5b0f66c | Susanna Siebert | 09 December 2013, 14:32:02 UTC | removed debug breakpoint | 11 December 2013, 21:06:07 UTC |
4c8ce81 | Susanna Siebert | 06 December 2013, 22:48:36 UTC | added wrapper to run EdgeR for ClinSeq including making the gene counts file and filtering | 11 December 2013, 21:06:01 UTC |
8efdb73 | Susanna Siebert | 06 December 2013, 21:46:56 UTC | added filtering functionality for gene counts files | 11 December 2013, 21:05:51 UTC |
2692834 | Susanna Siebert | 06 December 2013, 20:51:15 UTC | Make parameter names more intuitive | 11 December 2013, 21:05:42 UTC |
86f27b5 | Susanna Siebert | 11 December 2013, 20:43:07 UTC | empty genotype file is not a failure just return early | 11 December 2013, 20:43:17 UTC |
b4a5a2a | Eddie Belter | 11 December 2013, 18:45:16 UTC | MC16s: get SX results ind for each instdata when merging | 11 December 2013, 18:45:16 UTC |
33919c0 | APipe Tester | 11 December 2013, 13:18:19 UTC | Updated `gmt` tab completion. | 11 December 2013, 13:18:19 UTC |
ea9d10e | APipe Tester | 11 December 2013, 13:17:36 UTC | Updated `genome` tab completion. | 11 December 2013, 13:17:36 UTC |
4e2fbd9 | APipe Tester | 11 December 2013, 13:16:05 UTC | Updated class browser cache. | 11 December 2013, 13:16:05 UTC |
d00cef8 | Mark Burnett | 10 December 2013, 21:47:32 UTC | add support for Converge to WorkflowBuilder | 10 December 2013, 21:48:37 UTC |
0f00623 | Mark Burnett | 10 December 2013, 20:42:57 UTC | move responsibility for sorting input/output properties This will allow us to add new operation types that depend on particular sort order for their inputs and outputs (like Converge). | 10 December 2013, 21:48:36 UTC |
893065b | Charles Lu | 10 December 2013, 21:46:01 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 10 December 2013, 21:46:01 UTC |
6210aef | Charles Lu | 10 December 2013, 21:45:54 UTC | make --bmr-output option not required | 10 December 2013, 21:45:54 UTC |
ec64e62 | Chris Miller | 10 December 2013, 20:18:56 UTC | adding a new tool that appends Exome Variant Server allele frequencies to an annotation file | 10 December 2013, 20:19:29 UTC |
602528d | Jim Weible | 10 December 2013, 15:56:38 UTC | update rna-seq expected docs for cancer-annotation-db | 10 December 2013, 15:56:38 UTC |
faa715f | Jim Weible | 10 December 2013, 15:42:26 UTC | update apipe-test-rnaseq to remove cancer-annotation-db from the processing profile | 10 December 2013, 15:42:41 UTC |
1ebbc19 | Jim Weible | 10 December 2013, 15:41:48 UTC | make cancer_annoation_db an input rather than a processing-profile param | 10 December 2013, 15:42:40 UTC |
efccfb1 | Jim Weible | 10 December 2013, 15:02:01 UTC | Revert "update apipe-test-rnaseq to have new processing profile param" This reverts commit e587bedc1c4e174e1b01077d6e889dd9219d1688. cancer_annotation_db should never have been a processing profile param. It should be an input | 10 December 2013, 15:42:40 UTC |
8cb51ed | APipe Tester | 10 December 2013, 14:43:18 UTC | updated jenkins submodule to 73300ad | 10 December 2013, 14:43:18 UTC |
7dc8847 | APipe Tester | 10 December 2013, 13:17:26 UTC | Updated `genome` tab completion. | 10 December 2013, 13:17:26 UTC |
42e8ea7 | APipe Tester | 10 December 2013, 13:15:53 UTC | Updated class browser cache. | 10 December 2013, 13:15:53 UTC |
a521712 | Thomas Mooney | 09 December 2013, 23:33:43 UTC | Sort in the order we expect them to be sorted in. Same fix as 83ef80b86d83a1707040d22b1c276c9fdfd2f4d3. | 09 December 2013, 23:33:43 UTC |
0454870 | Adam Coffman | 09 December 2013, 22:45:33 UTC | dont resuse config hash references | 09 December 2013, 22:45:33 UTC |
d8981b5 | Thomas Mooney | 09 December 2013, 20:20:29 UTC | Fallback on any available GTF file for the annotation build. | 09 December 2013, 21:05:06 UTC |
a1da992 | Feiyu Du | 09 December 2013, 20:59:34 UTC | add solution for another case of indelfilter normal genotype | 09 December 2013, 20:59:34 UTC |
bfa13b1 | Adam Coffman | 09 December 2013, 18:41:40 UTC | update analysis project lister | 09 December 2013, 18:41:40 UTC |
cf12f8b | Adam Coffman | 09 December 2013, 17:00:01 UTC | small CQID fixes | 09 December 2013, 17:00:01 UTC |
83ef80b | Susanna Siebert | 09 December 2013, 16:29:25 UTC | sort instrument data by read group instead of date | 09 December 2013, 16:29:25 UTC |
e587bed | Jim Weible | 09 December 2013, 15:07:45 UTC | update apipe-test-rnaseq to have new processing profile param | 09 December 2013, 15:08:14 UTC |
8b10e7b | Jim Weible | 06 December 2013, 19:49:53 UTC | add Annotation to RnaSeq fusion detection | 09 December 2013, 15:08:13 UTC |
64117b2 | APipe Tester | 07 December 2013, 13:17:07 UTC | Updated `genome` tab completion. | 07 December 2013, 13:17:07 UTC |
c331c02 | APipe Tester | 07 December 2013, 13:15:30 UTC | Updated class browser cache. | 07 December 2013, 13:15:30 UTC |
d18093b | apregier | 06 December 2013, 22:31:12 UTC | Merge branch 'copy' into gb_master | 06 December 2013, 22:31:12 UTC |
7c7abe8 | apregier | 06 December 2013, 22:29:51 UTC | Use topTags to get adjusted p-value | 06 December 2013, 22:30:56 UTC |
995c846 | apregier | 06 December 2013, 22:11:16 UTC | Use topTags to get adjusted p-value | 06 December 2013, 22:30:55 UTC |
60b967f | Anthony Brummett | 06 December 2013, 21:20:55 UTC | tag the sqitch schema as synced with production | 06 December 2013, 21:36:13 UTC |
6e7f5ae | Anthony Brummett | 04 December 2013, 22:18:39 UTC | rename indexes to match the production database | 06 December 2013, 21:36:12 UTC |
0a331d7 | Anthony Brummett | 04 December 2013, 21:33:24 UTC | rename index to match what is in production DB | 06 December 2013, 21:36:12 UTC |
29ee6be | Anthony Brummett | 04 December 2013, 21:12:33 UTC | set permissions on config.instrument_data_analysis_project_bridge | 06 December 2013, 21:36:11 UTC |
c472f04 | Anthony Brummett | 04 December 2013, 21:01:48 UTC | change the name of the index to match what is in the production DB | 06 December 2013, 21:36:10 UTC |
7625257 | Anthony Brummett | 04 December 2013, 20:53:49 UTC | drop column disk.preserved and add NOT NULL to archive_after_time and status | 06 December 2013, 21:36:09 UTC |
24bcedc | apregier | 06 December 2013, 21:14:39 UTC | Merge branch 'copy' into gb_master | 06 December 2013, 21:14:39 UTC |
02157e4 | apregier | 06 December 2013, 21:12:48 UTC | Add header to counts_file | 06 December 2013, 21:12:48 UTC |
e88cb6d | apregier | 06 December 2013, 20:34:33 UTC | Don't explicitly set groups in DGEList object | 06 December 2013, 20:34:33 UTC |
90031cc | Susanna Siebert | 06 December 2013, 17:14:01 UTC | Replaced the rnaseq tumor and normal parameters with clinseq parameter | 06 December 2013, 20:16:23 UTC |
73f5ee2 | Susanna Siebert | 06 December 2013, 15:27:41 UTC | subjects_list and groups_list are optional parameters | 06 December 2013, 20:16:23 UTC |
4a506fa | Susanna Siebert | 05 December 2013, 22:36:28 UTC | Added test to ensure that the gene columns of the input files are identical | 06 December 2013, 20:16:22 UTC |
d421890 | Susanna Siebert | 05 December 2013, 22:30:33 UTC | Added test to ensure that the joined output file is as expected | 06 December 2013, 20:16:21 UTC |
c2b7cd1 | Susanna Siebert | 05 December 2013, 21:50:51 UTC | added new module to make a joined gene counts file for multiple RnaSeq builds | 06 December 2013, 20:16:21 UTC |
b405955 | Susanna Siebert | 04 December 2013, 17:57:02 UTC | Added validation and test to ensure that each subject is in each group at least once | 06 December 2013, 20:16:20 UTC |
3a1abe0 | Susanna Siebert | 04 December 2013, 17:36:47 UTC | Added validation and test to ensure that number of groups and subjects are the same | 06 December 2013, 20:16:20 UTC |
c7c7266 | Susanna Siebert | 04 December 2013, 17:28:18 UTC | Added validation and test to ensure that more than one subject is being used | 06 December 2013, 20:16:19 UTC |
783d23e | Susanna Siebert | 04 December 2013, 17:25:50 UTC | Added validation and test to ensure that each subject is being used more than once | 06 December 2013, 20:16:19 UTC |
e506ee9 | Susanna Siebert | 04 December 2013, 17:12:53 UTC | Added validation and test for having more than one group | 06 December 2013, 20:16:18 UTC |
e39bc2f | Susanna Siebert | 04 December 2013, 17:00:30 UTC | Factored out the validate params tests into Base.t | 06 December 2013, 20:16:17 UTC |
31fc275 | Susanna Siebert | 04 December 2013, 16:49:57 UTC | updated the documentation for the GLM module | 06 December 2013, 20:16:17 UTC |
6056ea0 | Susanna Siebert | 04 December 2013, 16:48:23 UTC | refactored the parameter validation | 06 December 2013, 20:16:16 UTC |
d8d8140 | Susanna Siebert | 03 December 2013, 22:41:27 UTC | added edgeR GLM functionality and tests | 06 December 2013, 20:16:16 UTC |
e08309c | Susanna Siebert | 03 December 2013, 22:40:33 UTC | factored out the generate_counts_file subroutine into the base class so it can be used by both tests for classic and glm | 06 December 2013, 20:16:15 UTC |
b6f9ab4 | Susanna Siebert | 03 December 2013, 21:30:28 UTC | updated documentation to correspond to edgeR's updated output file header names | 06 December 2013, 20:16:15 UTC |
57ff7aa | Susanna Siebert | 03 December 2013, 21:23:46 UTC | factored out common functionality into EdgeR::Base and made EdgeR::Classic a child class | 06 December 2013, 20:16:14 UTC |
c4cd085 | Gabriel Sanderson | 06 December 2013, 16:32:34 UTC | Merge branch 'master' into gb_master | 06 December 2013, 16:32:34 UTC |
0c260eb | Gabriel Sanderson | 06 December 2013, 16:31:24 UTC | Make sure we do not have double slashes causing an invalid URL | 06 December 2013, 16:31:24 UTC |
a907880 | Gabriel Sanderson | 06 December 2013, 16:16:29 UTC | Expanded Copy.t beyond just a use_ok | 06 December 2013, 16:24:11 UTC |
f06b9a3 | APipe Tester | 06 December 2013, 13:17:17 UTC | Updated `genome` tab completion. | 06 December 2013, 13:17:17 UTC |
e69195f | Chris Miller | 05 December 2013, 22:21:51 UTC | fixing bug with var allele matching | 05 December 2013, 22:23:50 UTC |
df8f213 | Chris Miller | 05 December 2013, 21:56:25 UTC | update AddRsid to handle the case where there are multiple variants at the same position. Also has the nice side effect of preserving the order of the input list | 05 December 2013, 22:23:50 UTC |
7729044 | Travis Abbott | 05 December 2013, 19:36:59 UTC | add max_output_files to split variant mtx to avoid running out of fds | 05 December 2013, 19:36:59 UTC |
e979a4f | Charles Lu | 05 December 2013, 17:52:22 UTC | Add a feature where if user specifies somatic_variation_id, readcounts will be done from the normal and tumor BAMs associated with the som_var_model | 05 December 2013, 17:52:22 UTC |
e260269 | Thomas Mooney | 05 December 2013, 14:44:57 UTC | Add "is_capture" for benefit of AP Config rule specification. | 05 December 2013, 14:44:57 UTC |
7996fcb | APipe Tester | 05 December 2013, 13:54:03 UTC | updated workflow submodule to 214c3f7 | 05 December 2013, 13:54:03 UTC |
7db41fa | APipe Tester | 05 December 2013, 13:17:03 UTC | Updated `genome` tab completion. | 05 December 2013, 13:17:03 UTC |
b6285eb | APipe Tester | 05 December 2013, 13:15:25 UTC | Updated class browser cache. | 05 December 2013, 13:15:25 UTC |
8ab2989 | APipe Tester | 05 December 2013, 05:00:02 UTC | updated workflow submodule to 6e78a48 | 05 December 2013, 05:00:02 UTC |
5c68ec0 | Thomas Mooney | 05 December 2013, 00:03:00 UTC | Test the module that is the namesake of our test! | 05 December 2013, 00:03:00 UTC |
72c4606 | Gabriel Sanderson | 04 December 2013, 23:55:33 UTC | Merge branch 'master' into gb_master | 04 December 2013, 23:55:33 UTC |
720f0d6 | Gabriel Sanderson | 04 December 2013, 23:54:57 UTC | Remove the hardcoded -m param. Allow default memory usage. RT95163 | 04 December 2013, 23:54:57 UTC |
3b284c6 | Thomas Mooney | 04 December 2013, 22:30:00 UTC | Skip user confirmation in the test. | 04 December 2013, 22:30:00 UTC |
87ff465 | Thomas Mooney | 04 December 2013, 22:27:05 UTC | Prompt for what kinds of analysis to run. | 04 December 2013, 22:27:05 UTC |
c1d9c56 | Adam Coffman | 04 December 2013, 22:19:19 UTC | add factory method for creating profiles from an already existing config file | 04 December 2013, 22:19:19 UTC |
8650ada | Adam Coffman | 04 December 2013, 21:42:12 UTC | make analysis menu items optional for config profile items | 04 December 2013, 21:42:12 UTC |
7090b25 | Adam Coffman | 04 December 2013, 21:39:31 UTC | change column to be nullable | 04 December 2013, 21:39:31 UTC |
3b3e5aa | Adam Coffman | 04 December 2013, 21:10:14 UTC | get test factory test for analysis projects working | 04 December 2013, 21:10:14 UTC |
996fed8 | Mark Burnett | 04 December 2013, 20:40:36 UTC | fix parallel by bug in WorkflowBuilder | 04 December 2013, 20:41:02 UTC |
1894923 | Mark Burnett | 04 December 2013, 15:58:12 UTC | improve error message of mandatory inputs | 04 December 2013, 20:41:02 UTC |
3e44c9c | Adam Coffman | 04 December 2013, 20:00:42 UTC | get analysis project test passing again | 04 December 2013, 20:00:42 UTC |
ff58c9b | Adam Coffman | 04 December 2013, 19:54:32 UTC | get CQID test passing again | 04 December 2013, 19:54:32 UTC |
92bda68 | Thomas Mooney | 04 December 2013, 19:50:47 UTC | If the aligner doesn't support multiple references only make one index. The specified annotation build will need to have the entirety of the desired annotation for this to work properly. | 04 December 2013, 19:50:47 UTC |
a231b9a | Adam Coffman | 04 December 2013, 19:44:12 UTC | fix class definitions so they are valid | 04 December 2013, 19:44:12 UTC |
345e9fd | Feiyu Du | 04 December 2013, 18:05:32 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 December 2013, 18:05:32 UTC |
1e264a5 | Thomas Mooney | 04 December 2013, 17:16:07 UTC | Merge AP configuration changes into branch 'master' of ssh://git/srv/git/genome Conflicts: lib/perl/Genome/Config/Set.pm lib/perl/Genome/Config/Set.t sqitch/gms/sqitch.plan | 04 December 2013, 17:16:07 UTC |
8b31f87 | Adam Coffman | 04 December 2013, 17:09:40 UTC | update CQID to use new analysis project config reader | 04 December 2013, 17:09:40 UTC |
740d7b1 | Adam Coffman | 04 December 2013, 17:08:56 UTC | add new CQID supporting classes | 04 December 2013, 17:08:56 UTC |
7fdfe50 | Adam Coffman | 04 December 2013, 17:07:17 UTC | remove unused config classes and references to them | 04 December 2013, 17:07:17 UTC |
8e93087 | Adam Coffman | 04 December 2013, 16:57:04 UTC | Add database migrations to support CQID custom config profiles. | 04 December 2013, 16:57:04 UTC |
a91e55b | Feiyu Du | 04 December 2013, 16:45:12 UTC | Merge branch 'master' of ssh://git/srv/git/genome | 04 December 2013, 16:45:12 UTC |
ab09272 | Feiyu Du | 04 December 2013, 16:45:04 UTC | fix unit test | 04 December 2013, 16:45:04 UTC |
f16e8c9 | APipe Tester | 04 December 2013, 13:18:20 UTC | Updated `gmt` tab completion. | 04 December 2013, 13:18:20 UTC |
193d684 | APipe Tester | 04 December 2013, 13:17:38 UTC | Updated `genome` tab completion. | 04 December 2013, 13:17:38 UTC |
31d354d | APipe Tester | 04 December 2013, 13:16:07 UTC | Updated class browser cache. | 04 December 2013, 13:16:07 UTC |