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Dockerfile
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####################################################################################
######## This is a Dockerfile to describe QIAGEN's read processing #########
######## runtime framework for spe-dna panels #########
####################################################################################
# Using a biocontainer base image
# Please see below for further details :
# https://github.com/BioContainers/containers/blob/master/biocontainers/Dockerfile
FROM biocontainers/biocontainers:latest
MAINTAINER Raghavendra Padmanabhan <[email protected]>
################ Create appropriate directory structure for code to run ################
USER root
RUN mkdir -p /srv/qgen/code && \
mkdir -p /srv/qgen/bin/downloads && \
mkdir -p /srv/qgen/data/genome && \
mkdir -p /srv/qgen/data/annotation && \
mkdir -p /srv/qgen/example/
################ Update package repository and install dependencies using apt-get ################
RUN apt-get -y update && \
apt-get -y install r-base
################ Install various version specific 3rd party tools ################
RUN conda install bedtools=2.25.0
################ Install python modules ################
## Install some modules with conda
RUN conda install scipy MySQL-python openpyxl pysam=0.9.0
RUN pip install statistics
################ R packages ################
RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile
RUN Rscript -e "install.packages('plyr')"
################ Add latest samtools version for sort by Tag feature ################
RUN wget https://github.com/samtools/samtools/releases/download/1.5/samtools-1.5.tar.bz2 -O /srv/qgen/bin/downloads/samtools-1.5.tar.bz2 && \
cd /srv/qgen/bin/downloads/ && \
tar -xvf samtools-1.5.tar.bz2 && \
cd samtools-1.5 && \
mkdir -p /srv/qgen/bin/samtools-1.5 && \
./configure --prefix /srv/qgen/bin/samtools-1.5 && \
make && \
make install
################ Add data directory ################
## Download genome files
RUN wget https://storage.googleapis.com/qiaseq-dna/data/genome/ucsc.hg19.dict \
https://storage.googleapis.com/qiaseq-dna/data/genome/ucsc.hg19.fa.gz -P /srv/qgen/data/genome/
RUN cd /srv/qgen/data/genome && \
gunzip ucsc.hg19.fa.gz && \
## Index the fasta using samtools
/srv/qgen/bin/samtools-1.5/bin/samtools faidx /srv/qgen/data/genome/ucsc.hg19.fa
## Download Annotation files
RUN wget https://storage.googleapis.com/qiaseq-dna/data/annotation/bkg.error.v2.RData \
https://storage.googleapis.com/qiaseq-dna/data/annotation/SR_LC_SL.full.bed \
https://storage.googleapis.com/qiaseq-dna/data/annotation/simpleRepeat.full.bed \
-P /srv/qgen/data/annotation/
## Add test files for smCounterv2
RUN mkdir -p /srv/qgen/test_smcounter-v2/
RUN wget https://storage.googleapis.com/qiaseq-dna/test_files/high.confidence.variants.bed \
https://storage.googleapis.com/qiaseq-dna/test_files/NB956-240-3-10_S1.highconfidence.bam \
https://storage.googleapis.com/qiaseq-dna/test_files/NB956-240-3-10_S1.highconfidence.VariantList.long.txt \
https://storage.googleapis.com/qiaseq-dna/test_files/NB956-240-3-10_S1.highconfidence.bam.bai \
-P /srv/qgen/test_smcounter-v2/
################ Update Environment Variables ################
ENV PYTHONPATH $PYTHONPATH:/opt/conda/lib/python2.7/site-packages/:/srv/qgen/code/qiaseq-dna/