| 423238b | apregier | 20 November 2014, 17:46:03 UTC | Merge pull request #223 from apregier/improve-showdocs-cli Allow singular versions of component types | 20 November 2014, 17:46:03 UTC |
| ad3d60c | Thomas B. Mooney | 20 November 2014, 15:54:20 UTC | Merge pull request #230 from tmooney/use_test_data Use fake data for this test. (Except the reference...) | 20 November 2014, 15:54:20 UTC |
| 2cd448e | Thomas B. Mooney | 20 November 2014, 15:41:24 UTC | Merge pull request #220 from tmooney/add_menuitem_relations Add accessors to configs and projects using the menu item. | 20 November 2014, 15:41:24 UTC |
| 86607d4 | Thomas Mooney | 20 November 2014, 14:44:46 UTC | Use fake data for this test. (Except the reference...) | 20 November 2014, 14:44:46 UTC |
| c05b79a | APipe Tester | 20 November 2014, 13:20:37 UTC | Updated `genome` tab completion. | 20 November 2014, 13:20:37 UTC |
| 94908d7 | APipe Tester | 20 November 2014, 13:17:09 UTC | Updated class browser cache. | 20 November 2014, 13:17:09 UTC |
| 44e0f67 | David Morton | 19 November 2014, 21:29:38 UTC | Merge pull request #214 from davidlmorton/process_run Genome::Processes can run and be viewed | 19 November 2014, 21:29:38 UTC |
| 7f3dcdb | Nathaniel Nutter | 19 November 2014, 20:12:38 UTC | Merge pull request #221 from nnutter/misc updated genome-snapshot-deps URL | 19 November 2014, 20:12:38 UTC |
| 020e2ba | apregier | 19 November 2014, 19:43:03 UTC | Allow singular versions of component types This makes the command line make more sense when you are looking at the detailed view for a single component | 19 November 2014, 19:43:03 UTC |
| 6448512 | apregier | 19 November 2014, 18:34:48 UTC | Merge pull request #211 from apregier/vr-show-docs VR show docs | 19 November 2014, 18:34:48 UTC |
| f51ca5b | Nathaniel Nutter | 19 November 2014, 17:58:14 UTC | Merge pull request #218 from nnutter/misc owner on GMSchema is optional | 19 November 2014, 17:58:14 UTC |
| d23d4f3 | Nathaniel Nutter | 19 November 2014, 17:56:59 UTC | updated genome-snapshot-deps URL genome-snapshot-deps has been migrated to GitHub so this updated the URL to point at the new location. | 19 November 2014, 17:56:59 UTC |
| 00508a9 | apregier | 19 November 2014, 16:49:01 UTC | Extract methods to clean up doc formating for properties Also, only say a property is undocumented if none of the doc fields are filled in | 19 November 2014, 16:49:01 UTC |
| 8f57d09 | Adam Coffman | 19 November 2014, 16:29:49 UTC | Merge pull request #219 from acoffman/remove_cell_type_from_sync Remove cell_type from GMS | 19 November 2014, 16:29:49 UTC |
| 705243f | apregier | 19 November 2014, 16:28:24 UTC | This code was just copied over and is not really needed | 19 November 2014, 16:28:24 UTC |
| f5a381f | apregier | 19 November 2014, 16:25:43 UTC | is_structural should already exclude id properties | 19 November 2014, 16:25:43 UTC |
| f96aa5f | apregier | 19 November 2014, 16:24:19 UTC | Clarify hash construction | 19 November 2014, 16:24:19 UTC |
| dbe5df2 | apregier | 19 November 2014, 16:17:44 UTC | Simplify property lookup | 19 November 2014, 16:17:44 UTC |
| c81850a | apregier | 19 November 2014, 16:12:45 UTC | WithTranslatedInputs inherits from Component::Base These generic classes also need the is_structural attribute on their properties | 19 November 2014, 16:12:45 UTC |
| d9291df | Thomas B. Mooney | 19 November 2014, 15:38:10 UTC | Merge pull request #216 from tmooney/minor_import_fix Use ceiling when estimating needed disk space for imports | 19 November 2014, 15:38:10 UTC |
| 56317fe | Thomas Mooney | 19 November 2014, 15:36:17 UTC | Add accessors to configs and projects using the menu item. This allows usage such as: genome analysis-project create --analysis-menu-items \ analysis_projects.id=12345 to copy all menu items to a new project. | 19 November 2014, 15:36:17 UTC |
| e3c8ef6 | Adam Coffman | 18 November 2014, 23:50:04 UTC | update number of expected misc update entries | 18 November 2014, 23:50:04 UTC |
| af6ac68 | Adam Coffman | 18 November 2014, 23:49:19 UTC | update number of properties to copy | 18 November 2014, 23:49:19 UTC |
| a5a1914 | Adam Coffman | 18 November 2014, 23:47:13 UTC | update test data dir for UpdateAnalysis | 18 November 2014, 23:47:13 UTC |
| 1ede725 | Adam Coffman | 18 November 2014, 23:40:42 UTC | remove cell_type value from expected output | 18 November 2014, 23:40:42 UTC |
| 4e20142 | Adam Coffman | 18 November 2014, 23:04:06 UTC | remove trailing tabs | 18 November 2014, 23:04:06 UTC |
| f21b3be | Adam Coffman | 18 November 2014, 22:53:52 UTC | remove cell_type from ClinSeq commands | 18 November 2014, 22:53:52 UTC |
| de54a2b | Adam Coffman | 18 November 2014, 22:53:30 UTC | update metadata expected outputs | 18 November 2014, 22:53:30 UTC |
| 0272de8 | Adam Coffman | 18 November 2014, 22:53:15 UTC | remove cell_type from export commands | 18 November 2014, 22:53:15 UTC |
| 89f7a5d | Adam Coffman | 18 November 2014, 22:52:09 UTC | remove cell_type from views | 18 November 2014, 22:52:45 UTC |
| 2bdea0c | Adam Coffman | 18 November 2014, 22:51:41 UTC | remove cell_type attribute from sample classes | 18 November 2014, 22:51:41 UTC |
| e7f79b5 | Adam Coffman | 18 November 2014, 22:51:05 UTC | remove cell_type from sync classes | 18 November 2014, 22:51:05 UTC |
| 1935787 | Nathaniel Nutter | 18 November 2014, 20:52:39 UTC | owner on GMSchema is optional When using the GENOME_TEST_FILLDB feature this object fails error checking due to `owner` being `undef`. To correct this the `owner` should be labeled as optional. | 18 November 2014, 20:52:39 UTC |
| f2ddd2a | apregier | 18 November 2014, 16:34:25 UTC | Don't compare warning messages | 18 November 2014, 16:35:05 UTC |
| 6b48bd7 | Thomas Mooney | 18 November 2014, 15:29:58 UTC | Spelling: excute to execute. | 18 November 2014, 16:05:52 UTC |
| 6a7dc44 | Thomas Mooney | 18 November 2014, 15:26:05 UTC | Use ceiling when estimating needed disk space. (In my case, I was testing with a file <1KB in size and it estimated needing 0 disk, which is clearly too small.) | 18 November 2014, 16:05:51 UTC |
| bae9384 | Thomas B. Mooney | 18 November 2014, 15:33:16 UTC | Merge pull request #212 from tmooney/update_example Update example file to not point to someone's homedir. | 18 November 2014, 15:33:16 UTC |
| aa25381 | APipe Tester | 18 November 2014, 13:22:19 UTC | Updated `gmt` tab completion. | 18 November 2014, 13:22:19 UTC |
| 2b9a8c7 | APipe Tester | 18 November 2014, 13:20:43 UTC | Updated `genome` tab completion. | 18 November 2014, 13:20:43 UTC |
| 4136d95 | APipe Tester | 18 November 2014, 13:17:31 UTC | Updated class browser cache. | 18 November 2014, 13:17:31 UTC |
| 962394a | dmorton | 18 November 2014, 02:28:59 UTC | Use Sys->read_file instead of File::Slurp | 18 November 2014, 02:28:59 UTC |
| 814cea3 | dmorton | 18 November 2014, 02:26:08 UTC | Use 'error_message' instead of 'status_message' | 18 November 2014, 02:26:08 UTC |
| aa7ebf4 | dmorton | 18 November 2014, 02:25:45 UTC | Eliminate spurious sprintf | 18 November 2014, 02:25:45 UTC |
| 41d1e13 | dmorton | 18 November 2014, 02:24:26 UTC | Make bsub'd workflows go to the workflow queue. | 18 November 2014, 02:24:26 UTC |
| 7cbfa03 | dmorton | 18 November 2014, 02:22:43 UTC | Use JSON library in a simpler way. | 18 November 2014, 02:22:43 UTC |
| ab0435a | dmorton | 18 November 2014, 02:20:33 UTC | Use %ENV instead of 'env' on cmd line | 18 November 2014, 02:20:33 UTC |
| 3d82bd7 | dmorton | 18 November 2014, 01:56:30 UTC | Reduce duplication between Viewers | 18 November 2014, 01:56:30 UTC |
| 0e82324 | dmorton | 18 November 2014, 01:22:37 UTC | Only set env variables if they aren't already set. | 18 November 2014, 01:22:37 UTC |
| d11f3d2 | dmorton | 18 November 2014, 01:14:34 UTC | Doc related touchups | 18 November 2014, 01:14:34 UTC |
| b10bfee | apregier | 17 November 2014, 23:07:43 UTC | Rename variable for clarity | 17 November 2014, 23:21:37 UTC |
| 0157fd2 | apregier | 17 November 2014, 23:06:08 UTC | Simplify property doc printing, which removes trailing spaces | 17 November 2014, 23:21:35 UTC |
| 5434e45 | apregier | 17 November 2014, 22:56:31 UTC | Fix types | 17 November 2014, 23:21:34 UTC |
| 4746b20 | apregier | 17 November 2014, 22:55:09 UTC | Add property type to docs | 17 November 2014, 23:21:33 UTC |
| 3960257 | apregier | 17 November 2014, 22:41:59 UTC | max_name_length isn't used anywhere | 17 November 2014, 23:21:32 UTC |
| d519109 | apregier | 17 November 2014, 22:40:38 UTC | Clean up how property lines are concatenated | 17 November 2014, 23:21:31 UTC |
| e614f02 | apregier | 17 November 2014, 21:52:42 UTC | Test to compare docs output for variant reporting | 17 November 2014, 23:21:30 UTC |
| e787dc0 | apregier | 17 November 2014, 21:46:55 UTC | Add required method | 17 November 2014, 23:21:28 UTC |
| 6bdb891 | dmorton | 17 November 2014, 21:54:22 UTC | bugfix: call execute instead of non-existing method | 17 November 2014, 21:54:22 UTC |
| 96637f3 | apregier | 17 November 2014, 21:46:18 UTC | Expose interface for type lookup to use in tests | 17 November 2014, 21:46:18 UTC |
| 8b890b2 | dmorton | 17 November 2014, 21:27:24 UTC | Processes can now be run The branch that bsub's and runs the workflow on LSF (with flow) has been pretty extensively hand-tested. It wasn't clear how to automate that testing until we have a test-database service that we can use. | 17 November 2014, 21:27:24 UTC |
| 4b6475b | dmorton | 17 November 2014, 21:18:40 UTC | Have create_disk_allocation create the log_directory | 17 November 2014, 21:25:26 UTC |
| 3bdf671 | dmorton | 17 November 2014, 05:25:12 UTC | Add 'genome process view' command | 17 November 2014, 21:25:26 UTC |
| 26f8206 | dmorton | 17 November 2014, 04:35:27 UTC | set status with 'update_status' not 'status' The way UR automatically creates undo-subroutines inside of transactions makes it so that when the transaction rolls back an invalid status transition will occur. If the status method has logic to disallow such transitions it will not allow us to roll back UR transactions, which is bad. | 17 November 2014, 21:25:25 UTC |
| 8fa54fb | dmorton | 16 November 2014, 21:23:50 UTC | Avoid using the ghost_class if possible My hand tests show that this has the same behavior of ensuring that the disk allocation is cleaned up when the current transaction commits but not if it gets rolled back. | 17 November 2014, 21:25:25 UTC |
| 6fb5bde | dmorton | 16 November 2014, 21:19:40 UTC | Ensure that disk-allocations get cleaned up upon rollback In the case we: 1) create transaction 2) call $process->create_disk_allocation 3) rollback transaction We need to be assured that the disk allocation is deleted. Since disk allocations are created in separate processes, there is no log in our transaction about the disk allocation creation, so we have to log it ourselves. | 17 November 2014, 21:25:25 UTC |
| 8d36b3f | APipe Tester | 17 November 2014, 21:20:32 UTC | updated ur submodule to 8a0a66b | 17 November 2014, 21:20:32 UTC |
| 73f98ed | David Morton | 17 November 2014, 21:17:32 UTC | Merge pull request #209 from davidlmorton/process_inputs Add Process inputs | 17 November 2014, 21:17:32 UTC |
| 55ad135 | dmorton | 17 November 2014, 21:07:02 UTC | fix name of foreign-key constraint | 17 November 2014, 21:07:51 UTC |
| 3785243 | apregier | 17 November 2014, 20:24:02 UTC | Add doc to full reporter | 17 November 2014, 20:24:02 UTC |
| aa99820 | apregier | 17 November 2014, 20:23:39 UTC | Add overview doc section | 17 November 2014, 20:23:39 UTC |
| 535f8e0 | Eddie Belter | 17 November 2014, 18:18:20 UTC | Merge pull request #202 from ebelter/genotype-microarray Genotype microarray | 17 November 2014, 18:18:20 UTC |
| 2ac09e0 | mkiwala | 17 November 2014, 17:53:17 UTC | Merge pull request #213 from mkiwala/revert-208 Revert "Merge branch 'ebelter-cghub'" | 17 November 2014, 17:53:17 UTC |
| 63fe898 | Eddie Belter | 17 November 2014, 17:12:25 UTC | GM: add Nathans suggestions | 17 November 2014, 17:12:25 UTC |
| ed633a5 | Eddie Belter | 17 November 2014, 16:08:22 UTC | Merge pull request #197 from ebelter/rdp-training-set Rdp training set | 17 November 2014, 16:08:22 UTC |
| 9403d0f | Michael J. Kiwala | 17 November 2014, 15:38:21 UTC | Revert "Import TCGA: fix compile error" This reverts commit 9823ad913ebac71740aa1d9c12b6098b50f37b36. | 17 November 2014, 15:38:21 UTC |
| 46ebe9d | Thomas Mooney | 17 November 2014, 15:29:41 UTC | Update example to not point to a homedir. | 17 November 2014, 15:29:41 UTC |
| 695d315 | Michael J. Kiwala | 17 November 2014, 15:25:33 UTC | Revert "Merge branch 'ebelter-cghub'" Reverts PR #208 This reverts commit 9113e05061af5b5ef5dd70662c84ea50c18940c1, reversing changes made to 85e0addf75bf6d49996815a7f9b4a41a08faa82f. | 17 November 2014, 15:25:33 UTC |
| 0828f2a | Thomas B. Mooney | 17 November 2014, 14:24:39 UTC | Merge pull request #206 from tmooney/remove_old_verify_headers_command Remove old `genome instrument-data alignment-result verify-headers`. | 17 November 2014, 14:24:39 UTC |
| 57ebeef | APipe Tester | 15 November 2014, 13:21:07 UTC | Updated `gmt` tab completion. | 15 November 2014, 13:21:07 UTC |
| 1b6c3b0 | APipe Tester | 15 November 2014, 13:19:43 UTC | Updated `genome` tab completion. | 15 November 2014, 13:19:43 UTC |
| 0391db4 | APipe Tester | 15 November 2014, 13:16:52 UTC | Updated class browser cache. | 15 November 2014, 13:16:52 UTC |
| 9823ad9 | Eddie Belter | 15 November 2014, 00:08:01 UTC | Import TCGA: fix compile error | 15 November 2014, 00:08:01 UTC |
| 9113e05 | Eddie Belter | 14 November 2014, 23:23:30 UTC | Merge branch 'ebelter-cghub' | 14 November 2014, 23:23:30 UTC |
| 85e0add | Eddie Belter | 12 November 2014, 00:02:28 UTC | GM: add b allele freq and vcf config | 14 November 2014, 23:23:23 UTC |
| 8fcbe37 | Eddie Belter | 12 November 2014, 00:00:34 UTC | GM ExtractTo/Write Csv: add b allele freq to valid fields | 14 November 2014, 23:23:22 UTC |
| 54294e8 | Eddie Belter | 12 November 2014, 00:00:10 UTC | GM ExtractToVcf: when resolving from model, set varition list build | 14 November 2014, 23:23:21 UTC |
| 03830ae | Eddie Belter | 11 November 2014, 23:59:26 UTC | GM: bump test data version to 7 | 14 November 2014, 23:23:21 UTC |
| 86d4df4 | Eddie Belter | 11 November 2014, 23:59:05 UTC | GM: combine extract to vcf tests into one since they all produce the same output. Added tests for resolving sources. | 14 November 2014, 23:23:20 UTC |
| 08f0158 | Eddie Belter | 14 November 2014, 23:22:19 UTC | Merge branch 'cghub' of github.com:ebelter/genome into ebelter-cghub Conflicts: lib/perl/Genome/InstrumentData/Command/Import/TcgaBam.pm | 14 November 2014, 23:22:19 UTC |
| 7f0e6ca | apregier | 14 November 2014, 21:13:56 UTC | Put all printing into show-docs Each component can add its own sections to the documentation which are all printed in a standard place | 14 November 2014, 22:17:45 UTC |
| 444baf7 | apregier | 13 November 2014, 22:25:04 UTC | Minimally functional version of show-docs for variant reporting | 14 November 2014, 22:17:44 UTC |
| b20bde0 | dmorton | 14 November 2014, 21:57:28 UTC | Sqitch: Add tag for deployment | 14 November 2014, 21:57:28 UTC |
| 3fa8c70 | dmorton | 14 November 2014, 21:54:42 UTC | Sqitch: Add columns to verify sql | 14 November 2014, 21:54:42 UTC |
| 363ae06 | dmorton | 14 November 2014, 21:15:35 UTC | Don't allow creation of Processes with missing inputs Because inputs are immutable they cannot be added to the Process later, so we should not allow the creation of un-savable objects. | 14 November 2014, 21:15:35 UTC |
| 96c219e | dmorton | 14 November 2014, 21:14:39 UTC | Always call $self->$property_name in list context | 14 November 2014, 21:14:39 UTC |
| ecd6a96 | Eddie Belter | 14 November 2014, 19:59:44 UTC | RDP: forgot to change the training set inferface in classifier base | 14 November 2014, 19:59:44 UTC |
| 16e32f7 | Avinash Ramu | 14 November 2014, 19:54:35 UTC | update clinseq blessed. This build has recent changes to the Circos output, the color scheme is inverted. | 14 November 2014, 19:54:35 UTC |
| c8e5954 | Avinash Ramu | 14 November 2014, 18:05:00 UTC | ignore stochastic files for diff | 14 November 2014, 18:05:00 UTC |
| f42ff00 | Susanna Siebert | 14 November 2014, 14:24:06 UTC | Merge pull request #205 from susannasiebert/resultify_generate_reports First round of removing memoize | 14 November 2014, 14:24:06 UTC |
| f92a5f3 | APipe Tester | 14 November 2014, 13:21:13 UTC | Updated `gmt` tab completion. | 14 November 2014, 13:21:13 UTC |
