| c14eeb1 | Thomas B. Mooney | 28 February 2017, 16:51:50 UTC | Use simpler means of validating LSF queue. Idea borrowed from Genome::ConfigValidator::LSFQueue. That module cannot "use Genome;" so can't be changed to refer to this version instead. | 02 March 2017, 20:28:04 UTC |
| 7941adb | Thomas B. Mooney | 23 February 2017, 20:45:28 UTC | Disable tests that relied on now-deleted production data. | 02 March 2017, 20:28:04 UTC |
| b81b423 | Feiyu Du | 23 February 2017, 20:58:04 UTC | update the unit test | 02 March 2017, 20:28:04 UTC |
| eecaa3a | Feiyu Du | 23 February 2017, 20:44:24 UTC | is rate, not percentage | 02 March 2017, 20:28:04 UTC |
| 66dc8b7 | Feiyu Du | 23 February 2017, 20:41:35 UTC | correct the variable names | 02 March 2017, 20:28:04 UTC |
| 5a1cef6 | Thomas B. Mooney | 23 February 2017, 20:29:19 UTC | Use files in test data directory. | 02 March 2017, 20:28:04 UTC |
| 3b02bf8 | Jason Walker | 23 February 2017, 16:48:32 UTC | spellcheck | 02 March 2017, 20:28:04 UTC |
| 1d1d51f | Jason Walker | 23 February 2017, 14:54:01 UTC | note about running builds in docs. | 02 March 2017, 20:28:04 UTC |
| c2b3dce | Jason Walker | 23 February 2017, 14:51:54 UTC | Improve documentation and stipulations. | 02 March 2017, 20:28:04 UTC |
| 02f24eb | Jason Walker | 23 February 2017, 14:46:21 UTC | Remove commented lines. | 02 March 2017, 20:28:04 UTC |
| c8be850 | Jason Walker | 22 February 2017, 22:31:44 UTC | Remove status messages. loop all builds. hash ref syntax fix. | 02 March 2017, 20:28:04 UTC |
| dc18228 | Jason Walker | 22 February 2017, 18:10:31 UTC | hash typo: curly for square brackets. | 02 March 2017, 20:28:04 UTC |
| a11b24f | Jason Walker | 22 February 2017, 17:50:38 UTC | Only look at last succeeded build. Avoid divide my zero errors. Status messages. | 02 March 2017, 20:28:04 UTC |
| 11a8fcc | Jason Walker | 20 February 2017, 22:09:43 UTC | Remove unnecessary import. | 02 March 2017, 20:28:04 UTC |
| 0695338 | Jason Walker | 20 February 2017, 22:02:52 UTC | Use separated value writer. | 02 March 2017, 20:28:04 UTC |
| 1c54ffe | Jason Walker | 20 February 2017, 21:51:20 UTC | improve docs. | 02 March 2017, 20:28:04 UTC |
| 1d772fe | Jason Walker | 20 February 2017, 21:36:59 UTC | Initial revision of command to report disk usage. WIP. | 02 March 2017, 20:28:04 UTC |
| c74d14a | Thomas B. Mooney | 20 February 2017, 17:53:30 UTC | Remove GMT WuBlast tree and dependent tools. The installation of WUBLAST is changing, so stop supporting it here. | 02 March 2017, 20:28:04 UTC |
| 3b9ee1d | Thomas B. Mooney | 15 February 2017, 20:27:06 UTC | In newer Perls, defined(@array) is disallowed. | 02 March 2017, 20:28:04 UTC |
| 1ab8ccb | Thomas B. Mooney | 15 February 2017, 20:25:52 UTC | In newer Perls qw() doesn't make something a list. | 02 March 2017, 20:28:04 UTC |
| f35c2a8 | Thomas B. Mooney | 14 February 2017, 21:39:03 UTC | Don't fail if a particular disk group configuration isn't set. | 02 March 2017, 20:28:04 UTC |
| 26fcd5d | Thomas B. Mooney | 14 February 2017, 21:38:36 UTC | Don't validate disk groups on get/create. | 02 March 2017, 20:28:04 UTC |
| 6fb7fa1 | Kilannin Krysiak | 13 February 2017, 23:38:22 UTC | Fixing header bug that led to repeat headers being printed | 02 March 2017, 20:28:04 UTC |
| d8a87f6 | Kilannin Krysiak | 09 February 2017, 00:10:56 UTC | Added code to disallow the annotation of indels since this code was not designed to handle them | 02 March 2017, 20:28:04 UTC |
| 3c1fe76 | Adam Coffman | 08 February 2017, 22:19:16 UTC | attempt to skip indels to avoid giving incorrect annotation | 02 March 2017, 20:28:04 UTC |
| 1efb3bb | Kilannin Krysiak | 08 February 2017, 21:41:33 UTC | Moved variable use to appropriate loop | 02 March 2017, 20:28:04 UTC |
| 76be932 | Kilannin Krysiak | 08 February 2017, 17:29:58 UTC | Adding decision functionality to support dbSNP VCFs with GMAF or CAF style reports | 02 March 2017, 20:28:04 UTC |
| 32f9338 | Thomas B. Mooney | 08 February 2017, 15:54:15 UTC | Use configurable network disk location. | 02 March 2017, 20:28:04 UTC |
| adb0620 | Thomas B. Mooney | 08 February 2017, 15:50:36 UTC | Remove `gmt sam r1`. | 02 March 2017, 20:28:04 UTC |
| f5ab97b | Thomas B. Mooney | 08 February 2017, 15:49:52 UTC | Remove commented-out code. | 02 March 2017, 20:28:04 UTC |
| 55d6410 | Thomas B. Mooney | 08 February 2017, 15:48:36 UTC | Stop writing unarchive logs to /gsc/var/tmp. | 02 March 2017, 20:28:04 UTC |
| 2c93c8c | Kilannin Krysiak | 07 February 2017, 22:14:02 UTC | Rework to keep the handling of the original VCF file types | 02 March 2017, 20:28:04 UTC |
| f1ee48d | Jason Walker | 05 December 2016, 19:49:30 UTC | Add sort to available versions | 02 March 2017, 20:28:04 UTC |
| 432e652 | Jason Walker | 30 November 2016, 17:53:55 UTC | Update manta to use new tool base class. | 02 March 2017, 20:28:04 UTC |
| d616365 | Jason Walker | 30 November 2016, 17:53:38 UTC | Add a base class for tools. Add Sambamba tool tree and basic implementation of sort command. | 02 March 2017, 20:28:04 UTC |
| 8ab6583 | Kilannin Krysiak | 07 February 2017, 18:34:13 UTC | Removing . for no information and cleaning up code | 07 February 2017, 18:34:13 UTC |
| 8ffc4d5 | Kilannin Krysiak | 07 February 2017, 05:33:43 UTC | Adding use of CAF values in newer dbSNP VCF files | 07 February 2017, 05:33:43 UTC |
| d43ba15 | Feiyu Du | 02 February 2017, 20:12:48 UTC | Merge pull request #1658 from dufeiyu/qc_error_rate Try to get error_rate from Genome::Qc::Result metrics | 02 February 2017, 20:12:48 UTC |
| 6c9ecc5 | Feiyu Du | 01 February 2017, 23:05:38 UTC | Update the unit test | 01 February 2017, 23:05:38 UTC |
| 16b5146 | Thomas B. Mooney | 01 February 2017, 16:01:50 UTC | Merge pull request #1654 from tmooney/anps_require_environment_specifications Analysis Projects Require Environment Specifications | 01 February 2017, 16:01:50 UTC |
| c9fc3c3 | Feiyu Du | 01 February 2017, 05:33:51 UTC | Try to get error_rate from Genome::Qc::Result metrics | 01 February 2017, 05:33:51 UTC |
| eb2d118 | Thomas B. Mooney | 30 January 2017, 19:35:53 UTC | Merge pull request #1641 from tmooney/stop_configuring_workflow_in_genome-env Remove "Workflow" from genome-env. | 30 January 2017, 19:35:53 UTC |
| c366766 | Thomas B. Mooney | 30 January 2017, 19:35:35 UTC | Merge pull request #1650 from tmooney/remove_gene_prediction_model_types Remove code for discontinued "GenePrediction" model types. | 30 January 2017, 19:35:35 UTC |
| 1f3f2c9 | Thomas B. Mooney | 25 January 2017, 14:05:06 UTC | Merge pull request #1657 from tmooney/fix_clinseq_tests_using_purged_data Fix/Disable ClinSeq tests using purged data | 25 January 2017, 14:05:06 UTC |
| 21e9939 | Thomas B. Mooney | 24 January 2017, 21:27:08 UTC | Remove obsolete comment. | 24 January 2017, 21:27:08 UTC |
| 9c6a270 | Thomas B. Mooney | 24 January 2017, 21:26:39 UTC | Skip tests that relied on production data instead of test data. | 24 January 2017, 21:26:39 UTC |
| e066ca5 | Thomas B. Mooney | 24 January 2017, 21:13:39 UTC | Fix test to use a fake build instead of relying on production data. | 24 January 2017, 21:13:39 UTC |
| b31524e | Thomas B. Mooney | 24 January 2017, 20:34:51 UTC | Use no-commit in test. | 24 January 2017, 20:34:51 UTC |
| 76dde10 | Thomas B. Mooney | 23 January 2017, 15:57:26 UTC | Merge pull request #1655 from tmooney/escape_filename_in_bam_readcounts Escape Sample Name Used as Filename in bam-readcounts | 23 January 2017, 15:57:26 UTC |
| 63fb747 | Thomas B. Mooney | 19 January 2017, 15:31:20 UTC | Require an environment configuration to be specified before releasing. | 23 January 2017, 15:56:10 UTC |
| 51c3037 | Thomas B. Mooney | 19 January 2017, 15:16:15 UTC | Include name of AnP in error message. | 23 January 2017, 15:56:09 UTC |
| 50f7356 | Thomas B. Mooney | 12 January 2017, 21:33:12 UTC | Rename "production" setting to "prod-builder" setting. This removes the overloaded concept of "production" from the term, and now refers specifically to running as that user just as the "cle" setting does. | 23 January 2017, 15:56:09 UTC |
| ff08f98 | Thomas B. Mooney | 23 January 2017, 14:29:05 UTC | Merge pull request #1653 from tmooney/request_four_cores_in_strelka Specify four CPUs in Strelka request. | 23 January 2017, 14:29:05 UTC |
| 723a8e7 | Thomas B. Mooney | 21 January 2017, 05:26:32 UTC | Merge pull request #1656 from tmooney/bwa_bhosts_check_removes_all_trailing_slashes Remove all trailing slashes from host-groups... not just one! | 21 January 2017, 05:26:32 UTC |
| 1c79790 | Thomas B. Mooney | 19 January 2017, 23:39:21 UTC | Remove all trailing slashes from host-groups... not just one! | 20 January 2017, 18:01:32 UTC |
| 3d07c40 | Thomas B. Mooney | 19 January 2017, 17:10:20 UTC | Check for the BAM's existence before bothering to create sample input. | 19 January 2017, 17:10:20 UTC |
| da65c61 | Thomas B. Mooney | 19 January 2017, 17:02:57 UTC | Sanitize the sample name before using it as a filename. | 19 January 2017, 17:08:57 UTC |
| bb7610d | Thomas B. Mooney | 19 January 2017, 16:53:57 UTC | Remove old contact line. | 19 January 2017, 16:53:57 UTC |
| a6562df | Thomas B. Mooney | 19 January 2017, 16:49:34 UTC | Get the number of CPUs from the environment. | 19 January 2017, 16:49:34 UTC |
| 30ff18f | Thomas B. Mooney | 19 January 2017, 16:10:16 UTC | Merge pull request #1651 from tmooney/gut_gm_report_getdataset_test Eliminate testcase that depends on MC16s build. | 19 January 2017, 16:10:16 UTC |
| dbed259 | Thomas B. Mooney | 18 January 2017, 18:25:41 UTC | Specify four CPUs in Strelka request. | 18 January 2017, 18:25:41 UTC |
| 1f2dffe | Thomas B. Mooney | 09 January 2017, 18:38:29 UTC | Eliminate testcase that depends on MC16s build. | 09 January 2017, 18:38:29 UTC |
| 3dec8bf | Thomas B. Mooney | 05 January 2017, 21:15:04 UTC | Merge pull request #1644 from tmooney/treat_errored_ptero_status_as_failure Treat "errored" PTero status as a failure condition. | 05 January 2017, 21:15:04 UTC |
| f9c5a64 | Thomas B. Mooney | 05 January 2017, 20:18:01 UTC | Merge pull request #1649 from tmooney/anp_take_and_uncomplete New AnP Commands to "Take Ownership" or "Uncomplete" AnPs. | 05 January 2017, 20:18:01 UTC |
| f3e25a0 | Thomas B. Mooney | 05 January 2017, 19:14:21 UTC | Remove code for discontinued "GenePrediction" model types. | 05 January 2017, 19:14:21 UTC |
| 1dda7f8 | Thomas B. Mooney | 04 January 2017, 20:52:45 UTC | New command to "uncomplete" an analysis project. Closes #1647. | 04 January 2017, 20:52:45 UTC |
| bd5b270 | Thomas B. Mooney | 04 January 2017, 20:42:11 UTC | New command to "take ownership" of an AnP. Closes #1648. | 04 January 2017, 20:49:41 UTC |
| bdb9952 | Feiyu Du | 20 December 2016, 16:38:22 UTC | Merge pull request #1645 from dufeiyu/update_cle_regression update the blessed build for germline model | 20 December 2016, 16:38:22 UTC |
| f9cd906 | Feiyu Du | 18 December 2016, 18:25:59 UTC | update the blessed build for germline model | 18 December 2016, 18:25:59 UTC |
| f877afd | Thomas B. Mooney | 12 December 2016, 23:33:20 UTC | Treat "errored" PTero status as a failure condition. This means we will now display the "execute" attempt if the "shortcut" attempt errors out. (Previously, the errored shortcut would be displayed even if the execute is running smoothly.) | 12 December 2016, 23:33:20 UTC |
| 11aaba9 | Thomas B. Mooney | 12 December 2016, 16:07:40 UTC | Merge pull request #1643 from tmooney/remove_old_disk_xsl Remove old disk view XSL. | 12 December 2016, 16:07:40 UTC |
| 5fc22cc | Thomas B. Mooney | 07 December 2016, 23:13:04 UTC | Remove old disk view XSL. The associated view module was removed in d9a16867c35a036d524f064df3c3cf18f972c284. | 07 December 2016, 23:13:04 UTC |
| 66d6a8f | Chris Miller | 07 December 2016, 15:08:04 UTC | Merge pull request #1642 from chrisamiller/master new copycat version requires bam-readcount v0.5, updated expected output files | 07 December 2016, 15:08:04 UTC |
| ba24d2e | Chris Miller | 07 December 2016, 05:05:27 UTC | new copycat version requires bam-readcount v0.5, updated expected output files | 07 December 2016, 05:05:59 UTC |
| a874a7d | APipe Tester | 06 December 2016, 13:18:13 UTC | Updated `gmt` tab completion. | 06 December 2016, 13:18:13 UTC |
| aeca5b7 | APipe Tester | 06 December 2016, 13:17:29 UTC | Updated `genome` tab completion. | 06 December 2016, 13:17:29 UTC |
| e63b098 | APipe Tester | 06 December 2016, 13:15:44 UTC | Updated class browser cache. | 06 December 2016, 13:15:44 UTC |
| 55e0408 | Thomas B. Mooney | 05 December 2016, 20:20:56 UTC | Update tests to stop testing for workflow options. | 05 December 2016, 22:10:55 UTC |
| 774ac69 | Thomas B. Mooney | 05 December 2016, 19:26:42 UTC | Remove "Workflow" from genome-env. | 05 December 2016, 19:26:42 UTC |
| 61322c5 | Jason Walker | 05 December 2016, 18:40:49 UTC | Merge pull request #1639 from jasonwalker80/config_disk_group_unarchive Use config to resolve disk group for unarchives. | 05 December 2016, 18:40:49 UTC |
| b442dc9 | Thomas B. Mooney | 05 December 2016, 18:36:40 UTC | Merge pull request #1638 from tmooney/lockproxy_test_uses_above Use above for loading Genome in LockProxy.t | 05 December 2016, 18:36:40 UTC |
| 6e47dfe | Thomas B. Mooney | 05 December 2016, 18:36:33 UTC | Merge pull request #1632 from tmooney/print_lock_name_when_waiting_on_lock Debug message for the resource when locking. | 05 December 2016, 18:36:33 UTC |
| 8246943 | Thomas B. Mooney | 05 December 2016, 18:36:15 UTC | Merge pull request #1636 from tmooney/is_mounted_trusts_symlinks Trust that symlinks are mounted. | 05 December 2016, 18:36:15 UTC |
| c739a43 | Thomas B. Mooney | 05 December 2016, 18:36:01 UTC | Merge pull request #1629 from tmooney/exclude_alignment_metrics_from_default_solexa_lister Exclude alignment metrics from default Solexa lister. | 05 December 2016, 18:36:01 UTC |
| 2b11c93 | Thomas B. Mooney | 05 December 2016, 18:35:53 UTC | Merge pull request #1640 from tmooney/remove_phred Remove tools that depend on `phred`. | 05 December 2016, 18:35:53 UTC |
| 93ee34d | Jason Walker | 05 December 2016, 18:25:16 UTC | Merge pull request #1622 from jasonwalker80/update_igv_refnames Update IGV ref name example values. | 05 December 2016, 18:25:16 UTC |
| e8bfa77 | Jason Walker | 05 December 2016, 17:36:11 UTC | Use estimated kb for allocation. | 05 December 2016, 17:36:11 UTC |
| 501c628 | APipe Tester | 02 December 2016, 13:17:46 UTC | Updated `gmt` tab completion. | 02 December 2016, 13:17:46 UTC |
| 19321b1 | APipe Tester | 02 December 2016, 13:17:02 UTC | Updated `genome` tab completion. | 02 December 2016, 13:17:02 UTC |
| 6fd17b4 | APipe Tester | 02 December 2016, 13:14:57 UTC | Updated class browser cache. | 02 December 2016, 13:14:57 UTC |
| 2a63ace | Thomas B. Mooney | 01 December 2016, 23:00:39 UTC | Remove tools that depend on `phred`. | 01 December 2016, 23:17:47 UTC |
| 5433da4 | Thomas B. Mooney | 01 December 2016, 19:41:07 UTC | Merge pull request #1637 from tmooney/remove_rdp Remove support for RDP. | 01 December 2016, 19:41:07 UTC |
| c604743 | Jason Walker | 01 December 2016, 19:28:03 UTC | Use config to resolve disk group for unarchives. | 01 December 2016, 19:28:03 UTC |
| e305e8d | Jason Walker | 01 December 2016, 17:54:10 UTC | Merge pull request #1634 from jasonwalker80/lookup_snvs_result SnvIndelReport standalone support | 01 December 2016, 17:54:10 UTC |
| 5dabb56 | Jason Walker | 01 December 2016, 16:41:06 UTC | Make target_gene_list and target_gene_list_name required and remove default. | 01 December 2016, 16:41:06 UTC |
| 2b5f8fb | Jason Walker | 01 December 2016, 16:39:49 UTC | Change order of operations for resolving annotated snvs vcf. Fail if shorcut does not work. | 01 December 2016, 16:39:49 UTC |
| d3be886 | Thomas B. Mooney | 01 December 2016, 16:18:33 UTC | Merge pull request #1635 from tmooney/use_db_for_breakannot Use Genome DB instead of hardcoded /gsc/ path. | 01 December 2016, 16:18:33 UTC |
| cd85786 | Thomas B. Mooney | 30 November 2016, 22:45:04 UTC | Use above for loading Genome in LockProxy.t | 30 November 2016, 22:45:04 UTC |
| d6aa6ea | Thomas B. Mooney | 30 November 2016, 22:12:11 UTC | Remove support for RDP. | 30 November 2016, 22:12:11 UTC |
| 73abdb3 | Thomas B. Mooney | 30 November 2016, 21:20:31 UTC | Trust that symlinks are mounted. | 30 November 2016, 21:20:31 UTC |
