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This commit is contained in:
Jeremy Goecks
2009-09-10 17:48:52 -04:00
parent 6f87a96051 140b458dbb
commit 1a2bd47618
2 changed files with 23 additions and 5 deletions
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cron/updateucsc.sh.sample
+22 -4
View File
@@ -6,7 +6,8 @@
# Edit this line to refer to galaxy's path:
GALAXY=/galaxy/path
export PYTHONPATH=${GALAXY}/lib
PYTHONPATH=${GALAXY}/lib
export PYTHONPATH
# setup directories
echo "Creating required directories."
@@ -32,7 +33,11 @@ echo "Updating builds.txt"
python ${GALAXY}/cron/parse_builds.py > ${GALAXY}/tool-data/shared/ucsc/new/builds.txt
if [ $? -eq 0 ]
then
cp -uf ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt
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
@@ -42,7 +47,11 @@ 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
cp -uf ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt
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
@@ -52,7 +61,16 @@ 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
cp -uf ${GALAXY}/tool-data/shared/ucsc/chrom/new/*.len ${GALAXY}/tool-data/shared/ucsc/chrom/
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
tools/new_operations/flanking_features.py
+1 -1
View File
@@ -129,7 +129,7 @@ def proximal_region_finder(readers, region, comments=True):
map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval
elif result_up:
map(outfields.append, result_up[res_ind].other)
else:
elif result_down:
map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval
yield outfields