f3fd98f1451f9c289fe9d43dbe1ba96446e4bad3 chinhli Thu Jan 12 16:33:56 2012 -0800 redmine track #6406 - tRNA track for several (44) assemblies. diff --git src/hg/htdocs/makefile src/hg/htdocs/makefile index 05eac54..b563f2a 100644 --- src/hg/htdocs/makefile +++ src/hg/htdocs/makefile @@ -1,82 +1,127 @@ 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 user: if test -d ${DOCUMENTROOT}-${USER}; then \ ${MAKE} doInstall destDir=${DOCUMENTROOT}-${USER} extra=doSymLink; \ fi alpha: ${MAKE} doInstall destDir=${DOCUMENTROOT} extra=doSymLink 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 # 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: 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/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: