78184d8baf8836108ec701aaad131935cac1bc52 braney Tue Jul 16 16:29:22 2013 -0700 changes to htdocs, trackDb, and genbank to support the lack of user logins on hgwbeta (refs #9708) diff --git src/hg/htdocs/makefile src/hg/htdocs/makefile index 669e3b8..3804011 100644 --- src/hg/htdocs/makefile +++ src/hg/htdocs/makefile @@ -1,132 +1,37 @@ include ../../inc/common.mk -# NOTES: -# - much of this is current repeats in the hgdownload htdocs makefile -# - all symlinks are built by the doSymLink target - - GIT = git GITUP = ${GIT} pull FIND=gitFiles ifeq (${DOCUMENTROOT_USER},) DOCUMENTROOT_USER=${DOCUMENTROOT}-${USER} endif user: if test -d ${DOCUMENTROOT_USER}; then \ - ${MAKE} doInstall destDir=${DOCUMENTROOT_USER} extra=doSymLink; \ + ${MAKE} doInstall destDir=${DOCUMENTROOT_USER} ; \ fi alpha: - ${MAKE} doInstall destDir=${DOCUMENTROOT} extra=doSymLink + ${MAKE} doInstall destDir=${DOCUMENTROOT} beta: - ${GITUP} - ${MAKE} doInstall destDir=${DOCUMENTROOT} extra=doSymLink - -alphaCancerPublic: - ${MAKE} doInstallCancerPublic destDir=${DOCUMENTROOT} extra=doSymLink - -alphaCancerSU2C: - ${MAKE} doInstallCancerSU2C destDir=${DOCUMENTROOT} extra=doSymLink - -alphaCancerTCGA: - ${MAKE} doInstallCancerTCGA destDir=${DOCUMENTROOT} extra=doSymLink - -# Recursive target to do install to destDir, with extra excludes excl and -# specific includes in incl. The variable extra are extra targets to depend -# on. This queries git to find out the list of files to install, so avoid the -# usual crud that collects in directories. -doInstall: doRsync ${extra} - -doInstallCancerPublic: doRsync ${extra} - mv ${destDir}/index.html ${destDir}/index.html.org - ln -sf ${destDir}/cancerGenomics/index.cancerGenomics.html ${destDir}/index.html - mv index.html index.html.org - -doInstallCancerSU2C: doRsync ${extra} - mv ${destDir}/index.html ${destDir}/index.html.org - ln -sf ${destDir}/cancerGenomics/index.cancerGenomics.su2c.html ${destDir}/index.html - mv index.html index.html.org - -doInstallCancerTCGA: doRsync ${extra} - mv ${destDir}/index.html ${destDir}/index.html.org - ln -sf ${destDir}/cancerGenomics/index.cancerGenomics.tcga.html ${destDir}/index.html - mv index.html index.html.org + #${GITUP} + ${MAKE} doInstall destDir=qateam@hgwbeta:${DOCUMENTROOT} # Run rsync. Care is taking to preserve times and mode on files. rsync is # smart about recreating file under the current users so that times and # permissions maybe modified. However, problems happen when a directory # is not owned by the current users. These options attemp to work around it. # use care in changing rsyncOpts = --times --recursive --omit-dir-times --relative --cvs-exclude --exclude='makefile' --exclude='cpAndLinkToResourceFiles.pl' --exclude='style/*' -doRsync: +doInstall: umask 002; rsync ${rsyncOpts} ${excl} ${incl} `$(FIND)` ${destDir} -# build symbolic links -doSymLink: doRsync - ln -sfn ../trash ${destDir}/trash - ln -sfn goldenPath ${destDir}/goldenpath - ln -sfn /gbdb/visiGene ${destDir}/visiGene - ln -sfn ENCODE ${destDir}/encode - ln -sfn Branchiostoma_lanceolatum.jpg ${destDir}/images/Branchiostoma_floridae.jpg - ln -sfn Rhesus_macaque.jpg ${destDir}/images/Macaca_mulatta.jpg - mkdir -p ${destDir}/RNA-img - ln -sfn /gbdb/hg18/RNA-img ${destDir}/RNA-img/hg18 - ln -sfn /gbdb/hg19/RNA-img ${destDir}/RNA-img/hg19 - ln -sfn /gbdb/mm9/RNA-img ${destDir}/RNA-img/mm9 - ln -sfn /gbdb/mm10/RNA-img ${destDir}/RNA-img/mm10 - ln -sfn /gbdb/rn4/RNA-img ${destDir}/RNA-img/rn4 - ln -sfn /gbdb/ailMel1/RNA-img ${destDir}/RNA-img/ailMel1 - ln -sfn /gbdb/caePb1/RNA-img ${destDir}/RNA-img/caePb1 - ln -sfn /gbdb/canFam2/RNA-img ${destDir}/RNA-img/canFam2 - ln -sfn /gbdb/danRer5/RNA-img ${destDir}/RNA-img/danRer5 - ln -sfn /gbdb/felCat3/RNA-img ${destDir}/RNA-img/felCat3 - ln -sfn /gbdb/gorGor3/RNA-img ${destDir}/RNA-img/gorGor3 - ln -sfn /gbdb/ornAna1/RNA-img ${destDir}/RNA-img/ornAna1 - ln -sfn /gbdb/panTro3/RNA-img ${destDir}/RNA-img/panTro3 - ln -sfn /gbdb/susScr2/RNA-img ${destDir}/RNA-img/susScr2 - ln -sfn /gbdb/anoCar2/RNA-img ${destDir}/RNA-img/anoCar2 - ln -sfn /gbdb/caePb2/RNA-img ${destDir}/RNA-img/caePb2 - ln -sfn /gbdb/cavPor3/RNA-img ${destDir}/RNA-img/cavPor3 - ln -sfn /gbdb/danRer6/RNA-img ${destDir}/RNA-img/danRer6 - ln -sfn /gbdb/felCat4/RNA-img ${destDir}/RNA-img/felCat4 - ln -sfn /gbdb/loxAfr3/RNA-img ${destDir}/RNA-img/loxAfr3 - ln -sfn /gbdb/oryCun2/RNA-img ${destDir}/RNA-img/oryCun2 - ln -sfn /gbdb/petMar1/RNA-img ${destDir}/RNA-img/petMar1 - ln -sfn /gbdb/taeGut1/RNA-img ${destDir}/RNA-img/taeGut1 - ln -sfn /gbdb/bosTau4/RNA-img ${destDir}/RNA-img/bosTau4 - ln -sfn /gbdb/caeRem2/RNA-img ${destDir}/RNA-img/caeRem2 - ln -sfn /gbdb/cb3/RNA-img ${destDir}/RNA-img/cb3 - ln -sfn /gbdb/danRer7/RNA-img ${destDir}/RNA-img/danRer7 - ln -sfn /gbdb/fr2/RNA-img ${destDir}/RNA-img/fr2 - ln -sfn /gbdb/melGal1/RNA-img ${destDir}/RNA-img/melGal1 - ln -sfn /gbdb/oryLat2/RNA-img ${destDir}/RNA-img/oryLat2 - ln -sfn /gbdb/ponAbe2/RNA-img ${destDir}/RNA-img/ponAbe2 - ln -sfn /gbdb/tetNig2/RNA-img ${destDir}/RNA-img/tetNig2 - ln -sfn /gbdb/bosTau6/RNA-img ${destDir}/RNA-img/bosTau6 - ln -sfn /gbdb/caeRem3/RNA-img ${destDir}/RNA-img/caeRem3 - ln -sfn /gbdb/ce4/RNA-img ${destDir}/RNA-img/ce4 - ln -sfn /gbdb/equCab1/RNA-img ${destDir}/RNA-img/equCab1 - ln -sfn /gbdb/galGal3/RNA-img ${destDir}/RNA-img/galGal3 - ln -sfn /gbdb/monDom5/RNA-img ${destDir}/RNA-img/monDom5 - ln -sfn /gbdb/oviAri1/RNA-img ${destDir}/RNA-img/oviAri1 - ln -sfn /gbdb/priPac1/RNA-img ${destDir}/RNA-img/priPac1 - ln -sfn /gbdb/xenTro3/RNA-img ${destDir}/RNA-img/xenTro3 - ln -sfn /gbdb/caeJap1/RNA-img ${destDir}/RNA-img/caeJap1 - ln -sfn /gbdb/calJac3/RNA-img ${destDir}/RNA-img/calJac3 - ln -sfn /gbdb/ce6/RNA-img ${destDir}/RNA-img/ce6 - ln -sfn /gbdb/equCab2/RNA-img ${destDir}/RNA-img/equCab2 - ln -sfn /gbdb/gasAcu1/RNA-img ${destDir}/RNA-img/gasAcu1 - ln -sfn /gbdb/nomLeu1/RNA-img ${destDir}/RNA-img/nomLeu1 - ln -sfn /gbdb/panTro2/RNA-img ${destDir}/RNA-img/panTro2 - ln -sfn /gbdb/rheMac2/RNA-img ${destDir}/RNA-img/rheMac2 - - # Other targets that may be invoked by ../makefile: compile: install: alpha clean: