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Dockerfile
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FROM debian:stretch
RUN apt-get update
################
#Install binaries dependencies
################
RUN apt-get install -y \
bedtools=2.26.0+dfsg-3 \
bowtie2=2.3.0-2 \
fastx-toolkit=0.0.14-3 \
gawk=1:4.1.4+dfsg-1 \
git \
perl \
python=2.7.13-2 \
r-base=3.3.3-1 \
r-base-dev=3.3.3-1 \
samtools=1.3.1-3 \
wget
################
#Install Wgsim
################
RUN mkdir -p /src; \
cd /src ; \
git clone https://github.com/lh3/wgsim.git; \
cd wgsim; \
gcc -g -O2 -Wall -o wgsim wgsim.c -lz -lm; \
mv wgsim /usr/bin/; \
cd /;
################
#Download Libraries
################
RUN mkdir -p /data/library/rep_annotation; \
cd /data/library/rep_annotation; \
wget --quiet -c -t0 "http://files2.gersteinlab.org/public-docs/2019/08.14/rep_annotation.hg38.tar.bz2" -O rep_annotation.hg38.tar.bz2; \
tar xjvf rep_annotation.hg38.tar.bz2; \
rm -Rf rep_annotation.hg38.tar.bz2
# DEPRECATED: 2017-02-14 - Only L1 subfamilies RPKM are estimated in the latest version
#RUN mkdir -p /data/library/kallisto; \
# cd /data/library/; \
# wget --quiet -c -t0 "https://www.dropbox.com/s/bd0vqqyedx7p0jv/kallisto_gencode23.hg38.tar.bz2?dl=1" -O kallisto_gencode23.hg38.tar.bz2; \
# tar xjvf kallisto_gencode23.hg38.tar.bz2; \
# rm -Rf kallisto_gencode23.hg38.tar.bz2
RUN mkdir -p /data/library/bowtie2; \
cd /data/library/bowtie2; \
wget --quiet -c -t0 "http://files2.gersteinlab.org/public-docs/2019/08.14/bowtie2.hg38.tar.bz2" -O bowtie2.hg38.tar.bz2; \
tar xjvf bowtie2.hg38.tar.bz2; \
rm -Rf bowtie2.hg38.tar.bz2
################
#Install R packages dependencies
################
#RUN cd /data/library/; \
# wget --quiet -c -t0 "https://cloud.r-project.org/src/contrib/Archive/penalized/penalized_0.9-49.tar.gz" -O penalized_0.9-49.tar.gz; \
# R CMD INSTALL penalized_0.9-49.tar.gz
RUN echo 'install.packages(c("penalized"), repos="http://cloud.r-project.org", dependencies=TRUE)' > /tmp/packages.R \
&& Rscript /tmp/packages.R
################
#Install TeXP
################
ADD https://api.github.com/repos/gersteinlab/texp/git/refs/heads/master version.json
RUN mkdir -p /src; \
cd /src ; \
git clone https://github.com/gersteinlab/texp.git
RUN chmod +x /src/texp/TeXP.sh /src/texp/TeXP_batch.sh; \
ln -s /src/texp/TeXP.sh /usr/bin/TeXP; \
ln -s /src/texp/TeXP.sh /usr/bin/TeXP.sh; \
ln -s /src/texp/TeXP_batch.sh /usr/bin/TeXP_batch;
WORKDIR /src/texp/
CMD ["/src/texp/TeXP.sh"]