Commits for hiram

v337_preview to v337_preview2 (2016-08-01 to 2016-08-08) v337

12037e4630802e31618c25c723df8ed8214c27e4 Mon Aug 1 10:27:58 2016 -0700

• adding gc5Base and windowMasker description pages refs #13553
  
  • src/hg/utils/automation/asmHubGc5Percent.pl - lines changed 69, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubWindowMasker.pl - lines changed 92, context: html, text, full: html, text

4236b638593ea428d9ed9efacaf7f3f63cb40f34 Mon Aug 1 10:30:53 2016 -0700

• adding gc5 trf and windowmasker description page scripts refs #13553
  
  • src/hg/utils/automation/makefile - lines changed 3, context: html, text, full: html, text

eaf7c0809178120da68607150595d7d9ce269c09 Mon Aug 1 16:19:50 2016 -0700

• starting an AsmHub.pm library for common routines refs #13533
  
  • src/hg/utils/automation/AsmHub.pm - lines changed 39, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubAssembly.pl - lines changed 13, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubCpG.pl - lines changed 11, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubGap.pl - lines changed 15, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubGatewayPage.pl - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubGc5Percent.pl - lines changed 11, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubHtml.pl - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubRmsk.pl - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubSimpleRepeat.pl - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubWindowMasker.pl - lines changed 14, context: html, text, full: html, text

9609da1a7bff8ac4576e830669b5f9b49e8c1bed Mon Aug 1 16:24:07 2016 -0700

• starting an AsmHub.pm library for common routines refs #13533
  
  • src/hg/utils/automation/makefile - lines changed 1, context: html, text, full: html, text

25a69a8e77d57796a6bfb2c49086d1cc1a39ef39 Mon Aug 1 21:16:05 2016 -0700

• adding panTro5 to the build refs #17817
  
  • src/hg/makeDb/trackDb/chimp/panTro5/description.html - lines changed 64, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro5/gap.html - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro5/gold.html - lines changed 36, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/chimp/panTro5/trackDb.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text

138ca64c20c808794cd930815016fe72545ef5fa Mon Aug 1 21:59:36 2016 -0700

• starting panTro5 build refs 17817
  
  • src/hg/makeDb/doc/panTro5/initialBuild.txt - lines changed 768, context: html, text, full: html, text

4560c66e919bcf4dee0edfff4a2670ac2189414b Tue Aug 2 08:57:08 2016 -0700

• adding panTro5 - Chimp refs #17817
  
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 20, context: html, text, full: html, text

72a6556b59b841454746ccfb60607ca5b4e8e656 Wed Aug 3 08:39:05 2016 -0700

• liftOver to panPan1 per user request refs #17776
  
  • src/hg/makeDb/doc/hg18.txt - lines changed 78, context: html, text, full: html, text

a5aafb2c5a1607b24d4e8e3cf04491a8043cb33c Thu Aug 4 10:01:57 2016 -0700

• update to grch38.p8 refs #16660
  
  • src/hg/utils/automation/grcRunIncidentUpdate.sh - lines changed 7, context: html, text, full: html, text

ee46dd2bd382e119fcdab2087d2f441df4119854 Thu Aug 4 10:19:25 2016 -0700

• adding panTro5 lastz chain net definitions refs #17817
  
  • src/hg/makeDb/trackDb/human/chainNetPanTro4.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetPanTro5.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/chainNetPrimate.ra - lines changed 15, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.primates.ra - lines changed 265, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/trackDb.chainNet.ra - lines changed 200, context: html, text, full: html, text

d2268a67d14ffbdfe295f07b5fda09e8a7c3c9b0 Thu Aug 4 10:48:36 2016 -0700

• new htslib compile on make requires some extra -lz library links refs #17833
  
  • src/blat/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslMap/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/gensub2/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/para/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraHub/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraHubStop/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraNode/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraNodeStart/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraNodeStatus/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraNodeStop/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/paraTestJob/makefile - lines changed 1, context: html, text, full: html, text
  • src/parasol/parasol/makefile - lines changed 1, context: html, text, full: html, text

48a94b926805e755347fd2e97fb5af41adafb510 Thu Aug 4 11:08:38 2016 -0700

• Added gorGor5 - Gorilla - refs #17580
  
  • 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

522bd043902bb034b50bd004550de23953307918 Thu Aug 4 21:33:11 2016 -0700

• lastz chain net on panTro5 refs #17817
  
  • src/hg/makeDb/doc/mm10.txt - lines changed 64, context: html, text, full: html, text

4753820862f79c9cd5e5f8e229860010cc4c31a6 Thu Aug 4 21:38:33 2016 -0700

• liftOver to panTro5 and some user requested lastz runs refs #17817
  
  • src/hg/makeDb/doc/panTro4.txt - lines changed 161, context: html, text, full: html, text

70999cafd8ac208d538f05c8faa164a33978f51b Thu Aug 4 21:41:05 2016 -0700

• lastz run to panTro5 refs #17817
  
  • src/hg/makeDb/doc/hg38/lastzRuns.txt - lines changed 74, context: html, text, full: html, text

271c01c105164ce102a3920e09101afdd7cd46e4 Thu Aug 4 21:51:03 2016 -0700

• genbank finally finished, liftOvers to and from gorGor4, augustus done, refs #17580
  
  • src/hg/makeDb/doc/gorGor5/initialBuild.txt - lines changed 73, context: html, text, full: html, text

a468d05863ec4b02a0606f3d802e3a37dc765748 Thu Aug 4 21:52:36 2016 -0700

• lastz done to pelSin1 refs #17168
  
  • src/hg/makeDb/doc/galGal5/lastzRuns.txt - lines changed 59, context: html, text, full: html, text

22879614cd1b3c208e12bbf436d6ed02ce2b2ff6 Thu Aug 4 21:55:00 2016 -0700

• almost everything done, genbank loading, liftOvers to panTro3 and 4, blat server setup refs #17817
  
  • src/hg/makeDb/doc/panTro5/initialBuild.txt - lines changed 266, context: html, text, full: html, text

4518da752aef97439e239b46d06c855c6a6fbdf0 Thu Aug 4 21:55:53 2016 -0700

• lastz to gorGor5 underway refs #17817 #17580
  
  • src/hg/makeDb/doc/panTro5/lastzRuns.txt - lines changed 78, context: html, text, full: html, text

71b909c8408071f0212343b4a51ad727996f4351 Thu Aug 4 22:02:05 2016 -0700

• finished lastz turTru2 to orcOrc1 refs #17425
  
  • src/hg/makeDb/doc/orcOrc1/lastzRuns.txt - lines changed 2, context: html, text, full: html, text

bfb80b7452b6bef82648c7669dd18494f7d9ef02 Fri Aug 5 08:20:21 2016 -0700

• adding panTro5 and gorGor5 refs #17817
  
  • src/hg/makeDb/schema/all.joiner - lines changed 10, context: html, text, full: html, text

42061eaf5e7526eae52a264c7378259568c0bae3 Mon Aug 8 09:01:00 2016 -0700

• Added panTro5 - chimp - Pan troglodytes refs #17817
  
  • 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

7bab4370ef9828d7b9b315f4d72d1548f81c2c95 Mon Aug 8 10:34:24 2016 -0700

• v337 preview2 refs #17689
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text