root/galaxy-central/cron/updateucsc.sh.sample

#!/bin/sh 
#
# Script to update UCSC shared data tables.  The idea is to update, but if
# the update fails, not replace current data/tables with error
# messages.

# Edit this line to refer to galaxy's path:
GALAXY=/galaxy/path
PYTHONPATH=${GALAXY}/lib
export PYTHONPATH

# setup directories
echo "Creating required directories."
DIRS="
${GALAXY}/tool-data/shared/ucsc/new
${GALAXY}/tool-data/shared/ucsc/chrom
${GALAXY}/tool-data/shared/ucsc/chrom/new
"
for dir in $DIRS; do
    if [ ! -d $dir ]; then
        echo "Creating $dir"
        mkdir $dir
    else
        echo "$dir already exists, continuing."
    fi
done

date
echo "Updating UCSC shared data tables."

# Try to build "builds.txt"
echo "Updating builds.txt"
python ${GALAXY}/cron/parse_builds.py > ${GALAXY}/tool-data/shared/ucsc/new/builds.txt
if [ $? -eq 0 ]
then
    diff ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt > /dev/null 2>&1
    if [ $? -ne 0 ]
    then
        cp -f ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt
    fi
else
    echo "Failed to update builds.txt" >&2
fi

# Try to build ucsc_build_sites.txt
echo "Updating ucsc_build_sites.txt"
python ${GALAXY}/cron/parse_builds_3_sites.py > ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt
if [ $? -eq 0 ]
then
    diff ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt > /dev/null 2>&1
    if [ $? -ne 0 ]
    then
        cp -f ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt
    fi
else
    echo "Failed to update builds.txt" >&2
fi

# Try to build chromInfo tables
echo "Building chromInfo tables."
python ${GALAXY}/cron/build_chrom_db.py ${GALAXY}/tool-data/shared/ucsc/chrom/new/ ${GALAXY}/tool-data/shared/ucsc/builds.txt
if [ $? -eq 0 ]
then
    for src in ${GALAXY}/tool-data/shared/ucsc/chrom/new/*.len
    do
        dst=${GALAXY}/tool-data/shared/ucsc/chrom/`basename $src`
        diff $src $dst > /dev/null 2>&1
        if [ $? -ne 0 ]
        then
            echo "cp -f $src $dst"
            cp -f $src $dst
        fi
    done
else
    echo "Failed to update chromInfo tables." >&2
fi

rm -rf ${GALAXY}/tool-data/shared/ucsc/new
rm -rf ${GALAXY}/tool-data/shared/ucsc/chrom/new
echo "Update complete."

#Perform Manual Additions here
echo "Adding Manual Builds."
python ${GALAXY}/cron/add_manual_builds.py ${GALAXY}/tool-data/shared/ucsc/manual_builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt ${GALAXY}/tool-data/shared/ucsc/chrom/
if [ $? -eq 0 ]
then
    echo "Manual addition was successful."
else
    echo "Manual addition failed" >&2
fi