Commits for hiram

2351b871084ddfbe26c56812d625b9ba3d6f9c47 Mon Jan 29 10:25:37 2018 -0800

exact equivalents UCSC db to NCBI RefSeq assembly refs #20215
- src/hg/utils/automation/dbAssemblyEquivalents.tab - lines changed 170, context: html, text, full: html, text

564f68b47e3af193949fc5b9af194601a4badc83 Mon Jan 29 18:27:46 2018 -0800

add cath email to reporting listings no redmine
- src/utils/qa/weeklybld/doNewBranch.csh - lines changed 1, context: html, text, full: html, text
- src/utils/qa/weeklybld/doNewReview.csh - lines changed 1, context: html, text, full: html, text
- src/utils/qa/weeklybld/doNewReview2.csh - lines changed 1, context: html, text, full: html, text

a6cdf21626f0dc03d6d1d0f2015e39a636822675 Wed Jan 31 11:09:03 2018 -0800

more general use of ensemblIdUrl from trackDb for ensGene refs #20696
- src/hg/hgc/hgc.c - lines changed 8, context: html, text, full: html, text

d0d0dd4b1b430349c117e6fffd3c9127e6f2605a Wed Jan 31 11:09:44 2018 -0800

fixup ensemblIdUrl with specific species name refs #20696
- src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.ra - lines changed 1, context: html, text, full: html, text

7b62fe211d818a5471b217f378c6658597bef32b Wed Jan 31 11:12:41 2018 -0800

fixup ensemblIdUrl with specific species name refs #20696
- src/hg/makeDb/trackDb/fugu/fr2/trackDb.ra - lines changed 4, context: html, text, full: html, text

f337553f95ea222f6502ff8748c2e2dbaca406ae Wed Jan 31 11:16:57 2018 -0800

fixup ensemblIdUrl with specific species name refs #20696
- src/hg/makeDb/trackDb/moleRat/hetGla1/trackDb.ra - lines changed 3, context: html, text, full: html, text
- src/hg/makeDb/trackDb/moleRat/hetGla2/trackDb.ra - lines changed 4, context: html, text, full: html, text

a0d229ef73611ba40e93e17d85c0d371afadce86 Wed Jan 31 11:19:35 2018 -0800

fixup ensemblIdUrl with specific species name refs #20696
- src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra - lines changed 4, context: html, text, full: html, text

d7ba35700e4cf209dd14aac4b38d6ebfe290f06c Wed Jan 31 13:10:08 2018 -0800

adding chromAlias table refs #20911
- src/hg/makeDb/doc/melGal5/initialBuild.txt - lines changed 33, context: html, text, full: html, text

36e2ae1f6f1df801b6d35a89272687d353a16ffb Thu Feb 1 11:39:59 2018 -0800

smart indexing of ncbiRefSeqOther.bed extra names refs #20215
- src/hg/utils/automation/ncbiRefSeqOtherIxIxx.pl - lines changed 102, context: html, text, full: html, text

da64eb14ea6dd47c3caf5631e06712172834ea8c Thu Feb 1 13:26:39 2018 -0800

recognize wormbase links and substitute into hgnc link refs #20215
- src/hg/utils/automation/gff3ToRefLink.pl - lines changed 7, context: html, text, full: html, text

f3e8212eceff94cb37f76470649f908c899c6ed3 Thu Feb 1 13:27:37 2018 -0800

use WormBase identifiers when present refs #20215
- src/hg/utils/automation/ncbiRefSeqOtherAttrs.pl - lines changed 2, context: html, text, full: html, text

3fe082c78f89149e7a35da9dd5f2a79066797e6a Thu Feb 1 13:28:16 2018 -0800

fixing up to work with ce11 wormbase links refs #20215
- src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 71, context: html, text, full: html, text

50a9e60e0b628bf6c083499a8cd1c234ec982a20 Thu Feb 1 13:29:04 2018 -0800

add noSuffix names and remove xxx: prefixes refs #20215
- src/hg/utils/automation/ncbiRefSeqOtherIxIxx.pl - lines changed 11, context: html, text, full: html, text

2b7dacf4d5f13c28b12263ff0d658c21587c6c74 Fri Feb 2 20:52:31 2018 -0800

clean up check on oreNil2 refs #20911
- src/hg/makeDb/schema/all.joiner - lines changed 4, context: html, text, full: html, text

b1245af3744adb9af6943f93b5671d33af2bbe20 Mon Feb 5 09:49:37 2018 -0800

could be an empty psl file from the gff3 refs #20215
- src/hg/utils/automation/doNcbiRefSeq.pl - lines changed 4, context: html, text, full: html, text

837fb343b0b0c433ff6baf30e75968b7febb001e Mon Feb 5 10:01:14 2018 -0800

v361 preview2 refs #20889
- src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text