due to missing inputs since the inputs have default values but aren't marked as optional. | 19 May 2014, 21:28:31 UTC |
| ef39c54 | Nathaniel Nutter | 19 May 2014, 21:24:47 UTC | since builds is_many should specify as array While Workflow might support passing singular items into is_many inputs it is better if the thing that has knowledege about the inputs (the model) specifies a list with one element. Flow does not wrap single elements in a list. | 19 May 2014, 21:28:29 UTC |
| 31c7d31 | apregier | 19 May 2014, 21:13:18 UTC | Removed vep params | 19 May 2014, 21:13:18 UTC |
| 6e3f7b3 | apregier | 19 May 2014, 19:36:31 UTC | Remove parameterization from vep so things always get run | 19 May 2014, 21:09:14 UTC |
| 36e2532 | apregier | 19 May 2014, 18:07:49 UTC | Added new outputs to vep interpreter | 19 May 2014, 20:29:33 UTC |
| b6369a3 | apregier | 19 May 2014, 16:57:11 UTC | New contains-tag filter | 19 May 2014, 20:29:33 UTC |
| 40d4d9e | apregier | 19 May 2014, 20:23:44 UTC | Keep using IPC::Run | 19 May 2014, 20:23:44 UTC |
| d21eb85 | Thomas Mooney | 19 May 2014, 20:03:39 UTC | Provide a reason when abandoning the builds. | 19 May 2014, 20:03:39 UTC |
| 729c25e | APipe Tester | 19 May 2014, 19:44:54 UTC | updated graphite submodule to be02103 | 19 May 2014, 19:44:54 UTC |
| 15a6f83 | dmorton | 19 May 2014, 17:19:21 UTC | die when no API path can be found This makes it so that less boilerplate is needed by consumers of this method as well as being more consistent with the way Sys->shellcmd works. | 19 May 2014, 18:06:38 UTC |
| 92d667d | dmorton | 19 May 2014, 17:18:30 UTC | Use Genome::Sys->shellcmd instead of IPC::Run 1) for status logging 2) for input/output file validation | 19 May 2014, 18:06:38 UTC |
| eefd30b | dmorton | 13 May 2014, 23:10:50 UTC | Invalid annotation plans cause builds to be unstartable | 19 May 2014, 18:06:37 UTC |
| 00eaeb0 | dmorton | 13 May 2014, 22:22:31 UTC | Vep correctly annotates multiple alternate alleles | 19 May 2014, 18:06:37 UTC |
| a2a369b | dmorton | 13 May 2014, 02:21:23 UTC | Fix imports related to File::Vcf::Differ | 19 May 2014, 18:06:37 UTC |
| 001833e | dmorton | 13 May 2014, 02:16:40 UTC | Add SplitAlternateAlleles and test This command splits vcf lines into multiple lines (one per alternate allele) and clears INFO fields. | 19 May 2014, 18:06:37 UTC |
| 730cd28 | dmorton | 12 May 2014, 22:58:56 UTC | Remove spurious execution return value checking | 19 May 2014, 18:06:37 UTC |
| e331d8b | dmorton | 12 May 2014, 20:23:44 UTC | Replace temp with methods | 19 May 2014, 18:06:37 UTC |
| e2bc1c7 | dmorton | 12 May 2014, 20:17:15 UTC | Replace temp with method (vep_params) | 19 May 2014, 18:06:37 UTC |
| 0d64f89 | dmorton | 12 May 2014, 20:16:37 UTC | Replace temp with method (custom_annotation_inputs) | 19 May 2014, 18:06:37 UTC |
| 99df226 | Avinash Ramu | 19 May 2014, 02:52:11 UTC | update clin-seq blessed | 19 May 2014, 02:52:42 UTC |
| 19c1d66 | Avinash Ramu | 19 May 2014, 01:43:45 UTC | update getvariant sources to handle mutect | 19 May 2014, 02:52:40 UTC |
| 3083d30 | Avinash Ramu | 16 May 2014, 17:11:02 UTC | extract method | 19 May 2014, 02:52:37 UTC |
| 8162c78 | Avinash Ramu | 16 May 2014, 16:04:55 UTC | refactor write output file | 19 May 2014, 02:52:37 UTC |
| 1f741c7 | Avinash Ramu | 16 May 2014, 15:20:34 UTC | minor refactor | 19 May 2014, 02:52:36 UTC |
| eb3fd72 | Avinash Ramu | 14 May 2014, 21:47:42 UTC | remove unused function | 19 May 2014, 02:52:36 UTC |
| d849156 | Avinash Ramu | 14 May 2014, 21:37:15 UTC | update description for cnv plot tool | 19 May 2014, 02:52:35 UTC |
| a19b00d | Adam Coffman | 16 May 2014, 20:12:31 UTC | make is_capture return explicit 1 or 0 | 16 May 2014, 20:12:31 UTC |
| 377b438 | Adam Coffman | 16 May 2014, 19:43:08 UTC | analysis project deletes now cascade | 16 May 2014, 19:43:08 UTC |
| b026682 | APipe Tester | 16 May 2014, 16:49:24 UTC | updated jenkins submodule to 5eb7e15 | 16 May 2014, 16:49:24 UTC |
| e7b8a5a | APipe Tester | 16 May 2014, 14:54:38 UTC | updated ur submodule to 48f2b46 | 16 May 2014, 14:54:38 UTC |
| 2d60b31 | APipe Tester | 16 May 2014, 12:19:50 UTC | Updated `gmt` tab completion. | 16 May 2014, 12:19:50 UTC |
| 774b570 | APipe Tester | 16 May 2014, 12:19:05 UTC | Updated `genome` tab completion. | 16 May 2014, 12:19:05 UTC |
| 151af66 | APipe Tester | 16 May 2014, 12:17:28 UTC | Updated class browser cache. | 16 May 2014, 12:17:28 UTC |
| 77e4543 | APipe Tester | 15 May 2014, 22:59:57 UTC | updated ur submodule to b35b1b1 | 15 May 2014, 22:59:57 UTC |
| fc9a49f | Chris Miller | 15 May 2014, 21:27:28 UTC | adding --clean-output option to avoid all of the symlinking junk. I'd prefer that it be clean by default with the option to turn on symlinks, but I suspect that would require changing dozens of places in the codebase | 15 May 2014, 22:24:39 UTC |
| 0989505 | Eddie Belter | 15 May 2014, 22:13:19 UTC | GM: add logic to test factory to set genotype file | 15 May 2014, 22:13:28 UTC |
| 51174fe | Dave Larson | 15 May 2014, 21:00:37 UTC | Append change frequency instead of prepend | 15 May 2014, 21:01:04 UTC |
| a1804a3 | Adam Coffman | 15 May 2014, 20:53:01 UTC | fall back on empty string rather than undef to avoid warnings | 15 May 2014, 20:53:01 UTC |
| b0b5e0e | Eddie Belter | 15 May 2014, 20:30:16 UTC | InstData GM: add snp hash getting to meethods installed to imported; misc cleanup | 15 May 2014, 20:30:35 UTC |
| 1b1e2dc | Eddie Belter | 15 May 2014, 19:57:15 UTC | InstData GM: move genotype_file methods to Microarray class; install genotype file methods from Microarray into Imported | 15 May 2014, 20:30:33 UTC |
| ba35887 | Eddie Belter | 15 May 2014, 19:56:30 UTC | InstData Imported: rm unused genotype microarray methods | 15 May 2014, 20:30:32 UTC |
| 9109e0a | Eddie Belter | 14 May 2014, 21:27:19 UTC | Genotype Microarray: genotype_file is a calculated method; do not use genotpe_file attr | 15 May 2014, 20:30:31 UTC |
| 99499ee | apregier | 15 May 2014, 20:22:49 UTC | Merge branch 'updated' into gb_master | 15 May 2014, 20:22:49 UTC |
| be901fd | apregier | 15 May 2014, 20:21:31 UTC | Add metric to track how many AF contribute to verifyBamId metrics | 15 May 2014, 20:21:46 UTC |
| bc5ebf8 | Thomas Mooney | 15 May 2014, 19:55:59 UTC | Be more stringent validating BD FASTQs; be more lenient in NovoRealign. This should allow cases with empty FASTQs to proceed through filtering, but hopefully catch the case of misconfigured Breakdancer sooner. | 15 May 2014, 19:55:59 UTC |
| dabd342 | Gabriel Sanderson | 15 May 2014, 19:16:49 UTC | All __profile_errors__ should call their super first in case of general behavior. | 15 May 2014, 19:32:15 UTC |
| 7933135 | Dave Larson | 15 May 2014, 19:21:19 UTC | * Don't print numerical labels unless the mutation is above the maximum frequency. * Add an option (--allow-floating-labels) to allow variable y positioning on each mutation's label | 15 May 2014, 19:22:51 UTC |
| 0682602 | Feiyu Du | 15 May 2014, 19:13:34 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 15 May 2014, 19:13:34 UTC |
| 27e42f6 | Feiyu Du | 15 May 2014, 19:13:22 UTC | add run parameter to handle unstranded instrument data | 15 May 2014, 19:13:22 UTC |
| 0e4e9a7 | Adam Coffman | 15 May 2014, 18:25:24 UTC | add reprocess option to add-config-file command | 15 May 2014, 18:25:24 UTC |
| 6e68870 | Susanna Siebert | 15 May 2014, 15:32:51 UTC | skip the vcf entry if there is no data for the sample | 15 May 2014, 15:36:09 UTC |
| 5bb77bc | Thomas Mooney | 15 May 2014, 15:35:21 UTC | Only add a number if needed, and respect that suffixes are at the end. | 15 May 2014, 15:35:21 UTC |
| b9a5a53 | Thomas Mooney | 15 May 2014, 14:44:35 UTC | Only increment the QC name when making a new model. Otherwise we can't find the existing ones! | 15 May 2014, 14:44:35 UTC |
| 93da51e | Thomas Mooney | 15 May 2014, 14:09:15 UTC | Ensure the value of "show" is set before listing. | 15 May 2014, 14:09:15 UTC |
| 4a63d06 | Susanna Siebert | 15 May 2014, 13:12:34 UTC | allow users to specify a suffix to the model names | 15 May 2014, 13:12:34 UTC |
| 2ecc408 | APipe Tester | 15 May 2014, 12:18:18 UTC | Updated `genome` tab completion. | 15 May 2014, 12:18:18 UTC |
| e55c860 | APipe Tester | 15 May 2014, 12:16:42 UTC | Updated class browser cache. | 15 May 2014, 12:16:42 UTC |
| 28c6794 | Anthony Brummett | 15 May 2014, 00:06:48 UTC | Update test diff file due to changes likely introduced in 6b3d60 | 15 May 2014, 00:06:48 UTC |
| 3fc23b1 | Anthony Brummett | 14 May 2014, 23:49:14 UTC | Change the property data types to UR data types The test Genome/Model/Command/Import_and_Export_Metadata.t was preloading Genome::Model::Build::Input objects which already existed in memory. Since PostgreSQL was returning these objects in a different order that UR had them sorted, the Loading Iterator concluded that a handful of them were actually deleted in the database. The test then thought it was IMPORTING them instead of FOUND them. Between the new support for "C" collation of text-type columns in UR::DS::Pg, and changing the data types, that preload get() no longer deletes those objects. | 14 May 2014, 23:49:14 UTC |
| 3714b07 | Avinash Ramu | 14 May 2014, 21:17:44 UTC | update test cases | 14 May 2014, 21:18:20 UTC |
| c14b956 | Avinash Ramu | 14 May 2014, 21:17:10 UTC | add snv files | 14 May 2014, 21:18:20 UTC |
| be692ad | Mark Burnett | 14 May 2014, 20:32:58 UTC | unify InstrumentData lister This changes makes the output of help not depend on the specified subclass, which means that it does not list the valid or default values for show. | 14 May 2014, 21:11:17 UTC |
| b740942 | apregier | 13 May 2014, 22:21:24 UTC | Translate CAF to AF in VCF results | 14 May 2014, 20:46:43 UTC |
| 56f9ddc | Avinash Ramu | 14 May 2014, 17:04:26 UTC | use NAs for missing columns | 14 May 2014, 18:47:10 UTC |
| ab56784 | Avinash Ramu | 13 May 2014, 19:00:50 UTC | make plotCNVs a part of clin-seq-converge | 14 May 2014, 18:47:09 UTC |
| cc691e6 | Nathaniel Nutter | 14 May 2014, 18:17:12 UTC | (sometimes) fix setgid being removed by Genome::Sys->create_directory | 14 May 2014, 18:46:10 UTC |
| 82cd129 | Nathaniel Nutter | 13 May 2014, 21:08:44 UTC | only chown if we have to We might want to just get rid of this chown and rely on setgid, etc. to control this. In fact, the reason to make the chown only execute if needed is because it removes setgid on root_squashed NFS volumes. | 14 May 2014, 18:46:09 UTC |
| b2a49ff | Nathaniel Nutter | 09 May 2014, 20:00:16 UTC | failing test for setgid | 14 May 2014, 18:46:08 UTC |
| d4545fe | Nathaniel Nutter | 14 May 2014, 18:45:10 UTC | increased model count in expected update-analysis output | 14 May 2014, 18:45:46 UTC |
| ea72fe2 | Mark Burnett | 14 May 2014, 18:22:10 UTC | microarray: relax errors while looking for instrument data | 14 May 2014, 18:22:10 UTC |
| aaa0578 | APipe Tester | 14 May 2014, 12:19:42 UTC | Updated `gmt` tab completion. | 14 May 2014, 12:19:42 UTC |
| 83a35c1 | APipe Tester | 14 May 2014, 12:18:58 UTC | Updated `genome` tab completion. | 14 May 2014, 12:18:58 UTC |
| 9553355 | APipe Tester | 14 May 2014, 12:17:21 UTC | Updated class browser cache. | 14 May 2014, 12:17:21 UTC |
| 3809fdb | APipe Tester | 13 May 2014, 21:21:05 UTC | updated ur submodule to a13ec70 | 13 May 2014, 21:21:05 UTC |
| 512f7ce | Eddie Belter | 13 May 2014, 20:45:47 UTC | GME Flexbar: add version 2.4 | 13 May 2014, 20:45:47 UTC |
| 2efcc7b | Feiyu Du | 13 May 2014, 18:52:39 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 13 May 2014, 18:52:39 UTC |
| 995132f | Thomas Mooney | 13 May 2014, 18:31:53 UTC | Fall back on the BED file stored in the ROI FeatureList. | 13 May 2014, 18:31:53 UTC |
| c7aa44a | Feiyu Du | 13 May 2014, 18:15:38 UTC | Add star unit test | 13 May 2014, 18:16:48 UTC |
| 6bdcd7f | Feiyu Du | 12 May 2014, 17:15:21 UTC | more tweaks to plug star in rna-seq pipeline | 13 May 2014, 18:16:48 UTC |
| 997101e | Feiyu Du | 06 May 2014, 19:03:03 UTC | Add star aligner to rna-seq pipeline | 13 May 2014, 18:16:48 UTC |
| 19f54d2 | Feiyu Du | 25 April 2014, 20:01:23 UTC | Add star aligner for rna-seq model | 13 May 2014, 18:16:47 UTC |
| 6ce4635 | Nathaniel Nutter | 13 May 2014, 17:49:50 UTC | remove transition code for created_by | 13 May 2014, 17:49:50 UTC |
| 6ea6cb9 | Nathaniel Nutter | 13 May 2014, 17:48:52 UTC | can't define with aliased property user_name | 13 May 2014, 17:49:45 UTC |
| 6b3d607 | Nathaniel Nutter | 13 May 2014, 15:17:03 UTC | remove transition code for created_by All snapshots (for awhile now) have created_by/run_as and all models (except 2 that had no user_name) have values. | 13 May 2014, 17:49:44 UTC |
| 0955494 | Thomas Mooney | 13 May 2014, 17:44:51 UTC | Add two more metrics for the benefit of the coverage report views. | 13 May 2014, 17:44:51 UTC |
| 78e3774 | Nathaniel Nutter | 13 May 2014, 15:30:37 UTC | allow run_as to be specified when defining models | 13 May 2014, 15:30:37 UTC |
| 538dca2 | Nathaniel Nutter | 13 May 2014, 15:30:03 UTC | update Genome/Model/Command/Define-docs.t expected output for run-as | 13 May 2014, 15:30:03 UTC |
| d254069 | Nathaniel Nutter | 13 May 2014, 15:07:40 UTC | allow run_as to be specified when defining models It is desired that production managers be able to create SomaticVariation models that can run as the production user (apipe-builder or cle). | 13 May 2014, 15:07:40 UTC |
| 53bea3f | apregier | 13 May 2014, 14:54:03 UTC | Skip useless test that fails all the time | 13 May 2014, 14:56:51 UTC |
| 1e4d29e | Nathaniel Nutter | 13 May 2014, 14:05:55 UTC | no longer need runtime default value for creation_time Remove the runtime default value for creation_time now that values have been backfilled in the database. | 13 May 2014, 14:51:18 UTC |
| 466f052 | Thomas Mooney | 13 May 2014, 14:28:54 UTC | Update due to updated updated_at (again). | 13 May 2014, 14:28:54 UTC |
| a813b85 | Nathaniel Nutter | 12 May 2014, 21:25:43 UTC | hard-code assumption about test Instead of depending on our current GENOME_SYS_UMASK hard-code in the value for the test. | 13 May 2014, 13:36:43 UTC |
| 64f68f3 | Nathaniel Nutter | 12 May 2014, 21:24:17 UTC | add test case Setting GENOME_SYS_UMASK='0027' for 'cle' user revealed that by not casting GENOME_SYS_UMASK as octal we were not using the expected umask. | 13 May 2014, 13:36:42 UTC |
| 8067ad1 | Nathaniel Nutter | 12 May 2014, 21:23:47 UTC | refactor test to use Genome::Utility::Test::Stat | 13 May 2014, 13:36:40 UTC |
| cf37205 | Nathaniel Nutter | 12 May 2014, 21:10:57 UTC | give tests default names | 13 May 2014, 13:36:39 UTC |
| f32fb72 | Nathaniel Nutter | 12 May 2014, 20:47:00 UTC | add Genome::Utility::Test::Stat | 13 May 2014, 13:36:37 UTC |
| 18f9fb3 | Thomas Mooney | 13 May 2014, 13:31:03 UTC | Newline at end of file. | 13 May 2014, 13:31:03 UTC |
| 91f5d4c | Thomas Mooney | 13 May 2014, 13:24:30 UTC | Update expected to account for updated updated_at time. | 13 May 2014, 13:24:30 UTC |
