| 7fbdd81 | Susanna Siebert | 24 December 2014, 14:50:30 UTC | Merge pull request #362 from susannasiebert/joinx_version use version package so that version comparison works for 1.10 and up | 24 December 2014, 14:50:30 UTC |
| c901f1b | Eddie Belter | 23 December 2014, 23:47:42 UTC | Merge pull request #364 from ebelter/rm-gsc-perl-from-tests Use /usr/bin/env genome-perl in tests instead of /gsc/bin/perl | 23 December 2014, 23:47:42 UTC |
| 6d11d16 | Eddie Belter | 23 December 2014, 23:31:26 UTC | Merge pull request #363 from ebelter/anp-cli-doc AnP CLI help and tests update. | 23 December 2014, 23:31:26 UTC |
| 07082ed | Eddie Belter | 23 December 2014, 23:13:14 UTC | AnP CLI: use env gneome-perl in test | 23 December 2014, 23:13:14 UTC |
| 1ecc9c2 | Eddie Belter | 23 December 2014, 23:09:18 UTC | Use /usr/bin/env genome-perl in tests instead of /gsc/bin/perl | 23 December 2014, 23:09:18 UTC |
| 23748f8 | Eddie Belter | 23 December 2014, 22:49:24 UTC | AnP CLI: add tests for disable config file | 23 December 2014, 22:49:24 UTC |
| 73c8aa4 | Eddie Belter | 23 December 2014, 22:48:54 UTC | AnP CLI: add test to config for instdata | 23 December 2014, 22:48:54 UTC |
| 2b45aed | Eddie Belter | 23 December 2014, 22:47:16 UTC | AnP CLI: add help brief to disable config file and config for instdata | 23 December 2014, 22:48:12 UTC |
| b3e1b00 | Susanna Siebert | 23 December 2014, 18:29:18 UTC | need to prepend 'v' to the version number so it gets parsed correctly | 23 December 2014, 18:29:18 UTC |
| de17f51 | Susanna Siebert | 23 December 2014, 16:39:50 UTC | use version package so that version comparison works for 1.10 and up | 23 December 2014, 17:00:32 UTC |
| 8595d1b | Susanna Siebert | 23 December 2014, 15:59:44 UTC | Merge pull request #359 from susannasiebert/epitope_prediction Use wildtype sequence length if it is shorter than desired peptide sequence length | 23 December 2014, 15:59:44 UTC |
| ace556a | APipe Tester | 23 December 2014, 13:16:57 UTC | Updated `gmt` tab completion. | 23 December 2014, 13:16:57 UTC |
| 917a2e4 | APipe Tester | 23 December 2014, 13:16:15 UTC | Updated `genome` tab completion. | 23 December 2014, 13:16:15 UTC |
| 9eae308 | APipe Tester | 23 December 2014, 13:14:38 UTC | Updated class browser cache. | 23 December 2014, 13:14:38 UTC |
| 43f79bd | Eddie Belter | 22 December 2014, 21:09:30 UTC | Merge pull request #334 from ebelter/cghub-import-instdata InstData Import: pull out retrieve file methods into separate modules | 22 December 2014, 21:09:30 UTC |
| 7a96079 | Mark Burnett | 22 December 2014, 21:07:31 UTC | Merge pull request #354 from mark-burnett/dv2-purged-allocations DV2 DetectionBase knows more about allocation statuses | 22 December 2014, 21:07:31 UTC |
| 8a3add5 | Thomas B. Mooney | 22 December 2014, 19:45:05 UTC | Merge pull request #344 from tmooney/import_instrument_data_sort_order_in_test Stop depending on being able to determine the order in which the two results were created. | 22 December 2014, 19:45:05 UTC |
| 7d3b7c5 | Eddie Belter | 22 December 2014, 19:42:55 UTC | InstData Import: spell/grammar check | 22 December 2014, 19:42:55 UTC |
| 75da1c4 | Mark Burnett | 22 December 2014, 19:23:52 UTC | fix missing `$_ eq` in grep | 22 December 2014, 19:23:52 UTC |
| d6e54b3 | Thomas Mooney | 22 December 2014, 18:48:47 UTC | Don't sort--grab the correct instrument data directly. | 22 December 2014, 18:48:47 UTC |
| fd9f651 | Thomas B. Mooney | 22 December 2014, 18:31:19 UTC | Merge pull request #340 from tmooney/remove_commented_code Clean Up Old Comments and Commented-Out Code | 22 December 2014, 18:31:19 UTC |
| 4c64a38 | Thomas B. Mooney | 22 December 2014, 18:28:55 UTC | Merge pull request #342 from tmooney/drop_featurelist_file_id Drop model.feature_list.file_id | 22 December 2014, 18:28:55 UTC |
| 9c908c3 | Thomas Mooney | 22 December 2014, 18:27:56 UTC | Tagged deployment of dropped file_id column. | 22 December 2014, 18:27:56 UTC |
| a1783c8 | Thomas Mooney | 18 December 2014, 15:42:56 UTC | Drop obsolete columns. | 22 December 2014, 18:22:20 UTC |
| ddc5a8a | Adam Coffman | 22 December 2014, 18:09:45 UTC | Merge pull request #324 from acoffman/migration_to_remove_unused_bx_params Remove unused SoftwareResult columns. | 22 December 2014, 18:09:45 UTC |
| ab6d12c | Adam Coffman | 22 December 2014, 18:09:22 UTC | tagged planfile | 22 December 2014, 18:09:22 UTC |
| 5ce8fd9 | Adam Coffman | 22 December 2014, 18:08:12 UTC | merge | 22 December 2014, 18:08:12 UTC |
| 141df27 | Adam Coffman | 22 December 2014, 18:06:07 UTC | Merge pull request #266 from acoffman/remove_model_group_column_from_anps Migration to remove model_group_id column from anps | 22 December 2014, 18:06:07 UTC |
| 26db964 | Adam Coffman | 22 December 2014, 18:05:11 UTC | tagged planfile | 22 December 2014, 18:05:11 UTC |
| 18de9a0 | Thomas B. Mooney | 22 December 2014, 18:04:09 UTC | Merge pull request #263 from tmooney/AT-667 Use Placeholder Objects for VR Planning/Documentation | 22 December 2014, 18:04:09 UTC |
| 8693451 | Adam Coffman | 22 December 2014, 18:03:27 UTC | merge | 22 December 2014, 18:03:27 UTC |
| bc1d6dd | Susanna Siebert | 22 December 2014, 17:16:26 UTC | remove unneeded braces | 22 December 2014, 17:16:26 UTC |
| 690a1d0 | Susanna Siebert | 22 December 2014, 17:03:37 UTC | typo fixes | 22 December 2014, 17:03:37 UTC |
| 4f9e4eb | Mark Burnett | 22 December 2014, 16:50:27 UTC | remove use of unstable ~~ operator | 22 December 2014, 16:50:27 UTC |
| ede2be1 | Mark Burnett | 22 December 2014, 16:47:52 UTC | do not make tarballs for symlinked data | 22 December 2014, 16:47:52 UTC |
| 2ab21e7 | Feiyu Du | 22 December 2014, 16:29:22 UTC | Merge pull request #356 from dufeiyu/path_update Update seq-grind path | 22 December 2014, 16:29:22 UTC |
| 23ab87d | Thomas B. Mooney | 22 December 2014, 16:21:33 UTC | Merge pull request #358 from tmooney/lock_build_requested_once Only need to lock once. After that it's ours to modify. | 22 December 2014, 16:21:33 UTC |
| 25cddae | Susanna Siebert | 22 December 2014, 16:00:44 UTC | fix else case to die instead of warn | 22 December 2014, 16:10:17 UTC |
| 31bb3c1 | Susanna Siebert | 22 December 2014, 15:59:05 UTC | use wildtype sequence length if it is shorter than desired peptide sequence length | 22 December 2014, 15:59:05 UTC |
| 36e58bc | Susanna Siebert | 22 December 2014, 15:19:26 UTC | Merge pull request #343 from susannasiebert/epitope_prediction Allow for a list of alleles to be used as input for epitope predirction | 22 December 2014, 15:19:26 UTC |
| ded4e83 | Thomas Mooney | 22 December 2014, 15:18:02 UTC | Only need to lock once. After that it's ours to modify. | 22 December 2014, 15:18:02 UTC |
| dfd7229 | APipe Tester | 20 December 2014, 13:17:25 UTC | Updated `gmt` tab completion. | 20 December 2014, 13:17:25 UTC |
| c5d43f7 | APipe Tester | 20 December 2014, 13:16:38 UTC | Updated `genome` tab completion. | 20 December 2014, 13:16:38 UTC |
| 7d9323b | Eddie Belter | 20 December 2014, 00:41:05 UTC | InstData Import: add https matches to retrieve methods for remote url | 20 December 2014, 00:41:05 UTC |
| c624230 | Eddie Belter | 20 December 2014, 00:35:59 UTC | InstData Import: reorg retrieve classes as requested from feedback | 20 December 2014, 00:35:59 UTC |
| 62468fb | Eddie Belter | 20 December 2014, 00:35:03 UTC | CgHub Metadata: amke file size for file retrun size in bytes not kb | 20 December 2014, 00:35:03 UTC |
| b39326c | Feiyu Du | 19 December 2014, 22:50:09 UTC | fix the tool name | 19 December 2014, 22:50:09 UTC |
| fdf7590 | Feiyu Du | 19 December 2014, 22:17:01 UTC | update seq-grind0.1 path | 19 December 2014, 22:17:01 UTC |
| 2f4ad5c | Mark Burnett | 19 December 2014, 21:11:07 UTC | Merge pull request #353 from mark-burnett/minor-nessy-fixups Minor nessy fixups | 19 December 2014, 21:11:07 UTC |
| e703246 | Chris Miller | 19 December 2014, 20:11:33 UTC | Merge pull request #336 from chrisamiller/master adding bam-readcount version parameter | 19 December 2014, 20:11:33 UTC |
| 21388ba | Chris Miller | 19 December 2014, 20:11:27 UTC | Merge pull request #335 from ernfrid/add_version_to_process_build_tools add option to specify bam-readcount version and also set its default to ... | 19 December 2014, 20:11:27 UTC |
| 05ce67f | Susanna Siebert | 19 December 2014, 20:00:13 UTC | Merge branch 'master' of https://github.com/genome/genome into epitope_prediction | 19 December 2014, 20:00:13 UTC |
| 39caa9d | Susanna Siebert | 19 December 2014, 19:52:49 UTC | use sub-workflow to achieve parallel by | 19 December 2014, 19:52:49 UTC |
| a253257 | Mark Burnett | 18 December 2014, 21:39:11 UTC | check for archived allocations | 19 December 2014, 18:46:23 UTC |
| 832211f | Mark Burnett | 18 December 2014, 21:35:23 UTC | unlink purged and invalid allocations | 19 December 2014, 18:46:23 UTC |
| 2de349b | Mark Burnett | 18 December 2014, 21:33:56 UTC | instrument symlink removal | 19 December 2014, 18:46:23 UTC |
| f164a69 | Mark Burnett | 18 December 2014, 21:18:55 UTC | simplify if statements instance_output is always a link here | 19 December 2014, 18:46:23 UTC |
| 648fabd | Mark Burnett | 18 December 2014, 21:18:05 UTC | extract _validate_missing_allocation | 19 December 2014, 18:46:23 UTC |
| 9252bf3 | Mark Burnett | 18 December 2014, 21:15:45 UTC | extract _validate_found_allocation | 19 December 2014, 18:46:23 UTC |
| 3aad81c | Mark Burnett | 18 December 2014, 21:06:46 UTC | simplify nested if (validate) | 19 December 2014, 18:46:22 UTC |
| d9f8974 | Mark Burnett | 18 December 2014, 21:05:57 UTC | simplify nested if (cleanup) | 19 December 2014, 18:46:22 UTC |
| b5aa344 | Mark Burnett | 18 December 2014, 20:59:25 UTC | restructure if/else block I removed one branch: else { die $class->error_message("Unexpected condition in " . __PACKAGE__ . "::_check_instance_output"); } This branch was essentially unreachable due to "_cleanup_legacy_non_software_result_data". I did not find any log messages containing "_check_instance_output" in the last 30 days. | 19 December 2014, 18:46:22 UTC |
| 75f34c6 | Mark Burnett | 18 December 2014, 20:46:18 UTC | extract _extract_allocation_owner_id | 19 December 2014, 18:46:22 UTC |
| 82efd24 | Mark Burnett | 18 December 2014, 20:31:32 UTC | extract methods from _check_instance_output | 19 December 2014, 18:46:22 UTC |
| 49e6e62 | Mark Burnett | 17 December 2014, 16:57:31 UTC | use getpwuid in scalar context Because it was being used in array context, we were generating a somewhat confusing user_data hash (some values redacted): "user_data": { "GID": "", "": "Mark Burnett", "lsf_id": "NONE", "requested_at": "Wed, 17 Dec 2014 10:52:31 -0600", "lsf_project": "NONE", "*": "UID", "pid": "19124", "host": "HOSTNAME", "user": "mburnett", "genome_build_id": "NONE", "HOMEDIR": "/bin/bash" } With this change, it looks more like this: "user_data": { "lsf_id": "NONE", "requested_at": "Wed, 17 Dec 2014 10:53:58 -0600", "lsf_project": "NONE", "pid": "19388", "host": "HOSTNAME", "user": "mburnett", "genome_build_id": "NONE" } | 19 December 2014, 18:27:24 UTC |
| 72aebb3 | Mark Burnett | 19 December 2014, 18:25:56 UTC | use config Nessy URL for testing | 19 December 2014, 18:25:56 UTC |
| b4ce218 | Mark Burnett | 19 December 2014, 18:22:36 UTC | use url specified in GENOME_NESSY_SERVER | 19 December 2014, 18:22:36 UTC |
| 2975063 | Mark Burnett | 19 December 2014, 18:19:18 UTC | fix bug: Sys::Lock::NessyBackend not used | 19 December 2014, 18:19:18 UTC |
| bcf677e | Mark Burnett | 19 December 2014, 16:48:35 UTC | Merge pull request #346 from mark-burnett/hide-deallocate Deprecate `genome disk allocation deallocate` | 19 December 2014, 16:48:35 UTC |
| d6b6794 | Susanna Siebert | 19 December 2014, 14:05:54 UTC | use new version of the test data | 19 December 2014, 14:05:54 UTC |
| 0577367 | APipe Tester | 19 December 2014, 13:17:09 UTC | Updated `gmt` tab completion. | 19 December 2014, 13:17:09 UTC |
| 3298778 | APipe Tester | 19 December 2014, 13:16:25 UTC | Updated `genome` tab completion. | 19 December 2014, 13:16:25 UTC |
| b6136c7 | APipe Tester | 19 December 2014, 13:14:39 UTC | Updated class browser cache. | 19 December 2014, 13:14:39 UTC |
| b9b709f | APipe Tester | 18 December 2014, 20:45:21 UTC | updated jenkins submodule to ad020c5 | 18 December 2014, 21:32:14 UTC |
| 9698f05 | Chris Miller | 18 December 2014, 21:04:03 UTC | Merge pull request #339 from chrisamiller/bsmap allowing user to input insert size params without being overridden | 18 December 2014, 21:04:03 UTC |
| b3f7309 | Thomas Mooney | 18 December 2014, 14:16:54 UTC | Update the expected test-case. | 18 December 2014, 20:48:33 UTC |
| 454ec3c | Thomas Mooney | 18 December 2014, 03:35:22 UTC | Remove old commented-out code. We must not want to ask, since we haven't come back to enable this! | 18 December 2014, 20:27:25 UTC |
| d577d1c | Thomas Mooney | 18 December 2014, 03:32:55 UTC | Remove commented-out code from before the redaction. | 18 December 2014, 20:27:25 UTC |
| 34113ad | Thomas Mooney | 18 December 2014, 03:30:11 UTC | Remove commented-out code from before the redaction. | 18 December 2014, 20:27:25 UTC |
| 73b129c | Thomas Mooney | 18 December 2014, 03:18:34 UTC | Remove old comments, and add an example that uses the name. | 18 December 2014, 20:27:24 UTC |
| 3133528 | Thomas Mooney | 18 December 2014, 03:15:20 UTC | Remove useless sorting. Even if it was once useful, the algorithm was mostly commented out and we now use UUIDs that don't sort in a meaningful order. | 18 December 2014, 20:27:24 UTC |
| 6d4e67b | Thomas Mooney | 18 December 2014, 03:11:03 UTC | Remove commented-out reference to ancient Picard version. | 18 December 2014, 20:25:45 UTC |
| 9e7731b | Thomas Mooney | 18 December 2014, 03:09:05 UTC | Remove commented out alternate logic. | 18 December 2014, 20:25:45 UTC |
| 4fdee07 | Thomas Mooney | 18 December 2014, 03:04:38 UTC | Remove commented-out obsolete property "file_id". This used to hold the ID of the file storage in LIMS... but it hasn't for a long time and they are discontinuing that storage, anyway. | 18 December 2014, 20:25:45 UTC |
| 0d5c4ba | Thomas Mooney | 18 December 2014, 03:02:17 UTC | I dare to remove parentheses (and quotation marks). | 18 December 2014, 20:25:32 UTC |
| 8c71f26 | Mark Burnett | 18 December 2014, 19:22:29 UTC | Deprecate `genome disk allocation deallocate` Users probably want `genome disk allocation purge` instead. For now we are simply hiding this command from non-admin users. | 18 December 2014, 19:22:29 UTC |
| 071d4a8 | Mark Burnett | 18 December 2014, 19:14:00 UTC | Merge pull request #331 from mark-burnett/add-purge-command Add `genome disk allocation purge` CLI | 18 December 2014, 19:14:00 UTC |
| 8ca2468 | Thomas Mooney | 18 December 2014, 16:46:28 UTC | Sort by a known distinguishing characteristic. import_date is sometimes identical and segment_id always is. | 18 December 2014, 16:46:28 UTC |
| 022e7cf | Chris Miller | 18 December 2014, 16:16:22 UTC | Merge branch 'master' of https://github.com/genome/genome into bsmap | 18 December 2014, 16:16:22 UTC |
| 4c251a4 | Chris Miller | 18 December 2014, 16:16:14 UTC | remove spurious 'my', simplify insert size checking | 18 December 2014, 16:16:14 UTC |
| 040ec76 | Susanna Siebert | 18 December 2014, 15:51:02 UTC | Allow for a list of alleles to be used as input | 18 December 2014, 15:51:02 UTC |
| c06722c | Susanna Siebert | 18 December 2014, 15:48:43 UTC | Merge pull request #337 from susannasiebert/epitope_prediction Remove duplicate sequences from fasta file | 18 December 2014, 15:48:43 UTC |
| 78b7abf | APipe Tester | 18 December 2014, 13:16:24 UTC | Updated `genome` tab completion. | 18 December 2014, 13:16:24 UTC |
| 0286502 | APipe Tester | 18 December 2014, 13:14:35 UTC | Updated class browser cache. | 18 December 2014, 13:14:35 UTC |
| 1f22afe | David Morton | 18 December 2014, 05:00:31 UTC | Merge pull request #314 from davidlmorton/merge_legends Merge legends | 18 December 2014, 05:00:31 UTC |
| c14ddc2 | APipe Tester | 18 December 2014, 03:03:10 UTC | updated jenkins submodule to 03a62f9 | 18 December 2014, 03:03:10 UTC |
| 12a313e | Thomas Mooney | 18 December 2014, 03:02:05 UTC | Remove commented-out condition. | 18 December 2014, 03:02:05 UTC |
| accd8d5 | Thomas Mooney | 18 December 2014, 02:56:26 UTC | Remove commented out code and redundant conditional next. If we decide this should complain about existing commands, we can bring back the confess in uncommented form. | 18 December 2014, 02:56:26 UTC |
| cdf1e54 | David Morton | 18 December 2014, 01:40:58 UTC | Merge pull request #325 from apregier/per_library_headers Vaf interpreters pass per-library fields separately to reporters | 18 December 2014, 01:40:58 UTC |
| e4df362 | Adam Coffman | 17 December 2014, 23:07:20 UTC | Merge pull request #333 from acoffman/remove_yaml_string Remove ununsed yaml_string methods | 17 December 2014, 23:07:20 UTC |
