Commits for hiram

v319_preview2 to v319_base (2015-07-06 to 2015-07-13) v319

• Added priPac3 - Pristionchus pacificus refs #15209
  
  • 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
• add information about column meanings in output in usage message refs #15635
  
  • src/utils/pslScore/pslScore.c - lines changed 3, context: html, text, full: html, text
• adding priPac3 definitions refs #15209
  
  • src/hg/makeDb/schema/all.joiner - lines changed 9, context: html, text, full: html, text
• liftOver to caeAng2 refs #15209
  
  • src/hg/makeDb/doc/caeAng1.txt - lines changed 17, context: html, text, full: html, text
• adding liftOvers haeCon1 and 2 both ways and the build of haeCon2 refs #15209
  
  • src/hg/makeDb/doc/haeCon1.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/haeCon2.txt - lines changed 445, context: html, text, full: html, text
• liftOvers from caeAng1 and 2 both ways and caeAng2 browser build refs #15209
  
  • src/hg/makeDb/doc/worms/caeAng2.txt - lines changed 117, context: html, text, full: html, text
• liftOvers from melInc1 and 2 both ways and melInc2 browser building refs #15209
  
  • src/hg/makeDb/doc/melInc1.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/melInc2.txt - lines changed 43, context: html, text, full: html, text
• liftOvers between priPac3 and priPac1 and 2 both ways and priPac3 browser build refs #15209
  
  • src/hg/makeDb/doc/priPac1.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/priPac2.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/priPac3.txt - lines changed 141, context: html, text, full: html, text
• done with haeCon2 lastz/chain/net refs #15209
  
  • src/hg/makeDb/doc/ce11/lastzRuns.txt - lines changed 57, context: html, text, full: html, text
• adding bruMal2 to the build refs #15209
  
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/bruMal2/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/bruMal2/gap.html - lines changed 31, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/bruMal2/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/bruMal2/trackDb.ra - lines changed 8, context: html, text, full: html, text
• starting build of bruMal2 refs #15209
  
  • src/hg/makeDb/doc/worms/bruMal2.txt - lines changed 459, context: html, text, full: html, text
• adding definitions for caeAng2 melInc2 priPac3 haeCon2 haeCon1 bruMal2 refs #15209
  
  • src/hg/makeDb/trackDb/worm/trackDb.chainNet.ra - lines changed 338, context: html, text, full: html, text
• photo from Mark Vinney/University of Bristol http://www.bristol.ac.uk/biology/people/mark-e-viney/index.html refs #15209
  
  • src/hg/htdocs/images/Strongyloides_ratti.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding strRat1 to the build refs #15209
  
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/strRat1/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/strRat1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/strRat1/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/strRat1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding strRat2 to the build refs #15209
  
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/strRat2/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/strRat2/gap.html - lines changed 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/strRat2/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/strRat2/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding gold table search rule refs #15209
  
  • src/hg/makeDb/trackDb/worm/strRat2/trackDb.ra - lines changed 5, context: html, text, full: html, text
• running up assemblies for caeSp51 strRat1 strRat2 and strRat2 is an organized assmbly so include scripts used refs #15209
  
  • src/hg/makeDb/doc/worms/caeSp51.txt - lines changed 463, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/strRat1.txt - lines changed 453, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/strRat2.txt - lines changed 447, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/ucscCompositeAgp.pl - lines changed 62, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/unlocalized.pl - lines changed 79, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/unplaced.pl - lines changed 48, context: html, text, full: html, text
• completed most tracks ready for lastz runs refs #15209
  
  • src/hg/makeDb/doc/worms/strRat1.txt - lines changed 60, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/strRat2.txt - lines changed 59, context: html, text, full: html, text
• don with caeSp111 bruMal2 caeSp51 refs #15209
  
  • src/hg/makeDb/doc/ce11/lastzRuns.txt - lines changed 171, context: html, text, full: html, text
• correct note of reference for photo refs #15209
  
  • src/hg/makeDb/trackDb/worm/strRat1/description.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/strRat2/description.html - lines changed 1, context: html, text, full: html, text
• photo from R.E. Pugh parasitology collection refs #15209
  
  • src/hg/htdocs/images/Dirofilaria_immitis.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding dirImm1 to the build refs #15209
  
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/dirImm1/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/dirImm1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/dirImm1/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/dirImm1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• reset assembly info link to WormBase refs #15209
  
  • src/hg/makeDb/trackDb/worm/dirImm1/description.html - lines changed 3, context: html, text, full: html, text
• adding burXyl1 to the build refs #15209
  
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/burXyl1/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/burXyl1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/burXyl1/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/burXyl1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding oncVol1 Onchocerca_volvulus from R.E. Pugh parasitology collection refs #15209
  
  • src/hg/htdocs/images/Onchocerca_volvulus.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding Onchocerca volvulus oncVol1 to the build refs #15209
  
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/oncVol1/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/oncVol1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/oncVol1/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/oncVol1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• add gold table search rule refs #15209
  
  • src/hg/makeDb/trackDb/worm/oncVol1/trackDb.ra - lines changed 5, context: html, text, full: html, text
• adding gold table search rule refs #15209
  
  • src/hg/makeDb/trackDb/worm/dirImm1/trackDb.ra - lines changed 5, context: html, text, full: html, text
• running up burXyl1 dirImm1 oncVol1 refs #15209
  
  • src/hg/makeDb/doc/worms/burXyl1.txt - lines changed 418, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/dirImm1.txt - lines changed 435, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/oncVol1.txt - lines changed 432, context: html, text, full: html, text
• add gold table search rule refs #15209
  
  • src/hg/makeDb/trackDb/worm/bruMal2/trackDb.ra - lines changed 6, context: html, text, full: html, text
• adding caeSp51 to the build refs #15209
  
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeSp51/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeSp51/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeSp51/gold.html - lines changed 33, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/caeSp51/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding gold table search rule refs #15209
  
  • src/hg/makeDb/trackDb/worm/caeSp51/trackDb.ra - lines changed 5, context: html, text, full: html, text
• done with initial tracks refs #15209
  
  • src/hg/makeDb/doc/worms/panRed1.txt - lines changed 72, context: html, text, full: html, text
• done with default set of tracks refs #15209
  
  • src/hg/makeDb/doc/worms/caeSp51.txt - lines changed 68, context: html, text, full: html, text
• finished with caeSp5 strRat2 strRat1 burXyl1 oncVol1 refs #15209
  
  • src/hg/makeDb/doc/ce11/lastzRuns.txt - lines changed 242, context: html, text, full: html, text
• adding caeSp51 panRed1 burXyl1 melHap1 strRat1 strRat2 oncVol1 refs #15209
  
  • src/hg/makeDb/trackDb/worm/trackDb.chainNet.ra - lines changed 392, context: html, text, full: html, text
• photo from CDC refs #15209
  
  • src/hg/htdocs/images/Trichinella_spiralis.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding Trichinella spiralis triSpi1 to the build refs #15209
  
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/triSpi1/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/triSpi1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/triSpi1/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/triSpi1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding gold table search rule refs #15209
  
  • src/hg/makeDb/trackDb/worm/triSpi1/trackDb.ra - lines changed 5, context: html, text, full: html, text
• photo from CDC public domain refs #15209
  
  • src/hg/htdocs/images/Trichuris_suis.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• adding Trichuris suis triSui1 refs #15209
  
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/triSui1/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/triSui1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/triSui1/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/triSui1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• adding gold table search rule refs #15209
  
  • src/hg/makeDb/trackDb/worm/triSui1/trackDb.ra - lines changed 5, context: html, text, full: html, text
• image from CDC public domain refs #15209
  
  • src/hg/htdocs/images/Loa_loa.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• addgin Loa loa loaLoa1 to the build refs #15209
  
  • src/hg/makeDb/trackDb/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/loaLoa1/description.html - lines changed 63, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/loaLoa1/gap.html - lines changed 30, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/loaLoa1/gold.html - lines changed 34, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/worm/loaLoa1/trackDb.ra - lines changed 8, context: html, text, full: html, text
• add gold table search rule refs #15209
  
  • src/hg/makeDb/trackDb/worm/loaLoa1/trackDb.ra - lines changed 5, context: html, text, full: html, text
• running up assemblies Trichinella spiralis, Trichuris suis, Loa loa refs #15209
  
  • src/hg/makeDb/doc/worms/loaLoa1.txt - lines changed 440, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/triSpi1.txt - lines changed 439, context: html, text, full: html, text
  • src/hg/makeDb/doc/worms/triSui1.txt - lines changed 443, context: html, text, full: html, text
• photo from CDC public domain refs #15209
  
  • src/hg/htdocs/images/Ascaris_suum.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• v319 final build refs #15624
  
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 3, context: html, text, full: html, text
• New version number v319
  
  • src/hg/inc/versionInfo.h - lines changed 1, context: html, text, full: html, text