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R2915/SIS/scicore_pipeline2_LSF/Dockerfile
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FROM centos:7.3.1611
RUN echo "Here we are installing software and other dependencies for the container!"
RUN echo "Installing bowtie2-2.2.9"
RUN yum -y install unzip wget
RUN cd /usr/local/src && wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.9/bowtie2-2.2.9-linux-x86_64.zip
RUN cd /usr/local/src && unzip bowtie2-2.2.9-linux-x86_64.zip
RUN cp bowtie2-2.2.9/bowtie2* /usr/local/bin/
RUN echo "Installing samtools-1.3.1"
RUN yum -y install make gcc gcc-c++ zlib-devel bzip2-devel ncurses-devel bzip2 wget
RUN cd /usr/local/src && wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2
RUN cd /usr/local/src && tar xf samtools-1.3.1.tar.bz2
RUN cd /usr/local/src/samtools-1.3.1 && ./configure && make && make install
RUN echo "Installing freebayes-1.1.0"
RUN yum -y install git cmake
RUN 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
RUN cd /usr/local/src/freebayes/ && git checkout 39e5e4b # this is the git commit for freebayes release 1.1.0
RUN cd /usr/local/src/freebayes/SeqLib && git checkout cce1e410ef6d2ac64972f5cacd8a0f9b86cecdd8
RUN cd /usr/local/src/freebayes/SeqLib/bwa && git checkout fbd4dbc03904eccd71cdca8cac7aa48da749c19c
RUN cd /usr/local/src/freebayes/SeqLib/htslib && git checkout 0f298ce22c5c825c506129bf242348a31630c382
RUN cd /usr/local/src/freebayes/SeqLib/fermi-lite && git checkout 5bc90f8d70e2b66184eccbd223a3be714c914365
RUN cd /usr/local/src/freebayes/bamtools && git checkout e77a43f5097ea7eee432ee765049c6b246d49baa
RUN cd /usr/local/src/freebayes/intervaltree && git checkout dbb4c513d1ad3baac516fc1484c995daf9b42838
RUN cd /usr/local/src/freebayes/vcflib && git checkout 5e3ce04f758c6df16bc4d242b18a24d725d2e6e5
RUN cd /usr/local/src/freebayes/vcflib/fsom && git checkout a6ef318fbd347c53189384aef7f670c0e6ce89a3
RUN cd /usr/local/src/freebayes/vcflib/intervaltree && git checkout b704f195e9b51d44dad68e33c209b06e63ebb353
RUN cd /usr/local/src/freebayes/vcflib/smithwaterman && git checkout 84c08d7eae7211d87fbcb1871dae20e6c2041e96
RUN cd /usr/local/src/freebayes/vcflib/fastahack && git checkout c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd
RUN cd /usr/local/src/freebayes/vcflib/filevercmp && git checkout 1a9b779b93d0b244040274794d402106907b71b7
RUN cd /usr/local/src/freebayes/vcflib/tabixpp/htslib/ && git checkout 0f298ce22c5c825c506129bf242348a31630c382
RUN cd /usr/local/src/freebayes/vcflib/tabixpp && git checkout 80012f86dc22b13c75b73baf38195956db92473e
RUN cd /usr/local/src/freebayes/vcflib/multichoose && git checkout 73d35daa18bf35729b9ba758041a9247a72484a5
RUN cd /usr/local/src/freebayes/vcflib/googletest/ && git checkout d225acc90bc3a8c420a9bcd1f033033c1ccd7fe0
RUN cd /usr/local/src/freebayes/ && make && make install
RUN echo "Installing vcftools-0.1.14"
RUN cd /usr/local/src && wget https://github.com/vcftools/vcftools/releases/download/v0.1.14/vcftools-0.1.14.tar.gz
RUN cd /usr/local/src && tar xf vcftools-0.1.14.tar.gz
RUN cd /usr/local/src && cd vcftools-0.1.14 && ./configure && make && make install
RUN echo "Installing seqtk-1.2-r94"
RUN cd /usr/local/src && wget https://github.com/lh3/seqtk/archive/v1.2.tar.gz
RUN cd /usr/local/src && tar xf v1.2.tar.gz
RUN cd /usr/local/src/seqtk-1.2/ && make
RUN cp /usr/local/src/seqtk-1.2/seqtk /usr/local/bin/
RUN echo "Installing SRA-Toolkit/2.8.1-3-centos_linux64"
RUN 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
RUN cd /usr/local/src && tar xf sratoolkit.2.8.1-3-centos_linux64.tar.gz
RUN cp -ra /usr/local/src/sratoolkit.2.8.1-3-centos_linux64/bin/* /usr/local/bin/
RUN rm -rf /usr/local/src/sratoolkit.2.8.1-3-centos_linux64/
RUN yum -y clean all
RUN mkdir /data
RUN mkdir /output
ENTRYPOINT ["echo", "-e", "This container includes the following apps:\\n\
Bowtie2/2.2.9 - http://bowtie-bio.sourceforge.net/bowtie2/index.shtml\\n\
SAMtools/1.3.1 - http://www.htslib.org/\\n\
freebayes/1.1.0 - https://github.com/ekg/freebayes\\n\
vcftools/0.1.14 - https://vcftools.github.io\\n\
Optional tools only used to download the public data and downsample it:\\n\
SRA-Toolkit/2.8.1-3-centos_linux64 - https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std \\n\
Seqtk/1.2 - https://github.com/lh3/seqtk\\n\
To execute a binary inside the container do \"singularity exec /path/to/container.img binary-name\""]
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