| ad7a859 | APipe Tester | 02 November 2012, 19:12:09 UTC | Merge remote-tracking branch 'origin/master' | 02 November 2012, 19:12:09 UTC |
| 5538baf | Eddie Belter | 02 November 2012, 19:11:43 UTC | Search Queue: add default value to timestamp so command works | 02 November 2012, 19:11:43 UTC |
| e64ee64 | Nathan Nutter | 02 November 2012, 15:43:08 UTC | reallocate on fail (and whitespace) Change-Id: Id53d70df61413922dee4806682ad6621ca2f3c2b | 02 November 2012, 15:45:01 UTC |
| e01e5ba | APipe Tester | 02 November 2012, 14:16:32 UTC | updated jenkins submodule to 0d2f07b | 02 November 2012, 14:16:32 UTC |
| 676b3c6 | Travis Abbott | 01 November 2012, 21:02:21 UTC | update test data to match expected results the previous test data was asserting that the code did the wrong thing (passed files to joinx in incorrect order due to filenames being hashed then iterating over the keys). | 01 November 2012, 21:14:01 UTC |
| df1bd18 | Eddie Belter | 01 November 2012, 20:33:31 UTC | AQID: using skipped as tgi_lims_status for inst data that had no models attempted | 01 November 2012, 20:33:37 UTC |
| c7f3aea | Eddie Belter | 01 November 2012, 18:58:09 UTC | AQID: add better error message for lack of sample/source/taxon. Add test for these failures | 01 November 2012, 20:33:37 UTC |
| a28026f | Travis Abbott | 01 November 2012, 20:22:10 UTC | fix plotting functionality in BurdenTestSummary Mutation diagrams were not being created due to specifying alternate alleles as bases where vcf indices were expected. | 01 November 2012, 20:22:10 UTC |
| 4ca2d7a | Jim Weible | 01 November 2012, 14:09:24 UTC | try to get around terribleness associated with copy number for mouse | 01 November 2012, 15:23:11 UTC |
| 49ddf1b | Thomas Mooney | 01 November 2012, 15:00:46 UTC | Mahalo, jlolofie. | 01 November 2012, 15:00:46 UTC |
| 591b88b | Nathaniel Nutter | 01 November 2012, 14:20:32 UTC | show subject_class in error message | 01 November 2012, 14:20:32 UTC |
| 70efbdc | Thomas Mooney | 01 November 2012, 13:43:30 UTC | Carry forward setting of content_type if it wasn't set initially. | 01 November 2012, 13:44:25 UTC |
| c852712 | Scott Smith | 31 October 2012, 23:32:50 UTC | Merge branch 'master' of ssh://git/srv/git/genome Conflicts: lib/perl/Genome/Model/Tools/BioSamtools/ErrorRate.pm | 31 October 2012, 23:32:50 UTC |
| 26b3fd8 | Travis Abbott | 31 October 2012, 21:56:37 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 31 October 2012, 21:56:37 UTC |
| b567b34 | Travis Abbott | 31 October 2012, 21:55:47 UTC | fix non-deterministic filename ordering in VcfMerge.pm files were being passed to joinx based on the order they appear in a hash. | 31 October 2012, 21:55:47 UTC |
| 7feede4 | Kyung Kim | 31 October 2012, 21:52:14 UTC | per rt#86752, update to remove distinction between euk and bacterial naming .. previously, euk samples were filtered out and not printed to interpro.ace file | 31 October 2012, 21:52:14 UTC |
| 0dcc1a1 | Scott Smith | 31 October 2012, 21:39:02 UTC | replaced calls to the old get_class_object with newer __meta__ | 31 October 2012, 21:39:02 UTC |
| fde012b | Eddie Belter | 31 October 2012, 19:59:31 UTC | AQID: Add tgi lims failed message when an inst data fails | 31 October 2012, 19:59:38 UTC |
| a9e2d2f | apregier | 31 October 2012, 19:44:35 UTC | Merge branch 'music' into gb_master | 31 October 2012, 19:44:35 UTC |
| 3deb4fe | apregier | 31 October 2012, 19:08:43 UTC | Assign dbsnp to AQID somatic variation models again | 31 October 2012, 19:44:17 UTC |
| 0945fca | apregier | 31 October 2012, 18:40:51 UTC | Add options to run only certain parts of play music | 31 October 2012, 19:44:17 UTC |
| 7750cb2 | Ian Ferguson | 31 October 2012, 19:38:02 UTC | Fixes for GMT::BioSamtools::ErrorRate Rearranged some code in ErrorRate and fixed an issue with single- vs paired-end reads. | 31 October 2012, 19:38:02 UTC |
| 0820b28 | Ian Ferguson | 31 October 2012, 19:25:45 UTC | Added support for bwa-0.6.2. Updated AlignmentResult and IntermediateAlignmentResult modules for bwa. Index files and log formats have changed with 0.6.2. | 31 October 2012, 19:25:45 UTC |
| 92510be | Travis Abbott | 31 October 2012, 19:05:36 UTC | more phenocorr updates for music output format change rename clinical correlation outputs -> tsv instead of csv, P-val in headers becomes Pval | 31 October 2012, 19:05:36 UTC |
| 73474a2 | Cyriac Kandoth | 31 October 2012, 18:56:01 UTC | Change output files names to .tsv to reflect tab-separation | 31 October 2012, 18:56:01 UTC |
| 1ab7a28 | Scott Smith | 31 October 2012, 18:51:02 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 31 October 2012, 18:51:02 UTC |
| 1dc56f9 | Scott Smith | 31 October 2012, 18:50:56 UTC | replaced calls to get_rule_for_params to define_boolexpr, since the former is deprecated and will not run outside of TGI | 31 October 2012, 18:50:56 UTC |
| 215030f | Travis Abbott | 31 October 2012, 18:44:17 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 31 October 2012, 18:44:17 UTC |
| 2457ed7 | Travis Abbott | 31 October 2012, 18:43:42 UTC | update phenocorr to cope with new music format | 31 October 2012, 18:43:42 UTC |
| 61ea612 | Mark Burnett | 31 October 2012, 18:21:29 UTC | Remove test for removed command | 31 October 2012, 18:21:29 UTC |
| 2e28de2 | Travis Abbott | 31 October 2012, 18:12:05 UTC | update to cope with new music output format | 31 October 2012, 18:12:05 UTC |
| 62a7991 | Travis Abbott | 31 October 2012, 17:43:19 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 31 October 2012, 17:43:19 UTC |
| de71cd7 | Travis Abbott | 31 October 2012, 17:42:36 UTC | point tigra-sv to /usr/bin, update test SvCalls test data | 31 October 2012, 17:42:36 UTC |
| 6bad744 | Nathaniel Nutter | 31 October 2012, 17:00:35 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 31 October 2012, 17:00:35 UTC |
| 8af8344 | Cyriac Kandoth | 31 October 2012, 16:57:00 UTC | Fix typos and other minor tweaks to formatting | 31 October 2012, 16:57:00 UTC |
| 3ae908c | Nathaniel Nutter | 31 October 2012, 16:55:33 UTC | Merge branch 'lockless_allocation_refactor' CHANGELOG: Allocations can now be created without requiring a lock on the volume. We expect this will decrease average allocation creation times from ~15-20 seconds down to ~3 seconds and will also provide a more consistent creation time. (The locking version has spikes as high several minutes.) Despite thoroughly testing these changes it is quite possible that unexpected issue may occur. If you notice any issues during allocation creation please let us know. | 31 October 2012, 16:55:33 UTC |
| 5a107fe | Nathaniel Nutter | 31 October 2012, 01:40:56 UTC | missed a total_kb call | 31 October 2012, 16:15:44 UTC |
| 246c92b | Nathaniel Nutter | 30 October 2012, 19:19:18 UTC | add logger role to sync-usage command | 31 October 2012, 16:15:44 UTC |
| b98fa21 | Nathaniel Nutter | 30 October 2012, 16:34:48 UTC | add shell_args_position property | 31 October 2012, 16:15:43 UTC |
| 7181769 | Nathaniel Nutter | 30 October 2012, 16:34:29 UTC | use reload since load is deprecated | 31 October 2012, 16:15:43 UTC |
| cb86a91 | Nathaniel Nutter | 30 October 2012, 16:34:03 UTC | use class's reload method | 31 October 2012, 16:15:43 UTC |
| c932804 | Nathaniel Nutter | 30 October 2012, 15:44:31 UTC | Revert "remove percent_used & percent_allocated from default show" This reverts commit fa13947a9a7054a137a4ba461cea48e4bdada840. | 31 October 2012, 16:15:42 UTC |
| 842a54c | Nathaniel Nutter | 30 October 2012, 15:43:39 UTC | remove above since used_libs is better/used | 31 October 2012, 16:15:42 UTC |
| d62d354 | Nathaniel Nutter | 30 October 2012, 15:39:49 UTC | remove useless AUTO_REMOVE_TEST_PATHS | 31 October 2012, 16:15:41 UTC |
| e4941bf | Nathaniel Nutter | 30 October 2012, 15:39:25 UTC | throw error only if specified mount path is also excluded | 31 October 2012, 16:15:41 UTC |
| 14b74e7 | Nathaniel Nutter | 30 October 2012, 15:25:59 UTC | reload after lock | 31 October 2012, 16:15:41 UTC |
| bb97543 | Nathaniel Nutter | 30 October 2012, 15:25:34 UTC | confess if mount_path and exclude_mount_paths are specified | 31 October 2012, 16:15:40 UTC |
| dac6ca3 | Nathaniel Nutter | 30 October 2012, 14:55:31 UTC | whitespace | 31 October 2012, 16:15:40 UTC |
| 55242a6 | Nathaniel Nutter | 30 October 2012, 14:48:53 UTC | remove unallocated_kb mutator calls - remove unallocated_kb mutator calls - test immutability of unallocated_kb - remove volume resize command | 31 October 2012, 16:15:39 UTC |
| b42a2a9 | Nathaniel Nutter | 29 October 2012, 23:49:18 UTC | make a default group for testing | 31 October 2012, 16:15:39 UTC |
| 892fb0b | Nathaniel Nutter | 29 October 2012, 23:48:49 UTC | remove debug line | 31 October 2012, 16:15:38 UTC |
| 9cd241c | Nathaniel Nutter | 29 October 2012, 23:33:19 UTC | rm unused code | 31 October 2012, 16:15:38 UTC |
| c3e2b48 | Nathaniel Nutter | 29 October 2012, 23:33:08 UTC | prevent warnings when self is undef | 31 October 2012, 16:15:38 UTC |
| 11bcbc8 | Nathaniel Nutter | 29 October 2012, 23:32:52 UTC | remove debug messages | 31 October 2012, 16:15:37 UTC |
| a56d664 | Nathaniel Nutter | 29 October 2012, 23:25:15 UTC | remove "duplicate" create dir | 31 October 2012, 16:15:37 UTC |
| 625eae2 | Nathaniel Nutter | 29 October 2012, 23:22:44 UTC | remove unused var | 31 October 2012, 16:15:36 UTC |
| a162094 | Nathaniel Nutter | 29 October 2012, 23:22:29 UTC | refactor absolute_path | 31 October 2012, 16:15:36 UTC |
| be1050f | Nathaniel Nutter | 29 October 2012, 23:16:12 UTC | remove old comment | 31 October 2012, 16:15:35 UTC |
| 2d55eb3 | Nathaniel Nutter | 29 October 2012, 23:15:33 UTC | remove unused methods | 31 October 2012, 16:15:35 UTC |
| 0bc99c9 | Nathaniel Nutter | 29 October 2012, 23:15:12 UTC | replace with equivalent so we can remove unallocatable_reserve_size | 31 October 2012, 16:15:35 UTC |
| 21abc40 | Nathaniel Nutter | 29 October 2012, 21:35:41 UTC | use real total_kb on test volumes | 31 October 2012, 16:15:34 UTC |
| 820a584 | Nathaniel Nutter | 29 October 2012, 21:34:38 UTC | add status/debug messages in is_over_soft_limit | 31 October 2012, 16:15:34 UTC |
| 809e5c0 | Nathaniel Nutter | 29 October 2012, 21:34:05 UTC | pretend all volumes are mounted during UR_DBI_NO_COMMIT | 31 October 2012, 16:15:33 UTC |
| 6e8279f | Nathaniel Nutter | 29 October 2012, 21:33:36 UTC | cap maximum reserved size for large volumes | 31 October 2012, 16:15:33 UTC |
| 3ec5025 | Nathaniel Nutter | 26 October 2012, 23:08:22 UTC | pretend dummy volumes are mounted | 31 October 2012, 16:15:32 UTC |
| a2e3f37 | Nathaniel Nutter | 26 October 2012, 22:23:31 UTC | rename old_unallocated_kb to cached_unallocated_kb | 31 October 2012, 16:15:32 UTC |
| e8525dc | Nathaniel Nutter | 26 October 2012, 21:18:36 UTC | add two more tests | 31 October 2012, 16:15:32 UTC |
| 7eb5056 | Nathaniel Nutter | 26 October 2012, 21:18:15 UTC | add available_kb | 31 October 2012, 16:15:31 UTC |
| e6c3320 | Nathaniel Nutter | 26 October 2012, 20:47:36 UTC | move hijacking to data source | 31 October 2012, 16:15:31 UTC |
| 1f90311 | Nathaniel Nutter | 26 October 2012, 19:22:39 UTC | use volume's is_over_soft_limit | 31 October 2012, 16:15:30 UTC |
| 9053140 | Nathaniel Nutter | 26 October 2012, 19:11:03 UTC | use df method in used_kb | 31 October 2012, 16:15:30 UTC |
| 26762df | Nathaniel Nutter | 26 October 2012, 19:10:30 UTC | create a df method that does error checking | 31 October 2012, 16:15:29 UTC |
| 7cf390e | Nathaniel Nutter | 26 October 2012, 19:01:55 UTC | add is_over_soft/hard_limit | 31 October 2012, 16:15:29 UTC |
| b2ab3dd | Nathaniel Nutter | 26 October 2012, 18:53:08 UTC | create symlink from absolute_path to old absolute_path | 31 October 2012, 16:15:29 UTC |
| b3f3b09 | Nathaniel Nutter | 25 October 2012, 21:54:51 UTC | prevent remove when no commit and adjust test accordingly | 31 October 2012, 16:15:28 UTC |
| 25d202d | Nathaniel Nutter | 25 October 2012, 21:23:27 UTC | switch allocation test class to use fuse | 31 October 2012, 16:15:28 UTC |
| 028d3d5 | Nathaniel Nutter | 24 October 2012, 18:33:30 UTC | use PERL5OPT instead of execute global | 31 October 2012, 16:15:27 UTC |
| 974b2f4 | Nathaniel Nutter | 16 October 2012, 18:14:26 UTC | add allocation create and tight fit tests | 31 October 2012, 16:15:27 UTC |
| febac15 | Nathaniel Nutter | 16 October 2012, 18:12:31 UTC | need to use "deeper" allocation_path to avoide pre-existing bugs | 31 October 2012, 16:15:26 UTC |
| 1c1997a | Nathaniel Nutter | 12 October 2012, 01:11:58 UTC | add brute force test | 31 October 2012, 16:15:26 UTC |
| b408744 | Nathaniel Nutter | 12 October 2012, 01:11:22 UTC | add LocalDataSource for testing | 31 October 2012, 16:15:26 UTC |
| 5018730 | Nathaniel Nutter | 19 October 2012, 23:14:23 UTC | remove MAX_VOLUMES limitation If we don't want to allocate to volumes we should just manage the volumes better rather than have code accounting for that. Additionally, the idea is complicated by the lockless algorithm. We would prefer thing not compete for the same volumes to improve performance though with lockless algorithm it is only really relevant as a volume reaches soft_limit_kb. | 31 October 2012, 16:15:25 UTC |
| 5d19a17 | Nathaniel Nutter | 19 October 2012, 23:11:59 UTC | show candidate volumes if unable to create allocation | 31 October 2012, 16:15:25 UTC |
| 3abfc01 | Nathaniel Nutter | 19 October 2012, 23:09:24 UTC | remove percent_used & percent_allocated from default show Having calculated properties in show often, as now, causes slow performance so I removed them from the default show. | 31 October 2012, 16:15:24 UTC |
| b13effe | Nathaniel Nutter | 16 October 2012, 19:13:14 UTC | add sync-usage and command | 31 October 2012, 16:15:24 UTC |
| d344aab | Nathaniel Nutter | 16 October 2012, 18:14:05 UTC | remove unused File::Copy (also fixes "move redefined" warnings) | 31 October 2012, 16:15:23 UTC |
| dc6537a | Nathaniel Nutter | 16 October 2012, 18:10:23 UTC | refactor _execute_system_command so it can be modified for testing | 31 October 2012, 16:15:23 UTC |
| b77e67b | Nathaniel Nutter | 16 October 2012, 18:08:30 UTC | show parent allocation_path when parent found | 31 October 2012, 16:15:23 UTC |
| 3d5cf07 | Nathaniel Nutter | 16 October 2012, 18:08:00 UTC | try each candidate volume three times | 31 October 2012, 16:15:22 UTC |
| 4dc940a | Nathaniel Nutter | 12 October 2012, 01:10:14 UTC | derive data source, table, etc. instead of hard-coding | 31 October 2012, 16:15:22 UTC |
| df0c56a | Nathaniel Nutter | 02 October 2012, 23:21:33 UTC | set display name of mount_path on volumes | 31 October 2012, 16:15:21 UTC |
| 338134b | Nathaniel Nutter | 18 October 2012, 14:19:00 UTC | check if SUPER::create succeeded | 31 October 2012, 16:15:21 UTC |
| a7919fb | Nathaniel Nutter | 24 October 2012, 16:25:05 UTC | over allocation check should be <= not < | 31 October 2012, 16:15:20 UTC |
| ec8ed40 | Mark Burnett | 10 October 2012, 15:57:30 UTC | Update archive/unarchive to lockless allocation scheme | 31 October 2012, 16:15:20 UTC |
| 2cb51a5 | Mark Burnett | 10 October 2012, 13:39:23 UTC | Add _commit_unless_testing to Disk::Allocation This lets us get the right behavior when we really run (committing in the right places), while still allowing other tests to build only partial object graphs that would not be consistent in the database if we called commit (that consistency is checked at commit time even when UR_DBI_NO_COMMIT is on). | 31 October 2012, 16:15:19 UTC |
| 0dcf0c8 | Mark Burnett | 03 October 2012, 13:37:00 UTC | Revert Allocation to using system instead of fork. | 31 October 2012, 16:15:19 UTC |
| b7958e9 | Mark Burnett | 28 September 2012, 11:39:18 UTC | Make allocation creation lockless Allocations also use fork() instead of system() | 31 October 2012, 16:15:19 UTC |
| 4264d10 | Mark Burnett | 28 September 2012, 17:48:22 UTC | Speed up allocation creation. Add hand written SQL for checking whether "child" allocations exist. | 31 October 2012, 16:15:18 UTC |
| b3ea6ce | Mark Burnett | 28 September 2012, 17:45:17 UTC | Allow GENOME_DB_PAUSE undef. Ignore PAUSE when NO_COMMIT | 31 October 2012, 16:15:18 UTC |
| 7a51919 | Nathan Nutter | 31 October 2012, 15:59:27 UTC | refactor diff command to add diff-blessed command | 31 October 2012, 15:59:56 UTC |
