InterProScan and Docker

Today I needed to generate a Docker image for InterProScan. I have found a solution at GitHub and modified it to fit my needs.

The Dockerfile contains:

FROM debian:buster
LABEL maintainer "me :D"

RUN apt-get update && \
    apt-get upgrade -y -q && \
    apt-get install -y -q \
    apt-utils \
    build-essential \
    cmake \
    g++ \
    gcc-multilib \
    git \
    gzip \
    libboost-filesystem-dev \
    libboost-iostreams-dev \
    libboost-system-dev \
    openjdk-11-jre \
    perl \
    python \
    software-properties-common \
    tcsh \
    wget \
    zlib1g-dev \
    zlibc

ENV JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64
ENV CLASSPATH=/usr/lib/jvm/java-11-openjdk-amd64/bin

RUN wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.39-77.0/interproscan-5.39-77.0-64-bit.tar.gz && \
    wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.39-77.0/interproscan-5.39-77.0-64-bit.tar.gz.md5 && \
    md5sum -c interproscan-5.39-77.0-64-bit.tar.gz.md5

RUN tar -pxvzf interproscan-5.39-77.0-64-bit.tar.gz && \
    rm interproscan-5.39-77.0-64-bit.tar.gz

WORKDIR /interproscan-5.39-77.0/data

RUN wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/data/panther-data-14.1.tar.gz && \
    wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/data/panther-data-14.1.tar.gz.md5 && \
    md5sum -c panther-data-14.1.tar.gz.md5

RUN tar -pxvzf panther-data-14.1.tar.gz && \
    rm panther-data-14.1.tar.gz.md5

ENV PATH="/interproscan-5.39-77.0/:${PATH}"

WORKDIR /interproscan-5.39-77.0

RUN mkdir /data
RUN chmod a+w /interproscan-5.39-77.0

Interesting to notice that the generated image is 105GB in total.

As a run example:

wget https://www.uniprot.org/uniprot/Q96IY4.fasta

docker run --rm -v $(pwd):/foo foo/interproscan \
bash -c "./interproscan.sh \
-cpu 8 \
-i /foo/Q96IY4.fasta \
-f tsv \
-b /foo/Q96IY4.fasta \
--goterms --pathways \
-appl Panther,Pfam,SUPERFAMILY"

The output:

sp|Q96IY4|CBPB2_HUMAN	36ceaff9909f2cef08f7aa9de5bc1561	423	Pfam	PF00246	Zinc carboxypeptidase	129	410	2.0E-91	T	10-12-2019	IPR000834	Peptidase M14, carboxypeptidase A	GO:0004181|GO:0006508|GO:0008270	
sp|Q96IY4|CBPB2_HUMAN	36ceaff9909f2cef08f7aa9de5bc1561	423	SUPERFAMILY	SSF53187		119	422	3.64E-100	T	10-12-2019
sp|Q96IY4|CBPB2_HUMAN	36ceaff9909f2cef08f7aa9de5bc1561	423	PANTHER	PTHR11705:SF17		3	423	0.0	T	10-12-2019
sp|Q96IY4|CBPB2_HUMAN	36ceaff9909f2cef08f7aa9de5bc1561	423	SUPERFAMILY	SSF54897		22	110	4.25E-20	T	10-12-2019
sp|Q96IY4|CBPB2_HUMAN	36ceaff9909f2cef08f7aa9de5bc1561	423	PANTHER	PTHR11705		3	423	0.0	T	10-12-2019
sp|Q96IY4|CBPB2_HUMAN	36ceaff9909f2cef08f7aa9de5bc1561	423	Pfam	PF02244	Carboxypeptidase activation peptide	33	105	2.1E-13	T	10-12-2019	IPR003146	Carboxypeptidase, activation peptide	GO:0004180|GO:0006508	

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