pgap_standalone.sh

#!/bin/bash
set -euo pipefail

case"${1:---help}"in
-u|--update)
shift

# Use curl (preferred) or wget as fallback.
if which curl 2>/dev/null
then
fetch-stdout() {
 curl -Ls "$1"
 }
fetch-file() {
echo"- Fetching $1: $2"
 curl -LC - "$2" -O
 }
elif which wget 2>/dev/null
then
fetch-stdout() {
 wget -O - "$1"
 }
fetch-file() {
echo"- Fetching $1: $2"
 wget -c "$2"
 }
else
echo>&2"ERROR: Cannot find 'curl' or 'wget' in PATH."
exit 1
fi

 VERSION=`fetch-stdout https://api.github.com/repos/ncbi/pgap/releases/latest | sed -n 's/^.*"tag_name": "\([^"]*\)".*/\1/p'`
iftest`cat VERSION 2>/dev/null` = "$VERSION"
then
echo"The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version $VERSION is up to date."
else
echo"Updating the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) to version $VERSION..."
echo"- Fetching Docker image"
 docker pull ncbi/pgap:"$VERSION"
 fetch-file "reference data" https://s3.amazonaws.com/pgap-data/input-"$VERSION".tgz
 fetch-file "test genomes" https://s3.amazonaws.com/pgap-data/test_genomes.tgz
echo"- Extracting reference data and test genomes"
 tar xzvf input-"$VERSION".tgz
 tar xzvf test_genomes.tgz
echo"- Done."
echo"$VERSION"> VERSION
fi
 ;;

-h|--help)
echo"NCBI Prokaryotic Genome Annotation Pipeline (PGAP)"
echo"Usage: $0 <input-YAML>"
exit ;;

-*)
echo"Invalid option $1; try: $0 --help"
exit 1 ;;
esac

iftest"$#" -ne 1
then
echo"Require exactly one input YAML file; try: $0 --help"
exit 1
fi

# Run PGAP.
VERSION=`<VERSION`
image="ncbi/pgap:$VERSION"
inDir=`cd $(dirname $1)&&pwd -P`
inFile=`basename $1`

# Create the input file
cat $1<(docker run -i "$image" cat /pgap/input.yaml)>$inDir/pgap_input.yaml

# Ensure needed files are setup
mkdir -p $inDir/input
mkdir -p output
ln -s /pgap/input_template $inDir/input_template

# Run the actual workflow
docker run -i \
 --volume $inDir:/pgap/user_input:ro \
 --volume $(pwd -P)/input-$VERSION:/pgap/user_input/input:ro \
 --volume $(pwd -P)/output:/pgap/output:rw \
"$image" \
 cwltool \
 --outdir ./outdir \
 wf_pgap_simple.cwl \
 user_input/pgap_input.yaml

# Cleanup
rmdir $inDir/input
rm $inDir/input_template