Commits for hiram

v344_preview to v344_preview2 (2017-01-16 to 2017-01-23) v344

07b468142183b0aa5218384c64ef003f330e82d7 Tue Jan 17 10:38:59 2017 -0800

• Added melGal5; refs #18656
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 17, context: html, text, full: html, text

2ba4e9dee785ef979c410dbb5301f98be7483545 Tue Jan 17 20:32:11 2017 -0800

• was missing melGal5.refseq.mrna.native.pslCDnaFilter refs #18656
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 1, context: html, text, full: html, text

8e7df7d2b7eeb9b8c97973b8333c3656e2e929b2 Wed Jan 18 08:12:36 2017 -0800

• liftOver to melGal5 refs #18656
  • src/hg/makeDb/doc/melGal1.txt - lines changed 19, context: html, text, full: html, text

596bbd93460cad45a66a0394a7dcca29f21216f3 Wed Jan 18 08:13:11 2017 -0800

• continuing alignments for 20-way multiz refs #18656
  • src/hg/makeDb/doc/rn6.txt - lines changed 625, context: html, text, full: html, text

77f43471b3d7ea5175c67703c6bb66d80c297fde Wed Jan 18 08:13:38 2017 -0800

• running up genbank refs #18656
  • src/hg/makeDb/doc/melGal5/initialBuild.txt - lines changed 145, context: html, text, full: html, text

815cc1bb7c76e07c5c1bd090444e87cc9e8b738b Wed Jan 18 13:53:17 2017 -0800

• Photo courtesy Ian Duffy, flickr/creative commons www.flickr.com/photos/38323841@N00/4322964957/ no redmine
  • src/hg/htdocs/images/Aptenodytes_forsteri.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

68321a736315c8bd0697fe44e00d1992b20f1186 Wed Jan 18 14:01:38 2017 -0800

• Alina Zienowicz, Wikimedia Commons, commons.wikimedia.org/wiki/File:Przewalski_horse_Warsaw_zoo.JPG no redmine
  • src/hg/htdocs/images/Equus_przewalskii.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

860c8075d55c79e2ecaf7bbc90c30f9aa4436c6c Wed Jan 18 14:45:13 2017 -0800

• Photo courtesy Appaloosa, Wikimedia Commons commons.wikimedia.org/wiki/File:P.t.altaica_Tomak_Male.jpg no redmine
  • src/hg/htdocs/images/Panthera_tigris_altaica.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

d51d27e90ec53fb41f227be45c81e6ad283ea563 Wed Jan 18 15:07:24 2017 -0800

• Photo courtesy John Hill, Wikimedia Commons commons.wikimedia.org/wiki/File:Wild_Bactrian_camel_on_road_east_of_Yarkand.jpg
  • src/hg/htdocs/images/Camelus_ferus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

b1d1fc34969d1c7b1cb7ace2b5afe9751fec6b4a Wed Jan 18 19:56:32 2017 -0800

• adding melGal5 to the update alignments refs #18656
  • src/hg/makeDb/genbank/etc/align.dbs - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 2, context: html, text, full: html, text

88dfe612b2d279ec6a964b4399215ef319f80b1c Wed Jan 18 20:04:56 2017 -0800

• adding melGal5 rules refs #18656
  • src/hg/makeDb/schema/all.joiner - lines changed 2, context: html, text, full: html, text

176f6c6de5aac4f766922556348e9a96e848cc41 Wed Jan 18 20:15:04 2017 -0800

• cleaner melGal5 keys check refs #18656
  • src/hg/makeDb/schema/all.joiner - lines changed 6, context: html, text, full: html, text

1985315adcd0c698dfc42f66084085e5bbd1983f Thu Jan 19 11:34:10 2017 -0800

• running up syntenicNet refs #18656
  • src/hg/makeDb/doc/rn6.txt - lines changed 419, context: html, text, full: html, text

7f3545e00af6cd43789922d10942b2987b7dd37c Fri Jan 20 10:38:24 2017 -0800

• fixup hgFindSpec for ncbiRefSeqProtein searches refs #13673
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 10, context: html, text, full: html, text

bfb1f3f57192f1cc6c6e34ab38911d4e02afea36 Fri Jan 20 11:00:27 2017 -0800

• adding chain net overrides to rn6 refs #18656
  • src/hg/makeDb/trackDb/rat/rn6/trackDb.chainNet.ra - lines changed 97, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn6/trackDb.ra - lines changed 2, context: html, text, full: html, text

3bebf4ab36e95c7e6219b310a5b59d8335a7a35c Fri Jan 20 11:10:44 2017 -0800

• catching up chain net definitions for melGal5 and rn6 alignments refs #18656
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text

9964cf5f43a2052378e200e37e81968cef66e3a2 Fri Jan 20 11:20:19 2017 -0800

• indicate requirement of photoReference.txt refs #18706
  • src/hg/utils/automation/prepConfig.pl - lines changed 26, context: html, text, full: html, text

ba33239d4e94b7da618beca11f61f7ac0559cd2f Fri Jan 20 13:23:18 2017 -0800

• fixup ncbiRefSeq rules refs #13673
  • src/hg/makeDb/schema/all.joiner - lines changed 3, context: html, text, full: html, text

ca618003f2631e20dc6ed8255fe5d28f5560cca0 Fri Jan 20 13:25:22 2017 -0800

• completed sequence for p8 version refs #13673
  • src/hg/makeDb/doc/hg38/ncbiRefSeq.txt - lines changed 39, context: html, text, full: html, text

52ac476a2c9590707df3233614146d4b44f898ad Fri Jan 20 14:26:57 2017 -0800

• wrapping up same set of alignments as melGal1 refs #17168
  • src/hg/makeDb/doc/galGal5/lastzRuns.txt - lines changed 178, context: html, text, full: html, text

218835549760828fe06e31e22be1e435e415fb84 Fri Jan 20 14:30:40 2017 -0800

• wrapping up same set of alignments as melGal1 refs #17168
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 72, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/doc/monDom5.txt - lines changed 65, context: html, text, full: html, text
  • src/hg/makeDb/doc/taeGut2.txt - lines changed 60, context: html, text, full: html, text

70c4f652dfcc3850671155ffbd0f4c25e3bf65d9 Fri Jan 20 14:33:03 2017 -0800

• wrapping up same set of alignments as melGal1 refs #17168
  • src/hg/makeDb/doc/melGal5/initialBuild.txt - lines changed 104, context: html, text, full: html, text
  • src/hg/makeDb/doc/melGal5/lastzRuns.txt - lines changed 117, context: html, text, full: html, text

a3fc9be264996bb181e9b0fc5d50043065716dbf Fri Jan 20 14:34:09 2017 -0800

• completed lastz alignments ready for 20-way refs #17168
  • src/hg/makeDb/doc/rn6.txt - lines changed 19, context: html, text, full: html, text

1454e6da154a2d5f516ae7f18c6e8e2b5572c338 Fri Jan 20 14:49:54 2017 -0800

• updated versions to latest for rn6 20-way refs #18656
  • src/hg/utils/phyloTrees/191way.nh - lines changed 5, context: html, text, full: html, text

9e555f7e91265c04840dc591d64278382b3885d2 Sat Jan 21 11:36:40 2017 -0800

• phylo image for rn6 20way refs #18656
  • src/hg/htdocs/images/phylo/rn6_20way.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)

fefe58073df93f30d4f6e1bf5bf04af38d9538f1 Mon Jan 23 10:06:35 2017 -0800

• v344 preview2 refs #18555
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text