Commits for lrnassar

v398_preview to v398_preview2 (2020-04-27 to 2020-05-04) v398

c1d89458d6796c16766ec77a62e96c38784f871f Mon Apr 27 10:18:26 2020 -0700

• Changing short and longLabel due to feedback refs #25297
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 2, context: html, text, full: html, text

aa4d2bf10307bd105eb11d0daf7d0278f8489af0 Mon Apr 27 10:37:45 2020 -0700

• Removing release tags for refseq genes update refs #24547
  • src/hg/makeDb/trackDb/armadillo/dasNov3/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/baboon/papAnu4/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/balAcu/balAcu1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/geoFor1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/birds/melUnd1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/bonobo/panPan2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/calMil/calMil1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chlorocebus/chlSab2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/criGri/criGriChoV1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/dog/canFam3/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/elephant/loxAfr3/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ferret/musFur1/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/frog/nanPar1/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/galVar/galVar1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/hedgehog/eriEur2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/latCha/latCha1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/lizard/anoCar2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macFas5/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/manatee/triMan1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/microbat/myoLuc2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/moleRat/hetGla2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/orangutan/ponAbe3/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/panda/ailMel1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/pika/ochPri3/trackDb.ra - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rabbit/oryCun2/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhino/cerSim1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/saiBol/saiBol1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/shrew/sorAra2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/squirrel/speTri2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tarsier/tarSyr2/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tasmanianDevil/sarHar1/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/xenTro/xenLae2/trackDb.ra - lines changed 1, context: html, text, full: html, text

e4a3deab7d351adfe571fd371171325dfa364639 Tue Apr 28 10:01:23 2020 -0700

• Adding pennantIcon and fixing some release tag issues refs #24547
  • src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/guineaPig/cavPor3/trackDb.refGene.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.refGene.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/refSeqComposite.ra - lines changed 1, context: html, text, full: html, text

8204f3686faa45ce0b031b2927f272fb1b11690e Tue Apr 28 14:30:03 2020 -0700

• Updating desc page for the crispr detection guides refs #25247
  • src/hg/makeDb/trackDb/virus/wuhCor1/crisprDet.html - lines changed 3, context: html, text, full: html, text

fc64e514e36c00b4d457d3bf0747853895dcc651 Tue Apr 28 14:48:13 2020 -0700

• Fixing up the desc page for cas13 CRISPR track refs #25344
  • src/hg/makeDb/trackDb/virus/wuhCor1/cas13Crispr.html - lines changed 50, context: html, text, full: html, text

c1dd96464056bde5c4a743be533d27c05535a7cb Tue Apr 28 15:04:01 2020 -0700

• Adding data access section for cas13 CRISPR track refs #25344
  • src/hg/makeDb/trackDb/virus/wuhCor1/cas13Crispr.html - lines changed 23, context: html, text, full: html, text

da125c7b2682fd607264cf3da6dc8e31ca19a36a Tue Apr 28 15:13:22 2020 -0700

• Fixing trackDb stanza for cas13 CRISPR to enable a score filter and shading by score refs #25344
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 4, context: html, text, full: html, text

1b57d6e546df31ddd01e6c521f52a0b4af8a4c53 Tue Apr 28 15:24:58 2020 -0700

• Adding data access section to ARTIC track refs #25416
  • src/hg/makeDb/trackDb/virus/wuhCor1/artic.html - lines changed 24, context: html, text, full: html, text

b64309c98f9f63c226fb0e72af7a6ececa5bca00 Tue Apr 28 15:48:25 2020 -0700

• Touching up description page for Rangan RNA, adding references refs #25228
  • src/hg/makeDb/trackDb/virus/wuhCor1/rnaStructRangan.html - lines changed 21, context: html, text, full: html, text

716c4d1035a1ee92d7c578294960a992fe1ba650 Tue Apr 28 15:49:11 2020 -0700

• Making small html fix for readability no RM
  • src/hg/makeDb/trackDb/virus/wuhCor1/cas13Crispr.html - lines changed 3, context: html, text, full: html, text

a4004610e414e50484185ea4a0f291deba0e12ec Tue Apr 28 16:05:04 2020 -0700

• Adding last includes plus pennantIcon to last missing dbs for refseq updates refs #24547
  • src/hg/makeDb/trackDb/bushbaby/otoGar3/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chicken/galGal6/refSeqComposite.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/horse/equCab3/trackDb.ra - lines changed 1, context: html, text, full: html, text

d64007232b5b5191becd4d3affa51a8641f09966 Tue Apr 28 16:12:38 2020 -0700

• News announcement for refSeq update refs #24547
  • src/hg/htdocs/goldenPath/newsarch.html - lines changed 117, context: html, text, full: html, text
  • src/hg/htdocs/indexNews.html - lines changed 14, context: html, text, full: html, text

edfe2154917b93dbca09f74b043c8d1d5dee2c34 Tue Apr 28 17:15:16 2020 -0700

• Making changes in response to CR refs #25448
  • src/hg/makeDb/trackDb/virus/wuhCor1/poranHla1.html - lines changed 5, context: html, text, full: html, text

3a0d7ebba74d84135ec239f3936da8bce479daa1 Wed Apr 29 08:17:01 2020 -0700

• Fixing up the protein interaction desc page refs #25247
  • src/hg/makeDb/trackDb/virus/wuhCor1/gordon2.html - lines changed 30, context: html, text, full: html, text

601daea1de754b9eaaf2b710a9e23e8e4d9c321d Wed Apr 29 12:39:14 2020 -0700

• Fixing up the kim transcriptome desc page refs #25468
  • src/hg/makeDb/trackDb/virus/wuhCor1/poranHla1.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/transcriptome.html - lines changed 61, context: html, text, full: html, text

a9c2124ec25e136c5395478728731a8432cfb78d Wed Apr 29 13:09:26 2020 -0700

• Fixing up desc page for rFAM refs #25464
  • src/hg/makeDb/trackDb/virus/wuhCor1/rfam.html - lines changed 30, context: html, text, full: html, text

26ad7e5fe96a1b5070432af743fda80a385d52e8 Wed Apr 29 13:28:42 2020 -0700

• Moving the track desc page down to the wuhCor1 level refs #25458
  • src/hg/makeDb/trackDb/targets.html - lines changed 28, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/targets.html - lines changed 28, context: html, text, full: html, text

80e84c909e7d3b1c2487911fdb44818b9eaf0305 Wed Apr 29 14:01:00 2020 -0700

• Fixing up desc page for T cell epitopes track refs #25458
  • src/hg/makeDb/trackDb/virus/wuhCor1/targets.html - lines changed 26, context: html, text, full: html, text

a67a875d9b30d3a5815f530c4685a03c3ea0e87f Wed Apr 29 14:42:36 2020 -0700

• Splitting transcriptome track to kim transcripts and transcriptomes refs #25468
  • src/hg/makeDb/trackDb/virus/wuhCor1/kim2020.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/kimTranscripts.html - lines changed 82, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/transcriptome.html - lines changed 16, context: html, text, full: html, text

7aef71a104ec1c3bb84dcff245b03dfc58d53358 Wed Apr 29 15:10:14 2020 -0700

• Fixing some forgot db declarations, no RM
  • src/hg/htdocs/goldenPath/newsarch.html - lines changed 2, context: html, text, full: html, text

851dd42ab83984ac7900a7a97c40bcb64d35407b Wed Apr 29 15:19:03 2020 -0700

• Adding wuhCor1 to the other nav bar, no RM
  • src/hg/htdocs/inc/gbPageStartHardcoded.html - lines changed 1, context: html, text, full: html, text

f21ea0504b247456a891e08e58877d644c2f483c Thu Apr 30 08:49:17 2020 -0700

• Capitalizing some shortLabels, no RM
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 3, context: html, text, full: html, text

893fb2be6044ef6697d9f199af3179d88a5a8616 Thu Apr 30 14:50:17 2020 -0700

• Fixing the name of the track, the name should not be all caps. No RM
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 2, context: html, text, full: html, text

432871a5ecd060804eccaed040a25f8d969981ef Thu Apr 30 16:01:34 2020 -0700

• Changing default selections to least-related sequences and making the labels more verbose refs #25090
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.119way.ra - lines changed 5, context: html, text, full: html, text

de0ea7557618ed71c31f0866eb351fb7a92c5e34 Fri May 1 10:24:22 2020 -0700

• Fixing labels, defaults, and shortLabel names for multiple alignment tracks refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.strainName119way.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.strainName44way.ra - lines changed 2, context: html, text, full: html, text

801f36c6c9fe7974ce8c89427dd7417697c28ef5 Fri May 1 16:11:51 2020 -0700

• News release for 2nd coronavirus data release refs #25343
  • src/hg/htdocs/goldenPath/newsarch.html - lines changed 109, context: html, text, full: html, text
  • src/hg/htdocs/indexNews.html - lines changed 12, context: html, text, full: html, text

c436774102f2cbc6e313ce1a36c885d433dd1d57 Sat May 2 11:43:22 2020 -0700

• Removing exon numbers and arrows from track refs #25482
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 2, context: html, text, full: html, text

7d43c2d37ecf3af7e749b575537717442135e2b3 Mon May 4 09:34:38 2020 -0700

• Adding CD8 RosettaMHC track refs #25482
  • src/hg/htdocs/goldenPath/newsarch.html - lines changed 7, context: html, text, full: html, text