Commits for galt

v370_base to v371_preview (2018-08-20 to 2018-08-27) v371

305cf5b58959929ced4acf3293ebd035bb35ff43 Mon Aug 20 14:08:40 2018 -0700

• Cleanup requested by Lowe Lab.
  • src/hg/hgc/lowelab.c - lines changed 16, context: html, text, full: html, text

5adcf6bc2904690de7b7b30a83ec8a7a0996abe9 Tue Aug 21 00:01:25 2018 -0700

• changing cse subdomain to soe
  • src/browserbox/home/browser/.bashrc - lines changed 6, context: html, text, full: html, text
  • src/browserbox/home/browser/.hg.conf - lines changed 3, context: html, text, full: html, text
  • src/browserbox/home/browser/downloadTools - lines changed 1, context: html, text, full: html, text
  • src/browserbox/home/browser/gbibAddTools - lines changed 1, context: html, text, full: html, text
  • src/browserbox/root/browserLogs/scripts/virtualBox.txt - lines changed 3, context: html, text, full: html, text
  • src/browserbox/root/hg.conf.offline - lines changed 3, context: html, text, full: html, text
  • src/browserbox/root/mirrorTrack - lines changed 1, context: html, text, full: html, text
  • src/browserbox/root/updateBrowser.sh - lines changed 8, context: html, text, full: html, text
  • src/browserbox/root/urlIsNotNewerThanFile - lines changed 1, context: html, text, full: html, text
  • src/browserbox/usr/local/apache/cgi-bin/hg.conf - lines changed 3, context: html, text, full: html, text
  • src/browserbox/var/spool/cron/crontabs/root - lines changed 2, context: html, text, full: html, text
  • src/gfServer/README.blat - lines changed 3, context: html, text, full: html, text
  • src/hca/toHca/hcaStormToBundles/testIt - lines changed 1, context: html, text, full: html, text
  • src/hg/cirm/cdw/cdwSummary/cdwSummary - lines changed 1, context: html, text, full: html, text
  • src/hg/das/tests/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/encodeCharts/encodeReportLib.py - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/encodeDownloadsPage/encodeDownloadsPage.pl - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/encodeQaCheckHgdownloadFiles/encodeQaCheckHgdownloadFiles - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/encodeQaInit/encodeQaInit - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/encodeStatus/hgShowEncodeSubmissions - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/newtest/config/cv.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/encodeValidate/test/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/encode/hgEncodeSubmit/README.FTP - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/hgEncodeSubmit/test/functional/account_controller_test.rb - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/hgEncodeSubmit/test/unit/user_test.rb - lines changed 1, context: html, text, full: html, text
  • src/hg/geoIp/README - lines changed 2, context: html, text, full: html, text
  • src/hg/hgBlatTest/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/hgMirror/hgMirror - lines changed 7, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/gbdDescriptionsOld.html - lines changed 10, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/mysql.html - lines changed 2, context: html, text, full: html, text
  • src/hg/htdocs/style/floretStyle.css - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/style/jWest.css - lines changed 1, context: html, text, full: html, text
  • src/hg/js/test/README - lines changed 2, context: html, text, full: html, text
  • src/hg/js/test/jsTestDriver.conf - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/crisprTrack/crisprAddGenome.py - lines changed 5, context: html, text, full: html, text
  • src/hg/makeDb/crisprTrack/lib/twobitreader/download.py - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/euronode-copy - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/etc/euronode-dbload - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/makefile - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/genbank/tests/tools/optimizeTables - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadWiggle/chkWiggleTable.sh - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/makeLoChain/makeLoChain-align.csh - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/README - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/checkMetaDb - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/beta/cv.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/public/cv.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/loadTracks - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/makeMetaDb - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/template.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/uniprot.html - lines changed 1, context: html, text, full: html, text
  • src/hg/near/hgNearTest/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/phyloPng/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/pyLib/hgLib.py - lines changed 1, context: html, text, full: html, text
  • src/hg/txGraph/algorithms.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/openStack/paraHubSetup.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/genomeQuality/genomeQuality.pl - lines changed 1, context: html, text, full: html, text
  • src/product/README.QuickStart - lines changed 5, context: html, text, full: html, text
  • src/product/README.building.source - lines changed 2, context: html, text, full: html, text
  • src/product/README.install - lines changed 3, context: html, text, full: html, text
  • src/product/README.local.git.source - lines changed 2, context: html, text, full: html, text
  • src/product/README.mysql.setup - lines changed 1, context: html, text, full: html, text
  • src/product/README.requirements - lines changed 3, context: html, text, full: html, text
  • src/product/ex.hg.conf - lines changed 3, context: html, text, full: html, text
  • src/product/minimal.hg.conf - lines changed 1, context: html, text, full: html, text
  • src/product/scripts/README - lines changed 4, context: html, text, full: html, text
  • src/product/scripts/activeDbList.sh - lines changed 1, context: html, text, full: html, text
  • src/product/scripts/browserEnvironment.txt - lines changed 3, context: html, text, full: html, text
  • src/product/scripts/fetchHgCentral.sh - lines changed 1, context: html, text, full: html, text
  • src/product/scripts/kentSrcUpdate.sh - lines changed 1, context: html, text, full: html, text
  • src/test/hgTest.pl - lines changed 1, context: html, text, full: html, text
  • src/userApps/Makefile - lines changed 1, context: html, text, full: html, text
  • src/userApps/README - lines changed 9, context: html, text, full: html, text
  • src/utils/qa/GS1.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/backupCentral.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/browserUsage.csh - lines changed 2, context: html, text, full: html, text
  • src/utils/qa/chain2.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/checkCoverage.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/checkGenomeMysql - lines changed 3, context: html, text, full: html, text
  • src/utils/qa/checkMetaAday.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/checkPushedFiles.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/checkStaticLinks.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/checkTrackUiLinks.csh - lines changed 2, context: html, text, full: html, text
  • src/utils/qa/compareHgFindSpecFast.csh - lines changed 2, context: html, text, full: html, text
  • src/utils/qa/compareHgFindSpecs.csh - lines changed 2, context: html, text, full: html, text
  • src/utils/qa/compareTrackDbFast.csh - lines changed 2, context: html, text, full: html, text
  • src/utils/qa/compareWholeTable.csh - lines changed 2, context: html, text, full: html, text
  • src/utils/qa/cronLinks.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/doRLUpdate.csh - lines changed 2, context: html, text, full: html, text
  • src/utils/qa/gc-stats.pl - lines changed 3, context: html, text, full: html, text
  • src/utils/qa/getDbSize.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/getField.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/getJoinerKeyErrors.pl - lines changed 3, context: html, text, full: html, text
  • src/utils/qa/getTableStatus.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/getVersion.csh - lines changed 2, context: html, text, full: html, text
  • src/utils/qa/hgFindSpecGlobal.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/igtc.csh - lines changed 2, context: html, text, full: html, text
  • src/utils/qa/knownGene.csh - lines changed 2, context: html, text, full: html, text
  • src/utils/qa/qaAutoTrack.sh - lines changed 2, context: html, text, full: html, text
  • src/utils/qa/qaEnsGenes.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/runBits.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/showTracks - lines changed 3, context: html, text, full: html, text
  • src/utils/qa/syncAday.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/qa/trackDbGlobal.csh - lines changed 1, context: html, text, full: html, text
  • src/utils/userApps/bigBedWigs.txt - lines changed 4, context: html, text, full: html, text
  • src/utils/userApps/fetchChromSizes - lines changed 5, context: html, text, full: html, text
  • src/utils/userApps/mkREADME.sh - lines changed 1, context: html, text, full: html, text
  • src/utils/wigTestMaker/timeNotes - lines changed 1, context: html, text, full: html, text

b448752a3bc70215db04d531b0841b7a9c49a459 Wed Aug 22 16:06:39 2018 -0700

• fixing genome-source URLs to use gitlist syntax
  • src/hg/htdocs/FAQ/FAQblat.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/FAQ/FAQformat.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/FAQ/FAQlicense.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/admin/git.html - lines changed 7, context: html, text, full: html, text
  • src/hg/htdocs/admin/jk-install.html - lines changed 5, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/gbdDescriptions.html - lines changed 3, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/bigBed.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/cram.html - lines changed 1, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/gbic.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/ebola/eboVir3/cons160way.html - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/altSequence.html - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 8, context: html, text, full: html, text
  • src/hg/utils/automation/doRecipBest.pl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/doSameSpeciesLiftOver.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/genbank/README.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/automation/openStack/paraHubSetup.sh - lines changed 1, context: html, text, full: html, text
  • src/product/README.building.source - lines changed 1, context: html, text, full: html, text
  • src/product/README.install - lines changed 1, context: html, text, full: html, text
  • src/product/README.mysql.setup - lines changed 1, context: html, text, full: html, text
  • src/product/installer/README.md - lines changed 2, context: html, text, full: html, text
  • src/product/installer/browserSetup.sh - lines changed 1, context: html, text, full: html, text
  • src/product/scripts/README - lines changed 1, context: html, text, full: html, text
  • src/product/scripts/README.trashCleaning - lines changed 1, context: html, text, full: html, text

c0559c7337852834308620733c839b69d07549d3 Fri Aug 24 15:33:17 2018 -0700

• Fixes problem with byterange and double redirect in net.c for example hubs and tracks hosted on hgwdev.
  • src/lib/net.c - lines changed 4, context: html, text, full: html, text

ab14d76f5c397c8c0da0192592b8600640b2669e Fri Aug 24 16:07:27 2018 -0700

• minor improvement
  • src/lib/tests/fetchUrlTest.c - lines changed 1, context: html, text, full: html, text