Merge branch 'interproscan-5.47-82.0' into 'master'

Interproscan 5.47 82.0

See merge request uniprot-public/unifire!13

docker/bin/run_unifire_docker.sh

@@ -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() {

docker/scripts/download-interproscan.sh

@@ -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

docker/scripts/unifire-workflow.sh

@@ -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}"