| 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 |
| 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 |
| 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 |
| 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 |
| 9ff84b4 | Thomas B. Mooney | 30 November 2016, 20:41:07 UTC | Use Genome DB instead of hardcoded /gsc/ path. | 30 November 2016, 20:41:07 UTC |
| 2eaf896 | Thomas B. Mooney | 30 November 2016, 14:57:52 UTC | Debug message for the resource when locking. This should make it easier to find out what we're waiting on when something else has the lock. This replaces the earlier pre-backend message that would output the entire contents of the file lock. * Can't use debug_message() here since we're not a UR::Object. * Genome::Logger might be better, but support for that isn't great. | 30 November 2016, 19:19:46 UTC |
| 6bf5853 | Jason Walker | 30 November 2016, 18:17:09 UTC | change precedence of SNV VCF lookup. Add correct user hash to command. | 30 November 2016, 18:17:09 UTC |
| e30f451 | Jason Walker | 30 November 2016, 02:55:26 UTC | inital attempt at looking up the result or shortcutting. | 30 November 2016, 02:55:26 UTC |
| c3c9b74 | Feiyu Du | 29 November 2016, 20:12:59 UTC | Merge pull request #1630 from dufeiyu/update_cletest Add PindelRegion region file feature list to CleTest | 29 November 2016, 20:12:59 UTC |
| a50942c | Feiyu Du | 29 November 2016, 17:37:33 UTC | Add PindelRegion region file feature list to CleTest | 29 November 2016, 17:37:33 UTC |
| f09971c | Feiyu Du | 23 November 2016, 20:08:46 UTC | Merge pull request #1628 from dufeiyu/update_cle Update CLE Test | 23 November 2016, 20:08:46 UTC |
| 71c29b9 | Thomas B. Mooney | 23 November 2016, 13:47:59 UTC | Exclude alignment metrics from default Solexa lister. When the LIMS was calculating these, they were quick lookups since they came as instrument data properties. Now that they're not, there's only the hacky "default_alignment_results" to get them. The question doesn't really make sense in a world where alignment can be done any number of ways. | 23 November 2016, 18:24:29 UTC |
| f34ac07 | Feiyu Du | 22 November 2016, 22:12:37 UTC | update CleTest with new processing profile and blessed builds/process | 22 November 2016, 22:12:37 UTC |
| 80af2cb | Thomas B. Mooney | 22 November 2016, 16:56:04 UTC | Merge pull request #1627 from tmooney/remove_bpdeluxe_module Remove top-level BPdeluxe.pm | 22 November 2016, 16:56:04 UTC |
| f071ff4 | APipe Tester | 22 November 2016, 13:18:26 UTC | Updated `gmt` tab completion. | 22 November 2016, 13:18:26 UTC |
| a15eed9 | APipe Tester | 22 November 2016, 13:17:43 UTC | Updated `genome` tab completion. | 22 November 2016, 13:17:43 UTC |
| c77af7a | APipe Tester | 22 November 2016, 13:16:13 UTC | Updated class browser cache. | 22 November 2016, 13:16:13 UTC |
| 87e6812 | Jason Walker | 21 November 2016, 20:56:58 UTC | Merge pull request #1621 from jasonwalker80/remove_instdata_limitation Remove imported restriction to assiging instrument data. | 21 November 2016, 20:56:58 UTC |
| 35ac6e1 | Jason Walker | 21 November 2016, 19:52:10 UTC | update sort order based on relevance. | 21 November 2016, 19:52:10 UTC |
| 6507ebe | Thomas B. Mooney | 21 November 2016, 19:26:54 UTC | Merge pull request #1617 from tmooney/bwamem_converts_fragment_bam_to_fastq_properly BWA-MEM: Only pass parameter for paired FASTQs if "-p" flag used. | 21 November 2016, 19:26:54 UTC |
| 3a2f9f1 | Jason Walker | 21 November 2016, 19:22:30 UTC | Add hg38 and mm10 as example values for IGV references. | 21 November 2016, 19:22:30 UTC |
| cea8865 | Jason Walker | 21 November 2016, 19:13:53 UTC | Remove imported restriction to assiging instrument data. | 21 November 2016, 19:13:53 UTC |
| 2d48d2d | Thomas B. Mooney | 21 November 2016, 19:10:04 UTC | Merge pull request #1618 from tmooney/remove_spurious_whitespace_in_jobiterator Remove spurious whitespace in regex. | 21 November 2016, 19:10:04 UTC |
| 9214d38 | Thomas B. Mooney | 21 November 2016, 19:09:50 UTC | Merge pull request #1615 from tmooney/remove_gmt_kmer Remove old `gmt kmer` tree. | 21 November 2016, 19:09:50 UTC |
| f46646e | Thomas B. Mooney | 21 November 2016, 19:09:43 UTC | Merge pull request #1612 from tmooney/use_testdata_for_adapter_file Use test input for adapter file instead of hardcoded path. | 21 November 2016, 19:09:43 UTC |
| 4204697 | Thomas B. Mooney | 21 November 2016, 19:09:26 UTC | Merge pull request #1609 from tmooney/analysis_project_view_includes_inactive_configs Add separate flag to control display of inactive configs. | 21 November 2016, 19:09:26 UTC |
| d602fe1 | Thomas B. Mooney | 21 November 2016, 19:09:15 UTC | Merge pull request #1604 from tmooney/remove_park_beta Remove "Park" beta. | 21 November 2016, 19:09:15 UTC |
| 656707d | Thomas B. Mooney | 21 November 2016, 18:41:06 UTC | Remove top-level BPdeluxe.pm There is another copy at: Genome/Model/Tools/Predictor/BPdeluxe.pm | 21 November 2016, 18:41:06 UTC |
| 5058219 | Thomas B. Mooney | 17 November 2016, 18:27:57 UTC | Merge pull request #1620 from tmooney/correct_operator_precedence_in_test_builder Test::Builder: Don't return before evaluating the entire expression. | 17 November 2016, 18:27:57 UTC |
| 44e515d | Thomas B. Mooney | 17 November 2016, 18:26:56 UTC | Merge branch 'master' into remove_park_beta Conflicts: lib/perl/Genome/Model/GenePrediction/Command/Pap/Blast/BladeBlastBatcher.pm lib/perl/Genome/Model/GenePrediction/Command/Pap/KEGGScan/RunKeggScan.pm | 17 November 2016, 18:26:56 UTC |
| 3052740 | Thomas B. Mooney | 17 November 2016, 18:24:28 UTC | Merge pull request #1611 from tmooney/configurable_memory_limit_for_picard Make Java heap and permgen configurable for calling Picard. | 17 November 2016, 18:24:28 UTC |
| 5b8e1fe | Thomas B. Mooney | 17 November 2016, 18:24:01 UTC | Merge pull request #1619 from tmooney/sr_avoid_calling_each_while_inserting_into_hash Avoid using `each()` in loop where we insert into the hash. | 17 November 2016, 18:24:01 UTC |
| ff05d0a | Thomas B. Mooney | 16 November 2016, 23:42:35 UTC | Don't return before evaluating the entire expression. This module really shouldn't be in the repository to begin with... but as long as we're supporting old systems it shall remain. | 16 November 2016, 23:42:35 UTC |
| c811b39 | Thomas B. Mooney | 16 November 2016, 22:37:56 UTC | Avoid using `each()` in loop where we insert into the hash. Newer Perl's provide this warning: > Use of each() on hash after insertion without resetting hash iterator > results in undefined behavior | 16 November 2016, 22:37:56 UTC |
| 9f9c7bd | Thomas B. Mooney | 16 November 2016, 22:24:29 UTC | Remove spurious whitespace in regex. Perl 5.22 warned of an unescaped "{". Seems like it was a quantifier gone wrong. The history of this module is obscured, though. | 16 November 2016, 22:24:29 UTC |
| 7399b54 | Thomas B. Mooney | 16 November 2016, 14:30:57 UTC | Only pass parameter for paired output if "-p" flag used in bwa-mem. | 16 November 2016, 14:30:57 UTC |
| 91fd81b | Joshua McMichael | 15 November 2016, 16:11:55 UTC | Merge pull request #1593 from tmooney/bugfix_coverage_html_table_structure Coverage Report: Use a wrapping <div> for the hiding. Apply dataTables to the <table>. | 15 November 2016, 16:11:55 UTC |
| 5413417 | APipe Tester | 11 November 2016, 13:18:03 UTC | Updated `gmt` tab completion. | 11 November 2016, 13:18:03 UTC |
| 91d6132 | APipe Tester | 11 November 2016, 13:17:20 UTC | Updated `genome` tab completion. | 11 November 2016, 13:17:20 UTC |
| 8667111 | APipe Tester | 11 November 2016, 13:15:46 UTC | Updated class browser cache. | 11 November 2016, 13:15:46 UTC |
| 9418845 | Thomas B. Mooney | 10 November 2016, 22:40:36 UTC | Merge pull request #1616 from tmooney/remove_obsolete_utilities Remove various "Genome::Utility" entries that seem disused. | 10 November 2016, 22:40:36 UTC |
| 558bd96 | Thomas B. Mooney | 10 November 2016, 16:52:41 UTC | Merge pull request #1610 from tmooney/make_it_possible_to_disable_fs_caching Make it possible to disable local filesystem caching. | 10 November 2016, 16:52:41 UTC |
| 1428b3f | Thomas B. Mooney | 10 November 2016, 16:51:56 UTC | Merge pull request #1613 from tmooney/remove_gmt_analysis_indels_dbsnpconcord Remove old `gmt analysis indels dbsnp-concord` tool. | 10 November 2016, 16:51:56 UTC |
| 31f52ca | Thomas B. Mooney | 10 November 2016, 16:51:43 UTC | Merge pull request #1614 from tmooney/remove_disabled_gmt_bedtools_coverage Remove old tool that was "disabled" in 2010. | 10 November 2016, 16:51:43 UTC |
| f9dd0b3 | APipe Tester | 10 November 2016, 13:18:52 UTC | Updated `gmt` tab completion. | 10 November 2016, 13:18:52 UTC |
| fd779ee | APipe Tester | 10 November 2016, 13:18:04 UTC | Updated `genome` tab completion. | 10 November 2016, 13:18:04 UTC |
| 07f318b | APipe Tester | 10 November 2016, 13:16:24 UTC | Updated class browser cache. | 10 November 2016, 13:16:24 UTC |
| 302c831 | Thomas B. Mooney | 09 November 2016, 22:57:13 UTC | Remove Genome::Utility::BioPerl tree. | 09 November 2016, 22:57:13 UTC |
| 786e7fc | Thomas B. Mooney | 09 November 2016, 22:52:15 UTC | Remove "Editor" Utility. I heartell this idea never got put to full use. | 09 November 2016, 22:52:15 UTC |
| d22285a | Thomas B. Mooney | 09 November 2016, 22:47:23 UTC | Remove TranscriptHelper Utility. | 09 November 2016, 22:47:23 UTC |
| 8675712 | Thomas B. Mooney | 09 November 2016, 22:43:22 UTC | Remove 454TrimFile Utility and tools. | 09 November 2016, 22:43:22 UTC |
| f3fc70c | Thomas B. Mooney | 09 November 2016, 22:41:56 UTC | Remove SeqcleanReport Utility and tool. | 09 November 2016, 22:41:56 UTC |
| da92807 | Thomas B. Mooney | 09 November 2016, 22:39:44 UTC | Remove Genome::Utility::IAValidate. | 09 November 2016, 22:39:44 UTC |
