Commit b60ce6c2 authored by Hermann Zellner's avatar Hermann Zellner

Updated usage information of run_unifire_docker.sh to display dynamically the...

Updated usage information of run_unifire_docker.sh to display dynamically the default version of the docker image
parent 6bdea795
......@@ -19,6 +19,13 @@
set -e
set -u
infile=""
outdir=""
workdir=""
cleanworkdir=0
docker_version="2020.4"
predictionfiles="predictions_unirule.out predictions_arba.out predictions_unirule-pirsr.out"
function usage() {
echo "usage: $0 -i <INPUT_FILE> -i <OUTPUT_FOLDER> [-v <VERSION> [-w <WORKING_FOLDER [-c]]]"
echo " -i: Path to multi-FASTA input file with headers in UniProt FASTA header format, containing at least"
......@@ -26,7 +33,7 @@ function usage() {
echo " -o: Path to output folder. All output files with predictions in TSV format will be available in this"
echo " folder at the end of the procedure. (Required)"
echo " -v: Version of the docker image to use, e.g. 2020.2. Available versions are listed under"
echo " https://gitlab.ebi.ac.uk/uniprot-public/unifire/container_registry. (Optional), DEFAULT: 2020.3"
echo " https://gitlab.ebi.ac.uk/uniprot-public/unifire/container_registry. (Optional), DEFAULT: ${docker_version}"
echo " -w: Path to an empty working directory. If this option is not given, then a temporary folder will be"
echo " created and used to store intermediate files. (Optional)"
echo " -c: Clean up temporary files. If set, then all temporary files will be cleaned up at the end of the"
......@@ -35,13 +42,6 @@ function usage() {
exit 1
}
infile=""
outdir=""
workdir=""
cleanworkdir=0
docker_version="2020.4"
predictionfiles="predictions_unirule.out predictions_arba.out predictions_unirule-pirsr.out"
while getopts "i:o:w:c:v:" optionName
do
case "${optionName}" in
......
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