https://github.com/genome/genome

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Revision Author Date Message Commit Date
aa0685c updated jenkins submodule to d3b251d 23 October 2015, 22:58:08 UTC
2e4e147 Merge pull request #1067 from brummett/remove-postgres-logging Remove obsolete postgres logging 23 October 2015, 20:56:17 UTC
ea348b4 Use Perl's built-in version checking for DBD::Pg LIMS is using a new enough version of DBD::Pg, so this special check isn't necessary anymore 23 October 2015, 15:32:15 UTC
41c52c9 Updated `genome` tab completion. 23 October 2015, 12:18:29 UTC
9860fd8 Updated class browser cache. 23 October 2015, 12:16:38 UTC
324c02b Merge pull request #1063 from ebelter/disk-under-allocated Disk Volume Under Allocated 22 October 2015, 22:49:32 UTC
ab89354 Merge pull request #1058 from ebelter/disk-move Disk Alloc Move: do not allow specifying target group and volume 22 October 2015, 22:49:26 UTC
0f41088 Merge pull request #1059 from ebelter/validate-disk-groups Disk Group Validate: add info_archive and update test 22 October 2015, 22:49:07 UTC
86182c7 Merge pull request #1064 from ebelter/build-event-view Build View Status XML: remove unused load jobs from lsf file methods 22 October 2015, 22:47:53 UTC
2857c8c Remove the code that generates the logs for CompareSyncTime These logs were used during the transition from Oracle to Postgres, to compare commit times, and to find errors in out implementation of Postgres. 22 October 2015, 20:42:14 UTC
bf4bf61 Remove obsolete CompareSyncTime command Used during our transition from Oracle to Postgres to compare the time it took to commit to the two databases. 22 October 2015, 20:41:49 UTC
8c45471 Merge pull request #1040 from brummett/unarchive-wait-for-lsf-jobs More efficient unarchive wait for lsf jobs 22 October 2015, 18:17:16 UTC
8c90a41 Merge pull request #1044 from tmooney/reference_sequence_buckets New SR to create "buckets" of chromosomes for a reference. 22 October 2015, 16:20:13 UTC
864e219 Merge pull request #924 from tmooney/alignment_dispatcher_uses_workflowbuilder Alignment Dispatcher uses WorkflowBuilder 22 October 2015, 13:14:03 UTC
9a89476 Updated `gmt` tab completion. 22 October 2015, 12:19:12 UTC
ad63289 Updated `genome` tab completion. 22 October 2015, 12:18:17 UTC
d964157 Updated class browser cache. 22 October 2015, 12:16:32 UTC
c4c82e2 Update workflow unit test to use WorkflowBuilder. 21 October 2015, 22:44:50 UTC
72aa6bb Cleanup: Removed unused variables. 21 October 2015, 22:44:50 UTC
85840d5 Couple refinement to merge. Callers expect not to see the "Merged" results if refined results are available, so we'll skip adding the merge to the outputs if refiners are being run. 21 October 2015, 22:44:50 UTC
b5dd26f Fixup: output_properties is not an arrayref. 21 October 2015, 22:44:50 UTC
422e012 Convert decorators to WorkflowBuilder. 21 October 2015, 22:44:50 UTC
8c52413 Stop using _add_link_to_workflow helper. 21 October 2015, 22:44:50 UTC
458ef74 Add ability to specify an input is optional. 21 October 2015, 22:44:50 UTC
28f49ed Use the DAG directly when running the workflow. 21 October 2015, 22:44:50 UTC
b6ff0a8 Remove UR optimization--it cloned objects with WorkflowBuilder links. 21 October 2015, 22:44:49 UTC
1d12e4f WorkflowBuilder requires that inputs/outputs be declared implicitly. 21 October 2015, 22:44:49 UTC
e4998b3 Remove disused property lists. 21 October 2015, 22:44:49 UTC
ff2b278 Move linking between steps to occur within each group. *The old master workflow generation is now completely parted out. 21 October 2015, 22:44:49 UTC
aaa7537 WIP: Convert Refine step to WorkflowBuilder 21 October 2015, 22:44:49 UTC
9a54edd Don't need to compute inputs and outputs any more. 21 October 2015, 22:44:49 UTC
0c998e7 WIP: Convert Merge step to WorkflowBuilder. 21 October 2015, 22:44:49 UTC
232b556 WIP: Convert "object" workflows to WorkflowBuilder (Align(AndMerge)) 21 October 2015, 22:44:49 UTC
dbc8c02 WIP: Convert first step of workflow generation (AlignerIndex) * Create master workflow in advance. * Create Block for aligner indices inside aligner index step. * Use constants to avoid needing to keep track of inputs. 21 October 2015, 22:43:49 UTC
1342dc5 Intermediate step: Convert object creation to WorkflowBuilder This is broken since WorkflowBuilder expects to learn of its inputs and outputs by the creation of links, but Workflow expects to be informed in advance of link creation so it can validate the links as they are added. 21 October 2015, 22:43:49 UTC
da090db Use _add_link_to_workflow helper. It uses the precomputed UR templates for efficiency. 21 October 2015, 22:37:57 UTC
e0789b8 Merge pull request #1038 from chrisamiller/concordance Addition of an option, cleanup of edge cases and tests 21 October 2015, 21:45:46 UTC
e2022dd adds another example SNP file for easy reference 21 October 2015, 21:35:18 UTC
47c8483 Merge pull request #1031 from susannasiebert/epitope_prediction Move variant sequence fasta generation into variant reporting framework and handle frameshifte and in frame indels 21 October 2015, 20:55:20 UTC
165cca8 Model Event View: rm commented out code 21 October 2015, 20:10:58 UTC
213fd73 Build View Status XML: remove unused load jobs from lsf file methods adn properties 21 October 2015, 18:33:23 UTC
f251710 Disk Alloc Move: do not specify the target group to the mover if we have a target volume 21 October 2015, 17:48:10 UTC
6dcd201 Disk Volume UderAlloc: test cleanup 21 October 2015, 17:38:55 UTC
ff47bbd Disk Volume UnderAlloc: use fake group, rename volume 21 October 2015, 17:35:34 UTC
7821697 Disk Volume UnderAlloc: return undef if under allocd volumes found 21 October 2015, 17:34:20 UTC
3618e9d Merge pull request #1056 from tmooney/refseq_df Use Filesys::Df to get available KB 21 October 2015, 14:24:50 UTC
8a7edd8 Merge pull request #1060 from tmooney/stop_testing_58 Stop testing that Genome classes work under older Perl. 21 October 2015, 13:14:20 UTC
cc8b659 Disk Alloc Move: check if target volume is in group is both are specified 21 October 2015, 01:01:23 UTC
2b6be0f Disk Alloc Move: fix idempotent move test 21 October 2015, 00:59:18 UTC
4a18780 updated ur submodule to 45bb80e 20 October 2015, 20:56:27 UTC
b186521 Disk Alloc: do not allow allcoations to be created in disk_group_archive 20 October 2015, 20:27:36 UTC
a697924 Disk Group: add is_archive method 20 October 2015, 20:26:50 UTC
c65add8 Merge pull request #1057 from tmooney/java7_in_gatk Make Java 1.7 the default for running GATK tools. 20 October 2015, 20:11:24 UTC
e6aa190 Disk Group Validate: use lives_ok in test 20 October 2015, 19:39:46 UTC
58c4230 Merge pull request #1055 from tmooney/remove_db_skip_postgres Remove old db_skip_postgres configuration variable. 20 October 2015, 19:12:49 UTC
eb5ccad Disk Under Allocated: use volume mock object 20 October 2015, 00:22:03 UTC
140f10a Disk Uder Allocated: convert to subtests 19 October 2015, 23:59:57 UTC
d3728fa Disk Uder Allocated: use is many for disk group names instead of splitting by commas 19 October 2015, 23:57:25 UTC
3fb96bb Disk Under Allocated: remove send alert feature 19 October 2015, 23:45:37 UTC
a983750 Disk Group Validate: use test::exception instead of test::fatal 19 October 2015, 23:39:49 UTC
49ba430 Disk Group Validate: remove db singles 19 October 2015, 23:37:06 UTC
71e9b38 Disk Group Validate: convert to subtests 19 October 2015, 23:36:07 UTC
e4b0b72 Disk Group Validate: add disk_group_archive to valid group names 19 October 2015, 23:35:21 UTC
3ee0181 Disk Alloc Move: only add existing alloc group if no target group and volume 19 October 2015, 23:24:12 UTC
a568448 Disk Alloc Move: function to get move params 19 October 2015, 23:20:46 UTC
ed0e639 Disk Alloc Mover: cannot specify target group and volume 19 October 2015, 23:07:13 UTC
0b13da1 Stop testing that Genome classes work under older Perl. 19 October 2015, 20:56:36 UTC
2f15f25 Make Java 1.7 the default for GATK. 19 October 2015, 19:39:51 UTC
07b6775 Use Filesys::Df instead of piping df output. 19 October 2015, 17:41:02 UTC
bcede52 Use -P to avoid wrapping lines. 19 October 2015, 16:13:08 UTC
6c94eb7 Merge pull request #1054 from tmooney/use_array_form_in_import_helper_shellcmd Use array form of shellcmd. 19 October 2015, 14:03:13 UTC
9bb4577 Disk Alloc Move: convert to subtests 15 October 2015, 22:20:56 UTC
9942417 updated workflow submodule to c0f1230 15 October 2015, 20:45:11 UTC
e88eb33 Remove comment. If preserving order is important, we'll already be handcrafting the bucket result instead of running this. It was confusing, anyway, since it didn't really apply to the code that was present. 15 October 2015, 20:31:10 UTC
dfe51e3 Remove old db_skip_postgres configuration variable. 15 October 2015, 20:24:32 UTC
13e2f3d Use array form of shellcmd. 15 October 2015, 19:15:31 UTC
f4e03af Merge pull request #1053 from tmooney/add_run_as_to_mc16s_test_factory_model Add run_as to test factory model. 15 October 2015, 16:49:11 UTC
c10972d Added LSF log output files 15 October 2015, 16:34:36 UTC
520b980 Merge pull request #1051 from tmooney/alignandmerge_lsf_resource_determination_to_command Move AlignAndMerge LSF Resource generation to the command. 15 October 2015, 16:21:25 UTC
3404f3e Add run_as to test factory model. That way G:SR:User->user_hash_for_build() can find a sponsor. 15 October 2015, 14:03:46 UTC
3e1c832 Merge pull request #1043 from tmooney/disable_indexing_in_mutect Disable index creation in `gmt mutect`. 14 October 2015, 20:10:04 UTC
c235827 updated jenkins submodule to b67763e 14 October 2015, 19:44:48 UTC
e1791c8 Merge pull request #1027 from davidlmorton/genome-ptero-lsf-integration Genome ptero lsf integration 14 October 2015, 19:38:43 UTC
7ff2f2d Merge pull request #1050 from tmooney/typos_in_instrument_data_launch Fix typos in InstrumentData Import Launcher 14 October 2015, 18:53:11 UTC
be94f1a Merge pull request #1052 from gatoravi/update_clinseq_blessed Build with results from https://github.com/genome/genome/pull/1012 14 October 2015, 17:51:57 UTC
73fdaa8 Updated `gmt` tab completion. 14 October 2015, 12:18:48 UTC
409a261 Updated `genome` tab completion. 14 October 2015, 12:17:58 UTC
8888d3e Merge pull request #1042 from ebelter/instdata-import-use-rgid-as-instdata-id Inst Data Import: use read group id as instdata id 13 October 2015, 21:45:14 UTC
62394e3 Update to reflect https://github.com/genome/genome/pull/1012 \#1012 switched to separatedvaluereader from an incorrect regex. The updated blessed-build has the correct results. 13 October 2015, 21:19:55 UTC
0f8ba75 InstData Import: die when setting headers/read groups 13 October 2015, 20:52:58 UTC
d648d98 InstData Import: chomp line 13 October 2015, 20:47:40 UTC
8f9afc6 InstData Import: set autogen uuid outside of helper sub 13 October 2015, 20:46:58 UTC
a22ed57 InstData Import: update debug msgs 13 October 2015, 20:45:09 UTC
f502619 InstData Import: die error instead of return undef 13 October 2015, 20:44:09 UTC
6122ee1 InstData Import: do not catch rv of _write_reads_based_on_read_group_and_pairedness 13 October 2015, 20:43:25 UTC
9d5d6ae In this new location, $class already holds the class we need. 13 October 2015, 20:01:05 UTC
243cf7b Move LSF Resource string generation to the command. 13 October 2015, 19:58:13 UTC
5ec6886 Merge pull request #1048 from tmooney/intervals_for_genotype_caller Add intervals parameter for GATK HaplotypeCaller 13 October 2015, 19:28:07 UTC
677d2e9 Merge pull request #1047 from tmooney/test_factory_for_speedseq_results Create a Test Factory for speedseq results. 13 October 2015, 19:27:56 UTC
6677317 Fix another typo, add serial comma and pluralization! 13 October 2015, 18:49:12 UTC
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