https://github.com/sanger-pathogens/Farm_blast
Tip revision: bb2346853c91798d4728f10d41fd590bc077aff0 authored by Christoph PĆ¼the on 07 April 2020, 07:08:12 UTC
Merge pull request #26 from sanger-pathogens/blastall
Merge pull request #26 from sanger-pathogens/blastall
Tip revision: bb23468
Dockerfile
FROM ubuntu:18.04
MAINTAINER path-help@sanger.ac.uk
ARG DEBIAN_FRONTEND=noninteractive
ARG BUILD_DIR=/tmp/local-install
ARG BLAST_VERSION="2.9.0"
ARG BLAST_DOWNLOAD_FILENAME="ncbi-blast-${BLAST_VERSION}+-x64-linux.tar.gz"
ARG BLAST_PLUS_URL="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLAST_VERSION}/${BLAST_DOWNLOAD_FILENAME}"
ARG PYFASTQ_VERSION=3.17.0
# Ubuntu
RUN apt-get update -qq -y && \
apt-get upgrade -qq -y
# Dependencies for singularity and python
RUN apt-get update -qq -y && \
apt-get install -qq -y \
python3 \
python3-pip \
wget && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
# NCBI blast+
RUN cd /opt && \
wget -q "$BLAST_PLUS_URL" -O "${BLAST_DOWNLOAD_FILENAME}" && \
tar xzvf "${BLAST_DOWNLOAD_FILENAME}" && \
rm "${BLAST_DOWNLOAD_FILENAME}"
ENV PATH "/opt/ncbi-blast-${BLAST_VERSION}+/bin:${PATH}"
# Legacy version of blast to get blastall executable (add to end of PATH)
ARG BLAST_LEGACY_VERSION="2.2.25"
ARG BLAST_LECAGY_DOWNLOAD_FILENAME="blast-${BLAST_LEGACY_VERSION}-x64-linux.tar.gz"
ARG BLAST_LEGACY_URL="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/${BLAST_LEGACY_VERSION}/${BLAST_LECAGY_DOWNLOAD_FILENAME}"
RUN cd /opt && \
wget -q ${BLAST_LEGACY_URL} -O ${BLAST_LECAGY_DOWNLOAD_FILENAME} && \
tar xzvf ${BLAST_LECAGY_DOWNLOAD_FILENAME} && \
rm ${BLAST_LECAGY_DOWNLOAD_FILENAME}
ENV PATH $PATH:/opt/blast-${BLAST_LEGACY_VERSION}/bin
# Farm blast
COPY . "${BUILD_DIR}"
RUN cd "${BUILD_DIR}" && \
pip3 install "pyfastaq==${PYFASTQ_VERSION}" && \
pip3 install . && \
rm -rf "${BUILD_DIR}"