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Lint updateucsc.sh.sample

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This commit is contained in:
Nicola Soranzo
2017-06-14 17:45:54 +01:00
parent f58f372a26
commit ebfdb598f6
1 changed files with 19 additions and 19 deletions
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cron/updateucsc.sh.sample
+19 -19
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@@ -1,4 +1,4 @@
#!/bin/sh
#!/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
@@ -9,7 +9,7 @@
PYTHONPATH=${GALAXY}/lib
export PYTHONPATH
# setup directories
# Setup directories
echo "Creating required directories."
DIRS="
${GALAXY}/tool-data/shared/ucsc/new
@@ -17,9 +17,9 @@ ${GALAXY}/tool-data/shared/ucsc/chrom
${GALAXY}/tool-data/shared/ucsc/chrom/new
"
for dir in $DIRS; do
if [ ! -d $dir ]; then
if [ ! -d "$dir" ]; then
echo "Creating $dir"
mkdir $dir
mkdir "$dir"
else
echo "$dir already exists, continuing."
fi
@@ -30,13 +30,13 @@ echo "Updating UCSC shared data tables."
# Try to build "builds.txt"
echo "Updating builds.txt"
python ${GALAXY}/cron/parse_builds.py > ${GALAXY}/tool-data/shared/ucsc/new/builds.txt
python "${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 ${GALAXY}/tool-data/shared/ucsc/builds.txt > /dev/null 2>&1
diff "${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 ${GALAXY}/tool-data/shared/ucsc/builds.txt
cp -f "${GALAXY}/tool-data/shared/ucsc/new/builds.txt" "${GALAXY}/tool-data/shared/ucsc/builds.txt"
fi
else
echo "Failed to update builds.txt" >&2
@@ -44,13 +44,13 @@ fi
# Try to build ucsc_build_sites.txt
echo "Updating ucsc_build_sites.txt"
python ${GALAXY}/cron/parse_builds_3_sites.py > ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt
python "${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 ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt > /dev/null 2>&1
diff "${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 ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt
cp -f "${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
@@ -58,30 +58,30 @@ fi
# Try to build chromInfo tables
echo "Building chromInfo tables."
python ${GALAXY}/cron/build_chrom_db.py ${GALAXY}/tool-data/shared/ucsc/chrom/new/ ${GALAXY}/tool-data/shared/ucsc/builds.txt
python "${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 $dst > /dev/null 2>&1
dst=${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 $dst
echo "cp -f \"$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 ${GALAXY}/tool-data/shared/ucsc/chrom/new
rm -rf "${GALAXY}/tool-data/shared/ucsc/new"
rm -rf "${GALAXY}/tool-data/shared/ucsc/chrom/new"
echo "Update complete."
#Perform Manual Additions here
# 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 ${GALAXY}/tool-data/shared/ucsc/chrom/
python "${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."