rhead: changes by file

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

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