Bootstrap: docker
From: ubuntu:bionic

%labels
Maintainer Sebastian Uhrig @ DKFZ

%post
# install dependencies
export DEBIAN_FRONTEND=noninteractive
apt-get update -y
apt-get install -y samtools r-base rna-star wget libcurl4-openssl-dev libxml2-dev
Rscript -e 'install.packages("circlize", repos="http://cran.r-project.org"); source("https://bioconductor.org/biocLite.R"); biocLite(c("GenomicRanges", "GenomicAlignments"))'

# install arriba
URL=$(wget -q -O - https://api.github.com/repos/suhrig/arriba/releases/latest | sed -n -e 's/.*"browser_download_url":\s*"\([^"]*\)".*/\1/p')
wget -q -O - "$URL" | tar -xzf -

# make wrapper for download_references.sh
echo '#!/bin/bash
cd /references
/arriba*/download_references.sh $1 $2 && \
cp /arriba*/database/*${1%+*}* /references' > /usr/local/bin/download_references.sh
chmod a+x /usr/local/bin/download_references.sh

# make wrapper script for run_arriba.sh
echo '#!/bin/bash
cd /output
/arriba*/run_arriba.sh /references/STAR_index_* /references/*.gtf /references/*.fa /references/blacklist_*.tsv.gz /read1.fastq.gz /read2.fastq.gz ${1-8}' > /usr/local/bin/arriba.sh
chmod a+x /usr/local/bin/arriba.sh

# make wrapper script for draw_fusions.R
echo '#!/bin/bash\n\
Rscript /arriba*/draw_fusions.R --annotation=$(ls /references/*.gtf) --fusions=/fusions.tsv --output=/output/fusions.pdf --proteinDomains=$(ls /references/protein_domains_*.gff3) --alignments=/Aligned.sortedByCoord.out.bam --cytobands=$(ls /references/cytobands_*.tsv)' > /usr/local/bin/draw_fusions.sh && \
chmod a+x /usr/local/bin/draw_fusions.sh

