Commits for hiram

v310_base to v311_preview (2015-01-05 to 2015-01-12) v311

• documentation for 17-way primates refs #14560
  • src/hg/makeDb/trackDb/human/hg38/cons17way.html - lines changed 448, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tarsier/tarSyr2/cons17way.html - lines changed 5, context: html, text, full: html, text
• description page for 17-way conservation refs #14560
  • src/hg/makeDb/trackDb/human/hg38/cons17way.html - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tarsier/tarSyr2/cons17way.html - lines changed 18, context: html, text, full: html, text
• description page for 17-way conservation refs #14560
  • src/hg/makeDb/trackDb/human/hg38/hg38primateChainNet.html - lines changed 2, context: html, text, full: html, text
• description page for 17-way conservation refs #14560
  • src/hg/makeDb/trackDb/human/hg38/trackDb.17way.ra - lines changed 2, context: html, text, full: html, text
• adding panPan1 refs #8231
  • src/hg/makeDb/schema/all.joiner - lines changed 8, context: html, text, full: html, text
• tweaking panPan1 to be clean joinerCheck refs #8231
  • src/hg/makeDb/schema/all.joiner - lines changed 7, context: html, text, full: html, text
• Added nasLar1; refs #14437
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text
• adding new sequences KP260799.1 KP260800.1 KP260801.1 KP260802.1 KP271018.1 KP271019.1 KP271020.1 refs #14278
  • src/hg/makeDb/trackDb/ebola/eboVir3/newSeqs.html - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.newSequences.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir3/trackDb.ra - lines changed 1, context: html, text, full: html, text
• fixup isolate description for two refs #14278
  • src/hg/makeDb/trackDb/ebola/eboVir3/newSeqs.html - lines changed 2, context: html, text, full: html, text
• bring up to date with Robert's latest code to help fix bugs refs #9741
  • src/hg/hgTracks/rmskJoinedTrack.c - lines changed 150, context: html, text, full: html, text
• allow pack squish modes refs #9741
  • src/hg/makeDb/trackDb/joinedRmsk.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/joinedRmskComposite.ra - lines changed 2, context: html, text, full: html, text
• photo from Rhett A. Butler mongabay.com refs #11174
  • src/hg/htdocs/images/Macaca_fascicularis.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• initial files from makeGenomeDb.ra refs #11174
  • src/hg/makeDb/trackDb/macaca/macFas5/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macFas5/gap.html - lines changed 32, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macFas5/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/macaca/macFas5/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding macFas5 to the build refs #11174
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
• can not use commands that fail in a csh -fe script since any command that fails stops the script immediately refs #11174
  • src/utils/qa/makeCytoBandIdeo.csh - lines changed 2, context: html, text, full: html, text
• Added macFas5; refs #11174
  • src/hg/makeDb/genbank/etc/genbank.conf - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbGenome.c - lines changed 2, context: html, text, full: html, text
• adding macFas5 rules refs #11174
  • src/hg/makeDb/schema/all.joiner - lines changed 16, context: html, text, full: html, text
• ready for pushQ after genbank is loaded refs #11174
  • src/hg/makeDb/doc/macFas5/initialBuild.txt - lines changed 480, context: html, text, full: html, text
  • src/hg/makeDb/doc/macFas5/ucscCompositeAgp.pl - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/doc/macFas5/unlocalized.pl - lines changed 66, context: html, text, full: html, text
  • src/hg/makeDb/doc/macFas5/unplaced.pl - lines changed 34, context: html, text, full: html, text
• finding equivalent names in GCA_000001405.17_GRCh38.p2_assembly_report.txt refs #14167
  • src/hg/makeDb/doc/hg38/scanAssemblyReport.pl - lines changed 87, context: html, text, full: html, text
• v311 preview1 refs #14648
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text