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FROM ubuntu:20.04
ENV DEBIAN_FRONTEND=noninteractive
#~~~~~~~~~~~~~~
# Install Preliminaries
#~~~~
RUN apt-get -qq update && apt-get -qq -y install \
automake \
build-essential \
bzip2 \
cmake \
curl \
default-jre \
fort77 \
ftp \
g++ \
gcc \
gfortran \
git \
libblas-dev \
libbz2-dev \
libcairo2-dev \
libcurl4-openssl-dev \
libdb-dev \
libghc-zlib-dev \
libjpeg-dev \
liblzma-dev \
libncurses-dev \
libncurses5-dev \
libpcre3-dev \
libpng-dev \
libreadline-dev \
libreadline-dev \
libssl-dev \
libtbb-dev \
libx11-dev \
libxml2-dev \
libxt-dev \
libzmq3-dev \
make \
nano \
perl \
pkg-config \
python3 \
python3-dev \
python3-distutils \
python3-pip \
python3-setuptools \
rsync \
texlive-latex-base \
tzdata \
unzip \
wget \
x11-common \
zlib1g-dev
## Perl stuff
RUN curl -L https://cpanmin.us | perl - App::cpanminus
RUN cpanm install DB_File
RUN cpanm install URI::Escape
#~~~~~~~~~~~
# Environmental Variables
#~~~~~~~~~~~
ENV SRC /usr/local/src
ENV BIN /usr/local/bin
# samtools
WORKDIR $SRC
ENV SAMTOOLS_VERSION 1.13
RUN wget https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
tar xvf samtools-${SAMTOOLS_VERSION}.tar.bz2 && \
cd samtools-${SAMTOOLS_VERSION} && \
./configure && make && make install
# blast
WORKDIR $SRC
ENV BLASTPLUS_VERSION 2.12.0
RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${BLASTPLUS_VERSION}/ncbi-blast-${BLASTPLUS_VERSION}+-x64-linux.tar.gz && \
tar xvf ncbi-blast-${BLASTPLUS_VERSION}+-x64-linux.tar.gz && \
cp ncbi-blast-${BLASTPLUS_VERSION}+/bin/* $BIN && \
rm -r ncbi-blast-${BLASTPLUS_VERSION}+
# Hmmer
WORKDIR $SRC
RUN wget http://eddylab.org/software/hmmer/hmmer.tar.gz && \
tar xvf hmmer.tar.gz && \
cd hmmer-3.3.2 && \
./configure && \
make && make install
# Trinotate
WORKDIR $SRC
ENV TRANSDECODER_CO=817d772325c8a354aec6b94ac58993b994ac7392
RUN git clone https://github.com/TransDecoder/TransDecoder.git && \
cd TransDecoder && \
git checkout $TRANSDECODER_CO && \
mv * $BIN
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