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FROM ubuntu:18.04
RUN apt-get update && \
apt-get install -y \
autoconf \
automake \
make \
gcc \
perl \
zlib1g-dev \
libbz2-dev \
liblzma-dev \
libcurl4-gnutls-dev \
libssl-dev \
libncurses5-dev \
libtool \
libboost-dev \
pkg-config \
wget
WORKDIR /soft
#htslib 1.15.1 released 2022-04-07
RUN wget https://github.com/samtools/htslib/releases/download/1.15.1/htslib-1.15.1.tar.bz2 && \
tar -vxjf htslib-1.15.1.tar.bz2 && \
rm -f htslib-1.15.1.tar.bz2 && \
cd htslib-1.15.1 && \
./configure --prefix=/soft/htslib-1.15.1 && \
make -j && \
make -j install
#libdeflate 1.11 relesed 2022-05-24
RUN wget https://github.com/ebiggers/libdeflate/archive/refs/tags/v1.11.tar.gz && \
tar -vxf v1.11.tar.gz && \
rm -f v1.11.tar.gz && \
cd libdeflate-1.11 && \
make -j && \
make -j install PREFIX=/soft/libdeflate-1.11
#samtools 1.15.1 released 2022-04-07
RUN wget https://github.com/samtools/samtools/releases/download/1.15.1/samtools-1.15.1.tar.bz2 && \
tar -vxjf samtools-1.15.1.tar.bz2 && \
rm -f samtools-1.15.1.tar.bz2 && \
cd samtools-1.15.1 && \
./configure --with-libdeflate=/soft/libdeflate-1.11 --with-htslib=/soft/htslib-1.15.1 --prefix=/soft/samtools-1.15.1 && \
make -j && \
make -j install
#gcc update for libmaus2 to work
RUN apt-get update && \
apt-get install software-properties-common -y && \
add-apt-repository ppa:ubuntu-toolchain-r/test && \
apt-get install gcc-11 g++-11 -y && \
update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-11 100 \
--slave /usr/bin/g++ g++ /usr/bin/g++-11 --slave /usr/bin/gcov gcov /usr/bin/gcov-11
#libmouse2 2.0.810-release-20220216151520 for biobambam2
RUN wget https://gitlab.com/german.tischler/libmaus2/-/archive/2.0.810-release-20220216151520/libmaus2-2.0.810-release-20220216151520.tar.bz2 && \
tar -vxjf libmaus2-2.0.810-release-20220216151520.tar.bz2 && \
rm -f libmaus2-2.0.810-release-20220216151520.tar.bz2 && \
cd libmaus2-2.0.810-release-20220216151520 && \
libtoolize && \
aclocal && \
autoreconf -i -f && \
./configure --prefix=/soft/libmaus2-2.0.810-release-20220216151520 && \
make -j && \
make -j install
#biobambam2 2.0.183-release-20210802180148
RUN wget https://gitlab.com/german.tischler/biobambam2/-/archive/2.0.183-release-20210802180148/biobambam2-2.0.183-release-20210802180148.tar.bz2 && \
tar -vxjf biobambam2-2.0.183-release-20210802180148.tar.bz2 && \
rm -f biobambam2-2.0.183-release-20210802180148.tar.bz2 && \
cd biobambam2-2.0.183-release-20210802180148 && \
autoreconf -if && \
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/soft/libmaus2-2.0.810-release-20220216151520/lib/pkgconfig && \
./configure --with-libmaus2=/soft/libmaus2-2.0.810-release-20220216151520 --prefix=/soft/biobambam2-2.0.183-release-20210802180148 && \
make -j install
ENV PATH=${PATH}:/soft/htslib-1.15.1/bin:/soft/libdeflate-1.11/bin:/soft/samtools-1.15.1/bin
ENV PATH=${PATH}:/soft/libmaus2-2.0.810-release-20220216151520/bin:/soft/biobambam2-2.0.183-release-20210802180148/bin