c4e2ae3a2c37b244143589fbeda66de7e52f4ad7 hiram Fri Apr 30 21:43:40 2021 -0700 correct usage message refs #26682 diff --git src/hg/utils/automation/pairLastz.sh src/hg/utils/automation/pairLastz.sh index f8abc69..48222de 100755 --- src/hg/utils/automation/pairLastz.sh +++ src/hg/utils/automation/pairLastz.sh @@ -10,31 +10,31 @@ And [tq]Clade is one of: primate|mammal|other Will create directory to work in, for example if, UCSC db: /hive/data/target/bed/lastzQuery.yyyy-mm-dd/ Or, in the assembly hub build directory: /hive/data/genomes/asmHubs/allBuild/GCA/002/844/635/GCA_002844635.1_USMARCv1.0/trackData/lastzQuery.yyyy-mm-dd Will set up a DEF file there, and a run.sh script to run all steps and output makeDoc text to document what happened. AND MORE, it will run the swap operation into the corresponding blastz.target.swap directory in the query genome work space. -e.g.: pairLastz.sh rn7 papAnu4 -qClade=mammal -tClade=primate\n" 1>&2 +e.g.: pairLastz.sh rn7 papAnu4 mammal primate\n" 1>&2 exit 255 fi # asmId - if assembly hub, determine GCx_012345678.9 name # if not, return the asmName (== UCSC database name) function asmId() { export asmName=$1 export id="${asmName}" case $asmName in GC[AF]_*) id=`echo $asmName | cut -d'_' -f1-2` ;; *) ;; esac