root/galaxy-central/setup.sh

#!/bin/sh

python ./scripts/check_python.py
[ $? -ne 0 ] && exit 1

SAMPLES="
datatypes_conf.xml.sample
reports_wsgi.ini.sample
tool_conf.xml.sample
tool_data_table_conf.xml.sample
universe_wsgi.ini.sample
tool-data/alignseq.loc.sample
tool-data/annotation_profiler_options.xml.sample
tool-data/annotation_profiler_valid_builds.txt.sample
tool-data/bfast_indexes.loc.sample
tool-data/binned_scores.loc.sample
tool-data/blastdb.loc.sample
tool-data/bowtie_indices.loc.sample
tool-data/bowtie_indices_color.loc.sample
tool-data/encode_datasets.loc.sample
tool-data/liftOver.loc.sample
tool-data/maf_index.loc.sample
tool-data/maf_pairwise.loc.sample
tool-data/microbial_data.loc.sample
tool-data/phastOdds.loc.sample
tool-data/quality_scores.loc.sample
tool-data/regions.loc.sample
tool-data/sam_fa_indices.loc.sample
tool-data/srma_index.loc.sample
tool-data/twobit.loc.sample
tool-data/shared/ucsc/builds.txt.sample
"

DIRS="
database
database/files
database/community_files
database/tmp
database/compiled_templates
database/job_working_directory
database/import
database/pbs
static/genetrack/plots
tool-data/shared/jars
"

for sample in $SAMPLES; do
    file=`echo $sample | sed -e 's/\.sample$//'`
    if [ -f $file ]; then
        echo "Not overwriting existing $file"
    else
        echo "Copying $sample to $file"
        cp $sample $file
    fi
done

for dir in $DIRS; do
    if [ ! -d $dir ]; then
        echo "Creating $dir"
        mkdir $dir
    fi
done

python ./scripts/fetch_eggs.py