mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
96 lines
2.3 KiB
Bash
96 lines
2.3 KiB
Bash
#!/bin/sh
|
|
|
|
cd `dirname $0`
|
|
|
|
: ${HOSTTYPE:=`uname -m`}
|
|
|
|
# link to HYPHY is arch-dependent
|
|
case "$OSTYPE" in
|
|
linux-gnu)
|
|
kernel=`uname -r | cut -f1,2 -d.`
|
|
HYPHY="/galaxy/software/linux$kernel-$HOSTTYPE/hyphy"
|
|
;;
|
|
darwin*)
|
|
this_minor=`uname -r | awk -F. '{print ($1-4)}'`
|
|
machine=`machine`
|
|
for minor in `jot - 3 $this_minor 1`; do
|
|
HYPHY="/galaxy/software/macosx10.$minor-$machine/hyphy"
|
|
[ -d "$HYPHY" ] && break
|
|
done
|
|
[ ! -d "$HYPHY" ] && unset HYPHY
|
|
;;
|
|
solaris2.10)
|
|
HYPHY="/galaxy/software/linux2.6-x86_64/hyphy"
|
|
;;
|
|
esac
|
|
|
|
LINKS="
|
|
/galaxy/data/location/alignseq.loc
|
|
/galaxy/data/annotation_profiler
|
|
/galaxy/data/annotation_profiler/annotation_profiler.loc
|
|
/galaxy/data/annotation_profiler/annotation_profiler_options.xml
|
|
/galaxy/data/annotation_profiler/annotation_profiler_valid_builds.txt
|
|
/galaxy/data/location/binned_scores.loc
|
|
/galaxy/data/location/blastdb.loc
|
|
/galaxy/data/location/bowtie_indices.loc
|
|
/galaxy/data/location/bowtie_indices_color.loc
|
|
/galaxy/data/location/bwa_index.loc
|
|
/galaxy/data/location/encode_datasets.loc
|
|
/galaxy/home/universe/encode_feature_partitions
|
|
/galaxy/data/location/lastz_seqs.loc
|
|
/galaxy/data/location/liftOver.loc
|
|
/galaxy/data/location/maf_index.loc
|
|
/galaxy/data/location/maf_pairwise.loc
|
|
/galaxy/data/location/microbes/microbial_data.loc
|
|
/galaxy/data/location/perm_base_index.loc
|
|
/galaxy/data/location/perm_color_index.loc
|
|
/galaxy/data/location/phastOdds.loc
|
|
/galaxy/data/location/quality_scores.loc
|
|
/galaxy/data/location/regions.loc
|
|
/galaxy/data/location/sam_fa_indices.loc
|
|
/galaxy/data/taxonomy
|
|
/galaxy/data/location/twobit.loc
|
|
"
|
|
|
|
SAMPLES="
|
|
datatypes_conf.xml.sample
|
|
universe_wsgi.ini.sample
|
|
"
|
|
|
|
DIRS="
|
|
database
|
|
database/files
|
|
database/tmp
|
|
database/compiled_templates
|
|
database/job_working_directory
|
|
database/import
|
|
database/pbs
|
|
"
|
|
|
|
for link in $LINKS; do
|
|
echo "Linking $link"
|
|
rm -f tool-data/`basename $link`
|
|
ln -sf $link tool-data
|
|
done
|
|
|
|
if [ -d "$HYPHY" ]; then
|
|
echo "Linking $HYPHY"
|
|
rm -f tool-data/HYPHY
|
|
ln -sf $HYPHY tool-data/HYPHY
|
|
fi
|
|
|
|
for sample in $SAMPLES; do
|
|
file=`echo $sample | sed -e 's/\.sample$//'`
|
|
echo "Copying $sample to $file"
|
|
cp $sample $file
|
|
done
|
|
|
|
for dir in $DIRS; do
|
|
if [ ! -d $dir ]; then
|
|
echo "Creating $dir"
|
|
mkdir $dir
|
|
fi
|
|
done
|
|
|
|
python ./scripts/fetch_eggs.py all
|