Commit 78a81d79 authored by Hermann Zellner's avatar Hermann Zellner

Interproscan 5.47 82.0

parent 8a18fe3b
......@@ -24,7 +24,7 @@ outdir=""
workdir=""
cleanworkdir=0
container_software="docker"
docker_version="2020.5"
docker_version="2020.6"
predictionfiles="predictions_unirule.out predictions_arba.out predictions_unirule-pirsr.out"
function usage() {
......
......@@ -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/5/5.45-80.0/interproscan-5.45-80.0-64-bit.tar.gz
wget -q ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.47-82.0/interproscan-5.47-82.0-64-bit.tar.gz
echo "Done."
wget -q ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.45-80.0/interproscan-5.45-80.0-64-bit.tar.gz.md5
wget -q ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.47-82.0/interproscan-5.47-82.0-64-bit.tar.gz.md5
ipr_check=`md5sum -c interproscan-5.45-80.0-64-bit.tar.gz.md5`
ipr_check=`md5sum -c interproscan-5.47-82.0-64-bit.tar.gz.md5`
if [[ ${ipr_check} != "interproscan-5.45-80.0-64-bit.tar.gz: OK" ]]
if [[ ${ipr_check} != "interproscan-5.47-82.0-64-bit.tar.gz: OK" ]]
then
exit 11
fi
......@@ -39,28 +39,14 @@ fi
mkdir -p ${ROOT_FOLDER}
cd ${ROOT_FOLDER}
echo "Extracting InterProScan..."
tar -pxzf ${DOWNLOAD_FOLDER}/interproscan-5.45-80.0-64-bit.tar.gz
tar -pxzf ${DOWNLOAD_FOLDER}/interproscan-5.47-82.0-64-bit.tar.gz
echo "Done."
cd ${DOWNLOAD_FOLDER}
echo "Downloading Panther data..."
wget -q ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/data/panther-data-14.1.tar.gz
echo "Done."
wget -q ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/data/panther-data-14.1.tar.gz.md5
panther_check=`md5sum -c panther-data-14.1.tar.gz.md5`
if [[ ${panther_check} != "panther-data-14.1.tar.gz: OK" ]]
then
exit 12
fi
cd ${ROOT_FOLDER}/interproscan-5.45-80.0/data
echo "Extracting Panther data..."
tar -pxzf ${DOWNLOAD_FOLDER}/panther-data-14.1.tar.gz
echo "Done."
echo "Initializing InerProScan..."
cd /opt/interproscan-5.47-82.0
python3 initial_setup.py
echo "Done iitializing InterProScan"
# Clean up tar to reduce the size of the image
rm -f ${DOWNLOAD_FOLDER}/interproscan-5.45-80.0-64-bit.tar.gz
rm -f ${DOWNLOAD_FOLDER}/interproscan-5.45-80.0-64-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
rm -f ${DOWNLOAD_FOLDER}/interproscan-5.47-82.0-64-bit.tar.gz
rm -f ${DOWNLOAD_FOLDER}/interproscan-5.47-82.0-64-bit.tar.gz.md5
......@@ -17,7 +17,7 @@
############################################################################
UNIFIRE_REPO="/opt/git/unifire"
INTERPROSCAN_REPO="/opt/interproscan-5.45-80.0"
INTERPROSCAN_REPO="/opt/interproscan-5.47-82.0"
ETE3FOLDER="/opt/ete3"
VOLUME=/volume
......@@ -27,7 +27,7 @@ ${UNIFIRE_REPO}/misc/taxonomy/fetchTaxonomicLineage.py -i ${VOLUME}/proteins.fas
-t ${ETE3FOLDER}/taxa.sqlite
${INTERPROSCAN_REPO}/interproscan.sh -f xml -dp -i ${VOLUME}/proteins_lineage.fasta \
--appl "Hamap,ProSiteProfiles,ProSitePatterns,Pfam,TIGRFAM,SMART,PRINTS,SFLD,CDD,Gene3D,ProDom,PIRSF,PANTHER,SUPERFAMILY" \
--appl "Hamap,ProSiteProfiles,ProSitePatterns,Pfam,TIGRFAM,SMART,PRINTS,SFLD,CDD,Gene3D,PIRSF,PANTHER,SUPERFAMILY" \
-o ${VOLUME}/proteins_lineage-ipr.xml
PATH="/usr/lib/jvm/java-8-openjdk-amd64/bin:${PATH}"
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment