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# MG-RAST pipeline Dockerfile
FROM ubuntu:18.10
MAINTAINER The MG-RAST team (folker@mg-rast.org)
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update && apt-get install -y \
cdbfasta \
cd-hit \
cmake \
dh-autoreconf \
emacs \
git \
libtbb-dev \
libcwd-guard-perl \
libberkeleydb-perl \
libdata-dump-streamer-perl \
libdatetime-perl \
libdatetime-format-iso8601-perl \
libdbi-perl \
libdigest-md5-perl \
libdigest-md5-file-perl \
libdbd-pg-perl \
libfile-slurp-perl \
libfilehandle-fmode-perl \
libgetopt-long-descriptive-perl \
libjson-perl \
liblist-allutils-perl \
libpq-dev \
libpng-dev \
libposix-strptime-perl \
libstring-random-perl \
libtbb-dev \
libtemplate-perl \
liburi-encode-perl \
libunicode-escape-perl \
libwww-perl \
liblog-log4perl-perl \
make \
nodejs \
python-biopython \
python-dev \
python-leveldb \
perl-modules \
python-numpy \
python-pika \
python-pip \
python-scipy \
python-sphinx \
unzip \
wget \
vim \
curl \
&& apt-get clean
### alphabetically sorted builds from source
### install latest bowtie2 release
RUN cd /root \
&& curl -s https://api.github.com/repos/BenLangmead/bowtie2/releases/latest \
| grep tarball_url | cut -f4 -d\" | wget -O download.tar.gz -qi - \
&& tar xzfp download.tar.gz \
&& rm -f download.tar.gz \
&& cd * \
&& make \
&& install bowtie2* /usr/local/bin/ \
&& cd /root \
&& rm -rf *bowtie2*
### install autoskewer (requires bowtie)
RUN cd /root \
&& git clone http://github.com/MG-RAST/autoskewer \
&& cd autoskewer \
&& make install \
&& cd /root \
&& rm -rf autoskewer
### install latest DIAMOND release
RUN cd /root \
&& curl -s https://api.github.com/repos/bbuchfink/diamond/releases/latest \
| grep tarball_url | cut -f4 -d\" | wget -O download.tar.gz -qi - \
&& tar xzfp download.tar.gz \
&& rm -f download.tar.gz \
&& cd * \
&& sh ./build_simple.sh \
&& install -s -m555 diamond /usr/local/bin \
&& cd /root \
&& rm -rf *diamond*
### install latest ea-utils release
RUN cd /root \
&& curl -s https://api.github.com/repos/ExpressionAnalysis/ea-utils/releases/latest \
| grep tarball_url | cut -f4 -d\" | wget -O download.tar.gz -qi - \
&& tar xzfp download.tar.gz \
&& rm -f download.tar.gz \
&& cd *ea-utils*/clipper \
&& make fastq-multx \
&& make fastq-join \
&& make fastq-mcf \
&& install -m755 -s fastq-multx /usr/local/bin \
&& install -m755 -s fastq-join /usr/local/bin \
&& install -m755 -s fastq-mcf /usr/local/bin \
&& cd /root \
&& rm -rf *ea-utils*
### install FragGeneScan from our patched source in github
RUN cd /root \
&& git clone https://github.com/MG-RAST/FGS.git FragGeneScan \
&& cd FragGeneScan \
&& make \
&& mkdir bin \
&& mv train bin/. \
&& mv *.pl bin/. \
&& cp -r bin/train /usr/local/bin/ \
&& install -s -m555 FragGeneScan /usr/local/bin/. \
&& install -m555 -t /usr/local/bin/. bin/*.pl \
&& make clean \
&& cd /root \
&& rm -rf FragGeneScan
### install jellyfish 2.2.6 from source (2.2.8 from repo is broken)
RUN cd /root \
&& wget -O jellyfish.tar.gz https://github.com/gmarcais/Jellyfish/releases/download/v2.2.6/jellyfish-2.2.6.tar.gz \
&& tar xfvz jellyfish.tar.gz \
&& rm -f jellyfish.tar.gz \
&& cd jelly* \
&& ./configure \
&& make install \
&& cd /root \
&& rm -rf *jelly*
### install latest prodigal release
RUN cd /root \
&& curl -s https://api.github.com/repos/hyattpd/Prodigal/releases/latest \
| grep tarball_url | cut -f4 -d\" | wget -O download.tar.gz -qi - \
&& tar xzfp download.tar.gz \
&& rm -f download.tar.gz \
&& cd *Prodigal* \
&& make \
&& make install \
&& strip /usr/local/bin/prodigal \
&& make clean \
&& cd /root \
&& rm -rf *Prodigal*
### install sortmerna 2.1b
RUN cd /root \
&& wget https://github.com/biocore/sortmerna/archive/2.1b.tar.gz \
&& tar xvf 2*.tar.gz \
&& cd sortmerna-2* \
&& sed -i 's/^\#define READLEN [0-9]*/#define READLEN 500000/' include/common.hpp \
&& ./configure \
&& make install \
&& make clean \
&& cd /root \
&& rm -rf sortmerna-2* 2*.tar.gz
### install skewer
RUN cd /root \
&& git clone --branch 0.2.2 https://github.com/relipmoc/skewer \
&& cd skewer \
&& make \
&& make install \
&& make clean \
&& cd /root \
&& rm -rf skewer
### install latest vsearch release
RUN cd /root \
&& curl -s https://api.github.com/repos/torognes/vsearch/releases/latest \
| grep tarball_url | cut -f4 -d\" | wget -O download.tar.gz -qi - \
&& tar xzfp download.tar.gz \
&& rm -f download.tar.gz \
&& cd * \
&& sh ./autogen.sh \
&& ./configure --prefix=/usr/local/ \
&& make \
&& make install \
&& make clean \
&& strip /usr/local/bin/vsearch* \
&& cd /root \
&& rm -rf *vsearch*
### install CWL runner
RUN pip install --upgrade pip
RUN pip install --upgrade cwlref-runner typing statistics
# for jellyfish (ugly)
ENV LD_LIBRARY_PATH=/usr/local/lib
# copy files into image
COPY CWL /CWL/
COPY mgcmd/* bin/* /usr/local/bin/
COPY lib/* /usr/local/lib/site_perl/