Merge branch 'generic_container'. Fixed #1

Author: suryasaha

5.36-75-cyverse/Dockerfile

@@ -0,0 +1,92 @@
+################## MultiStage build ######################
+
+################## Core ######################
+
+FROM busybox AS buildcore
+
+MAINTAINER Amanda Cooksey <amandamcooksey@gmail.com>
+
+ARG IPR=5
+ENV IPR $IPR
+ARG IPRSCAN=5.36-75.0
+ENV IPRSCAN $IPRSCAN
+
+RUN mkdir -p /opt/interproscan/bin/blast/ncbi-blast-2.9.0+
+RUN mkdir -p /opt/interproscan/bin/interproscan
+
+
+RUN wget -O /opt/interproscan-core-$IPRSCAN.tar.gz ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/$IPR/$IPRSCAN/alt/interproscan-core-$IPRSCAN.tar.gz
+RUN wget -O /opt/interproscan-core-$IPRSCAN.tar.gz.md5 ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/$IPR/$IPRSCAN/alt/interproscan-core-$IPRSCAN.tar.gz.md5
+
+
+WORKDIR /opt
+
+RUN md5sum -c interproscan-core-$IPRSCAN.tar.gz.md5
+
+RUN  tar -pxvzf interproscan-core-$IPRSCAN.tar.gz \
+    -C /opt/interproscan --strip-components=1 \
+    && rm -f interproscan-core-$IPRSCAN.tar.gz interproscan-core-$IPRSCAN.tar.gz.md5
+
+
+# Workaround bin/blast/ncbi-blast-2.9.0+/rpsblast: error while loading shared
+# libraries: libgnutls.so.28: cannot open shared object file: No such file or 
+# directory
+RUN wget -O /opt/ncbi-blast-2.9.0+-x64-linux.tar.gz ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.9.0/ncbi-blast-2.9.0+-x64-linux.tar.gz
+RUN tar xvf ncbi-blast-2.9.0+-x64-linux.tar.gz
+
+
+# copy the new version to the binary folder
+RUN cp /opt/ncbi-blast-2.9.0+/bin/rpsblast /opt/interproscan/bin/blast/ncbi-blast-2.9.0+/rpsblast
+#RUN cp /opt/interproscan/interproscan.sh /opt/interproscan/interproscan-5.jar /opt/interproscan/bin/interproscan
+
+################## BASE IMAGE ######################
+
+FROM ubuntu:16.04
+
+MAINTAINER Amanda Cooksey <amandamcooksey@gmail.com>
+LABEL  base_image="ubuntu:16.04" \
+       software="interproscan" \
+       software.version="5.36-75.0" \
+       version="1" \
+       about.summary="Scan sequences against the InterPro protein signature databases." \
+       about.home="https://www.ebi.ac.uk/interpro/interproscan.html" \
+       about.license="Apache-2.0" \
+       about.license_file="https://github.com/ebi-pf-team/interproscan/blob/dev/LICENSE" \
+       about.documentation="https://github.com/ebi-pf-team/interproscan/wiki" \
+       about.tags="biology::nucleic, biology::protein, field::biology, field::biology:bioinformatics, interface::commandline, role::program,:biological-sequence" \
+       extra.identifier.biotools="interproscan_5" \
+       extra.binaries="interproscan.sh"
+
+COPY --from=buildcore /opt/interproscan /opt/interproscan
+
+RUN mkdir -p /opt/interproscan/data
+RUN mkdir -p /data
+
+RUN apt-get update && \
+    apt-get upgrade -y && \
+    apt-get install -y \
+        parallel \
+        openjdk-8-jre   \
+        build-essential \
+        pkg-config      \
+        python3         \
+        bzip2           \
+	libdw1 \
+	nano \
+        ca-certificates && \
+    apt-get clean && \
+    apt-get purge && \
+    rm -rf /var/lib/apt/lists/* /tmp/*
+
+
+WORKDIR /opt/interproscan
+
+ENV PATH=$PATH:/opt/interproscan/bin
+
+ADD splitfasta.pl /usr/bin
+ADD iprs_wrapper.sh /usr/bin
+ADD cyverse_parse_ips_xml.pl /usr/bin
+
+
+ENTRYPOINT ["/bin/bash", "iprs_wrapper.sh"]
+##################### INSTALLATION END #####################

5.36-75-cyverse/README.md

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+# InterProScan
+
+This version is optimized for execution in the Cyverse environment.