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R2915/singularity-pipeline-runner/bioinformatics_pipeline2.singularity
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bioinformatics_pipeline2.singularity
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Bootstrap: docker
From: centos:7.3.1611
%runscript
#"I can put here whatever I want to happen by default when the user runs the container"
cat << EOF
This container includes the following apps:
Bowtie2/2.2.9 - http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
SAMtools/1.3.1 - http://www.htslib.org/
freebayes/1.1.0 - https://github.com/ekg/freebayes
vcftools/0.1.14 - https://vcftools.github.io
Optional tools only used to download the public data and downsample it:
SRA-Toolkit/2.8.1-3-centos_linux64 - https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std
Seqtk/1.2 - https://github.com/lh3/seqtk
To execute a binary inside the container do "singularity exec /path/to/container.img binary-name"
EOF
%post
echo "Here we are installing software and other dependencies for the container!"
echo "Installing bowtie2-2.2.9"
yum -y install unzip wget
cd /usr/local/src/
wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.9/bowtie2-2.2.9-linux-x86_64.zip
unzip bowtie2-2.2.9-linux-x86_64.zip
cp bowtie2-2.2.9/bowtie2* /usr/local/bin/
echo "Installing samtools-1.3.1"
yum -y install make gcc gcc-c++ zlib-devel bzip2-devel ncurses-devel bzip2
cd /usr/local/src/
wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2
tar xf samtools-1.3.1.tar.bz2
cd /usr/local/src/samtools-1.3.1
./configure
make
make install
echo "Installing freebayes-1.1.0"
yum -y install git cmake
cd /usr/local/src/
git clone --recursive git://github.com/ekg/freebayes.git
# the release system for freebayes does git --recursive which makes hard to reproduce the same installation
# To workaround it I do some git checkout to use the same source code installed in the scicore cluster
cd /usr/local/src/freebayes/ && git checkout 39e5e4b # this is the git commit for freebayes release 1.1.0
cd /usr/local/src/freebayes/SeqLib && git checkout cce1e410ef6d2ac64972f5cacd8a0f9b86cecdd8
cd /usr/local/src/freebayes/SeqLib/bwa && git checkout fbd4dbc03904eccd71cdca8cac7aa48da749c19c
cd /usr/local/src/freebayes/SeqLib/htslib && git checkout 0f298ce22c5c825c506129bf242348a31630c382
cd /usr/local/src/freebayes/SeqLib/fermi-lite && git checkout 5bc90f8d70e2b66184eccbd223a3be714c914365
cd /usr/local/src/freebayes/bamtools && git checkout e77a43f5097ea7eee432ee765049c6b246d49baa
cd /usr/local/src/freebayes/intervaltree && git checkout dbb4c513d1ad3baac516fc1484c995daf9b42838
cd /usr/local/src/freebayes/vcflib && git checkout 5e3ce04f758c6df16bc4d242b18a24d725d2e6e5
cd /usr/local/src/freebayes/vcflib/fsom && git checkout a6ef318fbd347c53189384aef7f670c0e6ce89a3
cd /usr/local/src/freebayes/vcflib/intervaltree && git checkout b704f195e9b51d44dad68e33c209b06e63ebb353
cd /usr/local/src/freebayes/vcflib/smithwaterman && git checkout 84c08d7eae7211d87fbcb1871dae20e6c2041e96
cd /usr/local/src/freebayes/vcflib/fastahack && git checkout c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd
cd /usr/local/src/freebayes/vcflib/filevercmp && git checkout 1a9b779b93d0b244040274794d402106907b71b7
cd /usr/local/src/freebayes/vcflib/tabixpp/htslib/ && git checkout 0f298ce22c5c825c506129bf242348a31630c382
cd /usr/local/src/freebayes/vcflib/tabixpp && git checkout 80012f86dc22b13c75b73baf38195956db92473e
cd /usr/local/src/freebayes/vcflib/multichoose && git checkout 73d35daa18bf35729b9ba758041a9247a72484a5
cd /usr/local/src/freebayes/vcflib/googletest/ && git checkout d225acc90bc3a8c420a9bcd1f033033c1ccd7fe0
cd /usr/local/src/freebayes/
make
make install
echo "Installing vcftools-0.1.14"
cd /usr/local/src
wget https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz
tar xf vcftools-0.1.14.tar.gz
cd vcftools-0.1.14
./configure
make
make install
echo "Installing seqtk-1.2-r94"
cd /usr/local/src
wget https://github.com/lh3/seqtk/archive/v1.2.tar.gz
tar xf v1.2.tar.gz
cd /usr/local/src/seqtk-1.2/
make
cp /usr/local/src/seqtk-1.2/seqtk /usr/local/bin/
echo "Installing SRA-Toolkit/2.8.1-3-centos_linux64"
yum -y install wget
cd /usr/local/src
wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.1-3/sratoolkit.2.8.1-3-centos_linux64.tar.gz
tar xf sratoolkit.2.8.1-3-centos_linux64.tar.gz
cp -ra /usr/local/src/sratoolkit.2.8.1-3-centos_linux64/bin/* /usr/local/bin/
rm -fr /usr/local/src/sratoolkit.2.8.1-3-centos_linux64/
yum -y clean all
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