| d30c66d | Eddie Belter | 29 August 2013, 21:37:13 UTC | Sync: add synchronize command tree | 29 August 2013, 23:21:51 UTC |
| dcf760a | Eddie Belter | 29 August 2013, 21:36:16 UTC | Sync: mv synchronize command into syncrhonize dir | 29 August 2013, 23:21:50 UTC |
| a30d22e | Eddie Belter | 29 August 2013, 21:05:39 UTC | Sync: fix tests expecting misc update skips to succeed b/c they now fail | 29 August 2013, 23:21:50 UTC |
| fb96196 | Eddie Belter | 29 August 2013, 20:57:52 UTC | Sync RMU: fix some typos | 29 August 2013, 23:21:49 UTC |
| c07ef50 | Eddie Belter | 29 August 2013, 20:57:05 UTC | Sync: sub attr success result is PASS | 29 August 2013, 23:21:49 UTC |
| 8e1e0fd | Eddie Belter | 29 August 2013, 20:20:15 UTC | Sync RMU: validate start is before stop | 29 August 2013, 23:21:48 UTC |
| 3241bba | Eddie Belter | 29 August 2013, 20:08:00 UTC | Sync RMU: change var names in __errors__ method | 29 August 2013, 23:21:48 UTC |
| 8c2c246 | Eddie Belter | 29 August 2013, 19:57:36 UTC | Sync RMU: use entities defined in test for multi misc update | 29 August 2013, 23:21:46 UTC |
| b13d576 | Eddie Belter | 29 August 2013, 19:56:50 UTC | Sync RMU: report updates and indels separately | 29 August 2013, 23:21:46 UTC |
| cec7cc1 | Eddie Belter | 29 August 2013, 19:56:10 UTC | Sync: misc update skip return value is undef | 29 August 2013, 23:21:45 UTC |
| 5ab4a7f | Eddie Belter | 29 August 2013, 19:50:51 UTC | Sync: subject attr failure result is FAIL; skipping return value is undef; updated tests | 29 August 2013, 23:21:45 UTC |
| 5aa5ad8 | Eddie Belter | 29 August 2013, 19:37:00 UTC | Sync: add test to skip sub attr update if subject does not exist; | 29 August 2013, 23:21:44 UTC |
| eeaca29 | Eddie Belter | 29 August 2013, 19:19:21 UTC | Sync: check subject exists before inserting subject attr | 29 August 2013, 23:21:44 UTC |
| cbb2e70 | Eddie Belter | 29 August 2013, 17:50:19 UTC | Sync RMU: change to giving start date and then playing all updates to present; load misc updates at once | 29 August 2013, 23:21:43 UTC |
| 44fc787 | APipe Tester | 29 August 2013, 21:50:55 UTC | updated ur submodule to f1915ea | 29 August 2013, 21:50:55 UTC |
| b0238c8 | apregier | 29 August 2013, 20:40:48 UTC | Merge branch 'generator' into gb_master | 29 August 2013, 20:40:48 UTC |
| 2ec7e25 | apregier | 29 August 2013, 20:39:46 UTC | Set the fusion file as an output property | 29 August 2013, 20:39:46 UTC |
| 9eda8ad | APipe Tester | 29 August 2013, 17:02:50 UTC | Updated `genome` tab completion. | 29 August 2013, 17:02:50 UTC |
| a5dd889 | APipe Tester | 29 August 2013, 17:01:03 UTC | Updated class browser cache. | 29 August 2013, 17:01:03 UTC |
| 8106a6b | Eddie Belter | 29 August 2013, 16:53:24 UTC | Sync: update testing taxon and ind to add organism in front | 29 August 2013, 16:53:24 UTC |
| 0b154d3 | APipe Tester | 29 August 2013, 15:00:21 UTC | updated ur submodule to 4de40f0 | 29 August 2013, 15:00:21 UTC |
| f4f7e1f | Eddie Belter | 28 August 2013, 22:12:55 UTC | Sync UAC: use sync class for pop group | 28 August 2013, 22:58:39 UTC |
| 43d707b | Eddie Belter | 28 August 2013, 21:20:11 UTC | Sync UAC: use sync classes for taxon and ind | 28 August 2013, 22:58:38 UTC |
| 1e6b961 | Eddie Belter | 28 August 2013, 19:48:36 UTC | Sync: moved/added organism to taxon and individual classes | 28 August 2013, 22:58:38 UTC |
| 8e162e6 | Scott Smith | 28 August 2013, 22:57:40 UTC | t Merge branch 'master' of ssh://git/srv/git/genome | 28 August 2013, 22:57:40 UTC |
| dd2bc2d | Scott Smith | 28 August 2013, 22:57:27 UTC | updated "genome model clin-seq update-inputs-from-model-group to handle tumor_rnaseq, normal_rnaseq | 28 August 2013, 22:57:27 UTC |
| 8671276 | APipe Tester | 28 August 2013, 22:11:51 UTC | Updated `gmt` tab completion. | 28 August 2013, 22:11:51 UTC |
| 018478c | APipe Tester | 28 August 2013, 22:10:57 UTC | Updated `genome` tab completion. | 28 August 2013, 22:10:57 UTC |
| 3c9998a | APipe Tester | 28 August 2013, 22:09:13 UTC | Updated class browser cache. | 28 August 2013, 22:09:13 UTC |
| 1260120 | Chris Miller | 28 August 2013, 21:59:26 UTC | revamped tool to work on newer file formats instead of just using Varscan input | 28 August 2013, 22:00:03 UTC |
| d27817f | APipe Tester | 28 August 2013, 19:40:11 UTC | Updated `genome` tab completion. | 28 August 2013, 19:40:11 UTC |
| 405928a | APipe Tester | 28 August 2013, 19:38:14 UTC | Updated class browser cache. | 28 August 2013, 19:38:14 UTC |
| 199db77 | Feiyu Du | 28 August 2013, 19:28:45 UTC | Add AnnotateGenesByDgidb.pm to ClinSeq | 28 August 2013, 19:29:43 UTC |
| d17f841 | Travis Abbott | 28 August 2013, 19:02:31 UTC | make gmt instrument-data import bam return 0/1 it was returning an instrument data id, and command v1 was expecting a number | 28 August 2013, 19:02:31 UTC |
| 4030736 | APipe Tester | 28 August 2013, 17:03:45 UTC | Updated `gmt` tab completion. | 28 August 2013, 17:03:45 UTC |
| f088c59 | APipe Tester | 28 August 2013, 17:02:46 UTC | Updated `genome` tab completion. | 28 August 2013, 17:02:46 UTC |
| 4f21616 | APipe Tester | 28 August 2013, 17:00:25 UTC | Updated class browser cache. | 28 August 2013, 17:00:25 UTC |
| b49682e | Chris Miller | 28 August 2013, 16:15:50 UTC | added option to plot whole chromosomes | 28 August 2013, 16:19:06 UTC |
| 8d1821e | Eddie Belter | 28 August 2013, 16:10:56 UTC | Sync UAC: update status msgs | 28 August 2013, 16:11:16 UTC |
| c8222f0 | Eddie Belter | 28 August 2013, 16:06:42 UTC | Sync UAC: update sql in genome project parts | 28 August 2013, 16:11:16 UTC |
| 936835b | Dave Larson | 28 August 2013, 15:41:35 UTC | fix missing semicolon error | 28 August 2013, 15:41:35 UTC |
| 2a3e33d | Dave Larson | 21 August 2013, 16:08:22 UTC | forgot the FT filter tag in the header. doh! | 28 August 2013, 15:38:50 UTC |
| 50fc9db | Dave Larson | 21 August 2013, 11:08:56 UTC | add FT field for better merging | 28 August 2013, 15:38:49 UTC |
| f58f64d | Dave Larson | 21 August 2013, 10:52:49 UTC | add the ability to skip header lines during the sort | 28 August 2013, 15:38:49 UTC |
| 60179b1 | Dave Larson | 21 August 2013, 10:50:49 UTC | set aligned_reads_sample name | 28 August 2013, 15:38:48 UTC |
| f7b80f4 | Dave Larson | 21 August 2013, 04:25:58 UTC | fix some file naming and take advantage of new line skipping functionality in the sort | 28 August 2013, 15:38:48 UTC |
| 5ff5305 | Dave Larson | 21 August 2013, 01:56:41 UTC | handle the case where depth is 0 in the FA contamination | 28 August 2013, 15:38:47 UTC |
| 1336329 | Adam Coffman | 28 August 2013, 15:04:41 UTC | sort on date rather than id | 28 August 2013, 15:04:41 UTC |
| 1700d13 | Thomas Mooney | 28 August 2013, 14:06:15 UTC | Lowercase the column names now that we're on PG. This clears up errors like: While committing, metadata for table input does not match class Genome::SoftwareResult::Input::Ghost. Table primary key columns are software_result_id, input_name class ID property columns software_result_id, INPUT_NAME | 28 August 2013, 14:06:15 UTC |
| 70037a4 | APipe Tester | 28 August 2013, 01:59:29 UTC | Updated `genome` tab completion. | 28 August 2013, 01:59:29 UTC |
| 2a7e5cf | APipe Tester | 28 August 2013, 01:57:25 UTC | Updated class browser cache. | 28 August 2013, 01:57:25 UTC |
| 2ffc52f | Travis Abbott | 28 August 2013, 01:28:42 UTC | fix typo: disk_allocation => disk_allocations. | 28 August 2013, 01:28:42 UTC |
| 24bd0ba | Obi Griffith | 28 August 2013, 00:26:49 UTC | blessed clinseq diffs related to limfo output | 28 August 2013, 00:26:49 UTC |
| 35fe10b | Eddie Belter | 27 August 2013, 21:13:19 UTC | Sync UAC: do not order by id | 27 August 2013, 21:18:41 UTC |
| 712226d | Eddie Belter | 27 August 2013, 21:12:21 UTC | Sync Expunge: do not delete [temporary] | 27 August 2013, 21:18:40 UTC |
| 5cdef50 | Eddie Belter | 27 August 2013, 21:11:53 UTC | Sync UAC: cleanup - rm test stuff and unused methods | 27 August 2013, 21:18:40 UTC |
| 70cc531 | Eddie Belter | 27 August 2013, 20:28:29 UTC | Sync UAC: calculate and add missing to report | 27 August 2013, 21:18:39 UTC |
| 2f4c2c3 | Eddie Belter | 27 August 2013, 20:20:17 UTC | Sync UAC: method for creating genome objects | 27 August 2013, 21:18:39 UTC |
| 880a40a | Eddie Belter | 27 August 2013, 19:41:43 UTC | Sync UAC: rm sync order | 27 August 2013, 21:18:38 UTC |
| 9ca4fbf | Eddie Belter | 27 August 2013, 19:40:21 UTC | Sync UAC: add get ids for class; rm all unneeded execute block | 27 August 2013, 21:18:38 UTC |
| aab72f2 | Eddie Belter | 27 August 2013, 19:20:53 UTC | Sync UAC: extract locking into separate methods | 27 August 2013, 21:18:37 UTC |
| 088a1a2 | Anthony Brummett | 27 August 2013, 21:08:46 UTC | typo | 27 August 2013, 21:08:46 UTC |
| 5e26e7d | Nathan Nutter | 27 August 2013, 20:50:33 UTC | IDs are Text now so have to be quoted in JSON... in XSL... in XML... | 27 August 2013, 20:50:55 UTC |
| d88a845 | APipe Tester | 27 August 2013, 20:46:48 UTC | Updated `genome` tab completion. | 27 August 2013, 20:46:48 UTC |
| 3a80cb7 | APipe Tester | 27 August 2013, 20:44:54 UTC | Updated class browser cache. | 27 August 2013, 20:44:54 UTC |
| 9cc0d97 | Anthony Brummett | 27 August 2013, 20:34:16 UTC | Instead of picking the "latest" library, exit when there are more than one with the given name As part of the postgres-id-sorting change, we can't rely on the "highest" ID being the newest thing anymore. There's no obvious time associated with a library so no good way to keep the old behavior, which seems bad anyway | 27 August 2013, 20:34:16 UTC |
| 8cd41b3 | Anthony Brummett | 27 August 2013, 20:33:54 UTC | Can't sort numerically be ID anymore | 27 August 2013, 20:33:54 UTC |
| f3bd359 | Anthony Brummett | 27 August 2013, 20:33:13 UTC | Can't sort things by ID as a surrogate for sorting by creation order | 27 August 2013, 20:33:13 UTC |
| 841cbb1 | Adam Coffman | 27 August 2013, 19:58:47 UTC | remove unused sub | 27 August 2013, 19:58:47 UTC |
| 3a7faf9 | Adam Coffman | 27 August 2013, 19:58:28 UTC | compare ids as strings instead of numbers | 27 August 2013, 19:58:28 UTC |
| 52f1a4e | Adam Coffman | 27 August 2013, 19:57:48 UTC | sort ids as strings instead of numbers | 27 August 2013, 19:57:48 UTC |
| 51bade9 | Adam Coffman | 27 August 2013, 19:57:28 UTC | sort on date_scheduled instead of build id | 27 August 2013, 19:57:28 UTC |
| 9ceb84e | Adam Coffman | 27 August 2013, 19:56:34 UTC | use last_succeeded_build | 27 August 2013, 19:56:34 UTC |
| c9de8fb | Adam Coffman | 27 August 2013, 19:55:43 UTC | sort bamqc result by new best_guess_date value on software results | 27 August 2013, 19:55:43 UTC |
| 48f6172 | Adam Coffman | 27 August 2013, 19:54:25 UTC | sort on creation_date and date_scheduled instead of id | 27 August 2013, 19:54:25 UTC |
| cf30083 | Adam Coffman | 27 August 2013, 19:54:02 UTC | sort instrument data ids as strings | 27 August 2013, 19:54:02 UTC |
| 730ae22 | Adam Coffman | 27 August 2013, 19:53:15 UTC | sort models on creation date instead of id | 27 August 2013, 19:53:15 UTC |
| 2478e2e | Adam Coffman | 27 August 2013, 19:52:24 UTC | sort models on creation date instead of id | 27 August 2013, 19:52:24 UTC |
| 10a5c10 | Adam Coffman | 27 August 2013, 19:51:57 UTC | sort instrument data ids as strings | 27 August 2013, 19:51:57 UTC |
| 9e4b959 | Adam Coffman | 27 August 2013, 19:51:35 UTC | sort build ids as strings instead of numbers | 27 August 2013, 19:51:35 UTC |
| 3e5f6ef | Adam Coffman | 27 August 2013, 19:51:18 UTC | sort builds on date_scheduled instead of id | 27 August 2013, 19:51:18 UTC |
| 647e572 | Adam Coffman | 27 August 2013, 19:42:00 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 27 August 2013, 19:42:00 UTC |
| 0fd5d84 | Adam Coffman | 27 August 2013, 19:41:49 UTC | add new best_guess_date sub for sorting software result | 27 August 2013, 19:41:49 UTC |
| 57ea583 | APipe Tester | 27 August 2013, 19:31:54 UTC | updated ur submodule to e3864f9 | 27 August 2013, 19:31:54 UTC |
| 5d5987f | APipe Tester | 27 August 2013, 19:24:34 UTC | updated graphite submodule to da9443f | 27 August 2013, 19:24:34 UTC |
| 255d147 | Nathan Nutter | 27 August 2013, 18:41:30 UTC | remove old datasources | 27 August 2013, 18:41:30 UTC |
| b99328f | Travis Abbott | 27 August 2013, 18:33:19 UTC | update model set coverage view to find correct builds it previously tried to sort builds by id, but build ids are no longer numeric. now, $model->builds returns builds newest first, which is what this thing wants anyway. | 27 August 2013, 18:34:33 UTC |
| f77e912 | Travis Abbott | 27 August 2013, 17:43:38 UTC | Genome::Model->builds now returns builds in order (newest first) they are ordered by date_scheduled (descending) | 27 August 2013, 18:34:33 UTC |
| 078c0df | APipe Tester | 27 August 2013, 18:17:56 UTC | updated graphite submodule to f4151f8 | 27 August 2013, 18:17:56 UTC |
| 02423fb | Gabriel Sanderson | 27 August 2013, 17:57:21 UTC | Merge branch 'master' into gb_master | 27 August 2013, 17:57:21 UTC |
| a88ea93 | Gabriel Sanderson | 27 August 2013, 17:56:26 UTC | Add a VERY rudimentary check to the beginning that will look for the common problem that we have "chr" chromosomes without a nimblegen reference sequence. | 27 August 2013, 17:56:26 UTC |
| 1eb3b61 | APipe Tester | 27 August 2013, 15:47:05 UTC | updated graphite submodule to 1629c7e | 27 August 2013, 15:47:05 UTC |
| 05b227e | Mark Burnett | 27 August 2013, 15:37:38 UTC | G:D:Allocation test -- seed RNG on fork This should fix the bug related to my previous commit. | 27 August 2013, 15:37:38 UTC |
| d98687b | Mark Burnett | 27 August 2013, 15:30:16 UTC | change G:D:A test allocation_paths This is an attempt to fix this error: ERROR: Failed to create directory (/tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/testing//tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/allocation_lock_testing_1_pKhDg6d) with return value = '', and error: Can't mkdir('/tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/testing'): File exists at /gscmnt/gc13001/info/model_data/apipe-ci/workspace/1-Genome-Perl-Tests/PERL_VERSION=5.10/PERL_VERSION/5.10/lib/perl/Genome/Sys.pm line 839 ERROR: Can't mkdir('/tmp/allocation_testing_2v2Wmv/test_volume_2_hibzxi6/testing'): File exists at /gscmnt/gc13001/info/model_data/apipe-ci/workspace/1-Genome-Perl-Tests/PERL_VERSION=5.10/PERL_VERSION/5.10/lib/perl/Genome/Sys.pm line 839 I could not reproduce the error, but this change should fix the odd, nested path. | 27 August 2013, 15:32:18 UTC |
| 4c1b012 | Thomas Mooney | 27 August 2013, 15:23:44 UTC | Take fail count into consideration when deciding which data to process. | 27 August 2013, 15:23:44 UTC |
| 1e078c6 | Mark Burnett | 27 August 2013, 13:33:39 UTC | G:M:T:Picard monitors both stdout and stderr for activity | 27 August 2013, 14:09:50 UTC |
| cf50bfc | Mark Burnett | 27 August 2013, 13:32:55 UTC | make sure InstrumentData::delete removes BamQc results | 27 August 2013, 14:09:49 UTC |
| c0325c1 | Mark Burnett | 23 August 2013, 14:56:16 UTC | add note indicating a build is run using flow | 27 August 2013, 14:09:49 UTC |
| 61bcd43 | Thomas Mooney | 27 August 2013, 14:05:30 UTC | Updates to account for transition to UUIDs. | 27 August 2013, 14:05:30 UTC |
| 29bd72e | Thomas Mooney | 27 August 2013, 13:49:27 UTC | Improve error message--print just class name instead of metaobject hash. | 27 August 2013, 13:49:27 UTC |
