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RIFTT.def
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RIFTT.def
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Bootstrap: debootstrap
OSVersion: focal
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
Include: apt
%post
mkdir /tools
mkdir /fcdata
mkdir /star_index
mkdir /outputfolder
touch /genome.fa
touch /anno.gtf
touch /read1.fastq.gz
touch /read2.fastq.gz
touch /clintable.xlsx
touch /blacklist_user.xlsx
apt-get install -y apt-utils
apt-get install -y locales
locale-gen en_US.UTF-8
export LANG=en_US.UTF-8
apt-get install -y software-properties-common
apt-get update
add-apt-repository universe
add-apt-repository multiverse
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'
apt-get update
apt-get install -y gzip
apt-get install -y unzip
apt-get install -y tar
apt-get install -y wget
apt-get install -y make
apt-get install -y gcc
apt-get install -y pigz
apt-get install -y libpng-dev
apt-get install -y python2
apt-get install -y python2-dev
ln -s /usr/bin/python2 /usr/bin/python
wget https://bootstrap.pypa.io/pip/2.7/get-pip.py -O /tools/get-pip.py
python /tools/get-pip.py
rm /tools/get-pip.py
pip2 install biopython==1.76
apt-get install -y r-base
apt-get install -y libxml2-dev
apt-get install -y libssl-dev
apt-get install -y parallel
apt-get install -y pandoc
apt-get install -y libcurl4-openssl-dev
apt-get install -y default-jre
apt-get install -y libgd3
apt-get install -y libgd-dev
cpan Math::Round Font::TTF::Font GD::Polyline List::MoreUtils Math::Bezier Readonly SVG Math::VecStat
cpan GD Clone Regexp::Common GD::Polyline Text::Format Set::IntSpan Statistics::Basic Params::Validate Config::General
Rscript /scripts/Rscripts/installrequiredRpackages.R
cd /tools
wget -O samtools.tar.bz2 https://github.com/samtools/samtools/releases/download/1.14/samtools-1.14.tar.bz2
bunzip2 samtools.tar.bz2
tar xf samtools.tar
rm samtools.tar
cd samtools-1.14
make
make install
cd ..
wget -O arriba.tar.gz https://github.com/suhrig/arriba/releases/download/v2.2.1/arriba_v2.2.1.tar.gz
tar xzf arriba.tar.gz
rm arriba.tar.gz
#sed -i 's#--outStd BAM_Unsorted#--outStd BAM_Unsorted --outFileNamePrefix "$mapbase/$sample_name/" --outTmpDir "$mapbase/$sample_name/"STARtemp#g' /tools/arriba_v2.2.1/run_arriba.sh
#sed -i 's#NoSharedMemory#NoSharedMemory --sjdbGTFfile "$ANNOTATION_GTF" --sjdbOverhang "$overhang"#g' /tools/arriba_v2.2.1/run_arriba.sh
#sed -i 's#-o fusions#-o "$arbase/$sample_name"/fusions#g' /tools/arriba_v2.2.1/run_arriba.sh
#sed -i 's#-O fusions#-O "$arbase/$sample_name"/fusions#g' /tools/arriba_v2.2.1/run_arriba.sh
#sed -i 's#Aligned#"$mapbase/$sample_name/$sample_name"#g' /tools/arriba_v2.2.1/run_arriba.sh
#sed -i 's#.sortedByCoord.out##g' /tools/arriba_v2.2.1/run_arriba.sh
#sed -i 's#-m $((40000/THREADS))M#-m 1G#g' /tools/arriba_v2.2.1/run_arriba.sh
#sed -i 's#-T tmp#-T "$mapbase/$sample_name/$sample_name".tmp#g' /tools/arriba_v2.2.1/run_arriba.sh
wget -O fusioncatcher.tar.gz https://github.com/ndaniel/fusioncatcher/archive/refs/tags/1.33.tar.gz
tar xzf fusioncatcher.tar.gz
rm fusioncatcher.tar.gz
sed -i 's/2.7.2b/2.7.10a/g' /tools/fusioncatcher-1.33/bin/fusioncatcher.py
wget -O picard.jar https://github.com/broadinstitute/picard/releases/download/2.25.5/picard.jar
mkdir /tools/picard
mv /tools/picard.jar /tools/picard
wget -O bowtie.zip https://github.com/BenLangmead/bowtie/releases/download/v1.2.3/bowtie-1.2.3-linux-x86_64.zip
unzip bowtie.zip -d /tools
rm bowtie.zip
wget -O bowtie2.zip https://github.com/BenLangmead/bowtie2/releases/download/v2.3.5.1/bowtie2-2.3.5.1-linux-x86_64.zip
unzip bowtie2.zip -d /tools
rm bowtie2.zip
wget -O seqtk.tar.gz https://github.com/ndaniel/seqtk/archive/refs/tags/1.2-r101c.tar.gz
tar xzf seqtk.tar.gz
rm seqtk.tar.gz
cd seqtk-1.2-r101c
make
cd ..
wget -O fastqtk.tar.gz https://github.com/ndaniel/fastqtk/archive/refs/tags/v0.27.tar.gz
tar xzf fastqtk.tar.gz
rm fastqtk.tar.gz
cd fastqtk-0.27
make
cd ..
wget -O star.tar.gz https://github.com/alexdobin/STAR/archive/refs/tags/2.7.10a.tar.gz
tar xzf star.tar.gz
rm star.tar.gz
wget -O bbmap.tar.gz https://downloads.sourceforge.net/project/bbmap/BBMap_38.96.tar.gz
tar xzf bbmap.tar.gz
rm bbmap.tar.gz
sed -i 's/38.44/38.96/g' /tools/fusioncatcher-1.33/bin/fusioncatcher.py
wget -O blat.zip https://users.soe.ucsc.edu/~kent/src/blatSrc35.zip
unzip blat.zip
rm blat.zip
MACHTYPE=x86_64
export MACHTYPE
mkdir /home/bin
mkdir /home/bin/$MACHTYPE
mkdir /tools/blat
HOME=/home
export HOME
cd blatSrc
make
mv /home/bin/$MACHTYPE/* /tools/blat
cd ..
rm -Rf /tools/blatSrc
wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver
chmod +x liftOver
mv liftOver /tools/blat
wget http://opengene.org/fastp/fastp.0.23.1
chmod a+x ./fastp.0.23.1
wget -O circos.tgz http://circos.ca/distribution/circos-0.69-9.tgz
tar xzf circos.tgz
chmod +x circos-0.69-9/bin/circos*
rm circos.tgz
%files
./scripts /
%environment
%runscript
/scripts/pipeline.sh
%help
This executes Part1 of the RIFTT pipeline.
Usage:
singularity run --bind <reference file>:/genome.fa,
<annotation file>:/anno.gtf,
<starindex folder>:/star_index,
<path to FusionCatcher data folder>:/fcdata,
<path to outputfolder>:/outputfolder,
<read1 compressed fastq file>:/read1.fastq.gz,
<read2 compressed fastq file>:/read2.fastq.gz
--env sample_name=<name of sample>,
strandness=<0 or 1 or 2>,
threads=<number of threads>,
genomebuild=<hg19 or hg38>,
tasks=<1 1 1 1 1 1> RIFTT.sif