jfroula/interproscan repository overview

# Created by: Lee Bergstrand 2018
#
# Discription:  A Dockerfile for building a container containing InterProScan5. It is based-off the Dockerfile used by
#               EBI Metagenomics team (https://github.com/EBI-Metagenomics/InterProScan) but has been modified to
#               provide code and data for all InterProScan5 analyses with the exception of SignalP, Phobius, Tmhmm.
#               These are exluded as they require licence agreements
#               (https://github.com/ebi-pf-team/interproscan/wiki/ActivatingLicensedAnalyses).
#
# Building: docker build https://raw.githubusercontent.com/Micromeda/InterProScan-Docker/master/Dockerfile -t micromeda/interproscan-docker
#
# Usage: docker run --rm --name interproscan -v /tmp:/tmp micromeda/interproscan-docker -dp --goterms --pathways -f tsv
#                   --appl "PfamA,TIGRFAM,PRINTS,PrositePatterns,Gene3d" -o /tmp/out.ipr -i /tmp/test.fasta


FROM openjdk:8

MAINTAINER Lee Bergstrand


ARG IPR=5
ENV IPR $IPR
ENV IPRSCAN "$IPR.35-74.0"

RUN mkdir -p /opt

RUN curl -o /opt/interproscan-$IPRSCAN-64-bit.tar.gz ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.35-74.0/interproscan-5.35-74.0-64-bit.tar.gz
RUN curl -o /opt/interproscan-$IPRSCAN-64-bit.tar.gz.md5 ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.35-74.0/interproscan-5.35-74.0-64-bit.tar.gz.md5

WORKDIR /opt

# Install InterProScan5.
RUN md5sum -c interproscan-$IPRSCAN-64-bit.tar.gz.md5

RUN mkdir -p /opt/interproscan

RUN  tar -pxvzf interproscan-$IPRSCAN-64-bit.tar.gz \
    --exclude="interproscan-$IPRSCAN/data/phobius" \
    --exclude="interproscan-$IPRSCAN/data/tmhmm" \
    --exclude="interproscan-$IPRSCAN/data/cdd" \
    --exclude="interproscan-$IPRSCAN/data/smart" \
    --exclude="interproscan-$IPRSCAN/data/gene3d" \
    --exclude="interproscan-$IPRSCAN/data/hamap" \
    --exclude="interproscan-$IPRSCAN/data/pirsf" \
    --exclude="interproscan-$IPRSCAN/data/prints" \
    --exclude="interproscan-$IPRSCAN/data/prodom" \
    --exclude="interproscan-$IPRSCAN/data/prosite" \
    --exclude="interproscan-$IPRSCAN/data/sfld" \
    -C /opt/interproscan --strip-components=1

# total list
# cdd/  freemarker/  gene3d/  hamap/  pfam/  phobius/  pirsf/  prints/  prodom/  prosite/  sfld/	smart/	superfamily/  tigrfam/	tmhmm/

RUN rm -f interproscan-$IPRSCAN-64-bit.tar.gz interproscan-$IPRSCAN-64-bit.tar.gz.md5
ENV PATH /opt/interproscan:$PATH

# remove code that checks java version since this errors when run with cromwell
RUN sed -i '30,42d' /opt/interproscan/interproscan.sh