rhead: changes by commit

review to branch (2009-04-21 to 2009-04-28) v205

• Changed default position.
  • src/hg/makeDb/doc/hg19.txt 1.5 - lines changed: 7, context: html, text, full: html, text
• Changed back to sourcing the qaConfig file using which, after specifying PATH in the crontab that was having problems running this script.
  • src/utils/qa/tableDumpDates.csh 1.4 - lines changed: 2, context: html, text, full: html, text
• Changed hard-coded tracknames to real ones from trackDb, added checks for mgcFullMrna and orfeomeMrna, changed echoes so that they reflect same command as is run, general cleanup.
  • src/utils/qa/doGenbankTests 1.7 - lines changed: 56, context: html, text, full: html, text
• Fixed link to Baylor conditions for use.
  • src/hg/makeDb/trackDb/apis/apiMel1/description.html 1.17 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/apiMel2/description.html 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau1/description.html 1.14 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau2/description.html 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau3/description.html 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dp2/description.html 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac1/description.html 1.8 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/urchin/strPur1/description.html 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/urchin/strPur2/description.html 1.6 - lines changed: 1, context: html, text, full: html, text
• Fixed honeybee links to Baylor.
  • src/hg/makeDb/trackDb/apis/apiMel1/description.html 1.18 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/apiMel2/description.html 1.7 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/apiMel2/gold.html 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/apis/apiMel2/scaffolds.html 1.3 - lines changed: 2, context: html, text, full: html, text
• Fixed cow links to Baylor.
  • src/hg/makeDb/trackDb/cow/bosTau1/description.html 1.15 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau2/contigOrient.html 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau2/description.html 1.7 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau3/description.html 1.7 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau3/scaffold.html 1.2 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau4/description.html 1.10 - lines changed: 1, context: html, text, full: html, text
• Fixed fly links to Baylor.
  • src/hg/makeDb/trackDb/drosophila/dm1/axtNetDp1.html 1.7 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dm1/netDp1.html 1.8 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dp2/description.html 1.6 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/netDp2.html 1.7 - lines changed: 1, context: html, text, full: html, text
• Got carried away with the http's. Fixed Baylor links again.
  • src/hg/makeDb/trackDb/cow/bosTau1/description.html 1.16 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau2/contigOrient.html 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau2/description.html 1.8 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau3/description.html 1.8 - lines changed: 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cow/bosTau3/scaffold.html 1.3 - lines changed: 2, context: html, text, full: html, text
• Fixed rat links to Baylor.
  • src/hg/makeDb/trackDb/human/hg13/syntenyRat.html 1.10 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg15/syntenyRat.html 1.8 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg16/syntenyRn3.html 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/ensRatMusHom.html 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg17/syntenyRn3.html 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm4/syntenyRn3.html 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn1/description.html 1.3 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn1/ensRatMusHom.html 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn2/description.html 1.13 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn3/description.html 1.20 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn3/ensRatMusHom.html 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rat/rn4/description.html 1.3 - lines changed: 2, context: html, text, full: html, text
• Fixed rhesus links to Baylor.
  • src/hg/makeDb/trackDb/rhesus/rheMac1/description.html 1.9 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac2/ctgPos.html 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/rhesus/rheMac2/description.html 1.10 - lines changed: 2, context: html, text, full: html, text
• Fixed urchin links to Baylor.
  • src/hg/makeDb/trackDb/urchin/strPur1/description.html 1.6 - lines changed: 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/urchin/strPur2/description.html 1.7 - lines changed: 2, context: html, text, full: html, text
• Clarified the type of BED file for chromTrf.tar.gz.
  • src/hg/utils/automation/makeDownloads.pl 1.21 - lines changed: 1, context: html, text, full: html, text
• Reset default position.
  • src/hg/makeDb/doc/hg19.txt 1.6 - lines changed: 3, context: html, text, full: html, text
• Commented out more missing pieces + minor edits.
  • src/hg/makeDb/trackDb/human/hg19/description.html 1.7 - lines changed: 8, context: html, text, full: html, text
• added hg19
  • src/hg/makeDb/genbank/etc/rr.dbs 1.81 - lines changed: 1, context: html, text, full: html, text
• Changed PARs to match gold.fragStart and gold.fragEnd fields.
  • src/hg/makeDb/trackDb/human/hg19/description.html 1.8 - lines changed: 2, context: html, text, full: html, text
• Format bit about the PARs.
  • src/hg/makeDb/trackDb/human/hg19/description.html 1.9 - lines changed: 7, context: html, text, full: html, text
• Added an explanation of the chromosome names, plus an example search with the new chrUn_contigName chrom name.
  • src/hg/makeDb/trackDb/human/hg19/description.html 1.10 - lines changed: 17, context: html, text, full: html, text