Commit b6195b5d authored by Hermann Zellner's avatar Hermann Zellner

2020 03

parent a3f50e7b
......@@ -65,7 +65,7 @@ The only input data that need to be provided are the protein sequence data in mu
### Usage
```
usage: run_unifire_docker.sh -i <INPUT_FILE> -i <OUTPUT_FOLDER> [-v <VERSION> [-w <WORKING_FOLDER [-c]]]
-i: Path to multi-FASTA input file with headers in UniProt FASTA header format, containing at least
-i: Path to multi-FASTA input file with headers in UniProt FASTA header format, containing at least
OX=<taxid>. (Required)
-o: Path to output folder. All output files with predictions in TSV format will be available in this
folder at the end of the procedure. (Required)
......
......@@ -26,7 +26,7 @@ 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: 2020.2"
echo " https://gitlab.ebi.ac.uk/uniprot-public/unifire/container_registry. (Optional), DEFAULT: 2020.3"
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"
......@@ -39,7 +39,7 @@ infile=""
outdir=""
workdir=""
cleanworkdir=0
docker_version="2020.2"
docker_version="2020.3"
predictionfiles="predictions_unirule.out predictions_saas.out predictions_unirule-pirsr.out"
while getopts "i:o:w:c:v:" optionName
......
......@@ -25,13 +25,13 @@ DOWNLOAD_FOLDER="/opt/download"
mkdir -p ${DOWNLOAD_FOLDER}
cd ${DOWNLOAD_FOLDER}
echo "Downloading InterProScan..."
wget -q ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.41-78.0/interproscan-5.41-78.0-64-bit.tar.gz
wget -q ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.44-79.0/interproscan-5.44-79.0-64-bit.tar.gz
echo "Done."
wget -q ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.41-78.0/interproscan-5.41-78.0-64-bit.tar.gz.md5
wget -q ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.44-79.0/interproscan-5.44-79.0-64-bit.tar.gz.md5
ipr_check=`md5sum -c interproscan-5.41-78.0-64-bit.tar.gz.md5`
ipr_check=`md5sum -c interproscan-5.44-79.0-64-bit.tar.gz.md5`
if [[ ${ipr_check} != "interproscan-5.41-78.0-64-bit.tar.gz: OK" ]]
if [[ ${ipr_check} != "interproscan-5.44-79.0-64-bit.tar.gz: OK" ]]
then
exit 11
fi
......@@ -39,7 +39,7 @@ fi
mkdir -p ${ROOT_FOLDER}
cd ${ROOT_FOLDER}
echo "Extracting InterProScan..."
tar -pxzf ${DOWNLOAD_FOLDER}/interproscan-5.41-78.0-64-bit.tar.gz
tar -pxzf ${DOWNLOAD_FOLDER}/interproscan-5.44-79.0-64-bit.tar.gz
echo "Done."
cd ${DOWNLOAD_FOLDER}
......@@ -54,13 +54,13 @@ then
exit 12
fi
cd ${ROOT_FOLDER}/interproscan-5.41-78.0/data
cd ${ROOT_FOLDER}/interproscan-5.44-79.0/data
echo "Extracting Panther data..."
tar -pxzf ${DOWNLOAD_FOLDER}/panther-data-14.1.tar.gz
echo "Done."
# Clean up tar to reduce the size of the image
rm -f ${DOWNLOAD_FOLDER}/interproscan-5.41-78.0-64-bit.tar.gz
rm -f ${DOWNLOAD_FOLDER}/interproscan-5.41-78.0-64-bit.tar.gz.md5
rm -f ${DOWNLOAD_FOLDER}/interproscan-5.44-79.0-64-bit.tar.gz
rm -f ${DOWNLOAD_FOLDER}/interproscan-5.44-79.0-64-bit.tar.gz.md5
rm -f ${DOWNLOAD_FOLDER}/panther-data-14.1.tar.gz
rm -f ${DOWNLOAD_FOLDER}/panther-data-14.1.tar.gz.md5
......@@ -17,7 +17,7 @@
############################################################################
UNIFIRE_REPO="/opt/git/unifire"
INTERPROSCAN_REPO="/opt/interproscan-5.41-78.0"
INTERPROSCAN_REPO="/opt/interproscan-5.44-79.0"
VOLUME=/volume
infilename=infile.fasta
......
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