diff --git a/docker/Dockerfile b/docker/Dockerfile index 629a100..e7b73a6 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -2,39 +2,43 @@ FROM centos:6.10 COPY CentOS-Base.repo /etc/yum.repos.d/ + RUN yum update -y && \ yum upgrade -y && \ yum install -y xz git libzip-devel curl wget zlib-devel xz-devel bzip2-devel openssl-devel libcurl-devel -RUN wget http://people.centos.org/tru/devtools-2/devtools-2.repo -O /etc/yum.repos.d/devtools-2.repo && \ +RUN wget --no-check-certificate http://people.centos.org/tru/devtools-2/devtools-2.repo -O /etc/yum.repos.d/devtools-2.repo && \ yum install -y devtoolset-2-gcc RUN yum install -y devtoolset-2-binutils devtoolset-2-gcc-c++ && \ source scl_source enable devtoolset-2 && \ echo "source scl_source enable devtoolset-2" >> ~/.bashrc && \ - echo "source scl_source enable devtoolset-2" >> ~/.bash_profile && \ - wget --quiet https://ftp.gnu.org/gnu/m4/m4-1.4.18.tar.gz + echo "source scl_source enable devtoolset-2" >> ~/.bash_profile + RUN source scl_source enable devtoolset-2 && \ - wget --quiet https://ftp.gnu.org/gnu/m4/m4-1.4.18.tar.gz && \ + wget --quiet --no-check-certificate https://ftp.gnu.org/gnu/m4/m4-1.4.18.tar.gz && \ tar xzf m4-1.4.18.tar.gz && cd m4* && ./configure && make && make install && cd .. && rm -rf m4* && \ - wget --quiet http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz && \ + wget --no-check-certificate --quiet http://ftp.gnu.org/gnu/autoconf/autoconf-2.69.tar.gz && \ tar xzf autoconf-2.69.tar.gz && \ cd autoconf* && ./configure && make && make install && cd .. && rm -rf autoconf* && \ git clone --depth 1 https://github.com/ebiggers/libdeflate.git && \ cd libdeflate && make -j 2 CFLAGS='-fPIC -O3' libdeflate.a && \ cp libdeflate.a /usr/local/lib && cp libdeflate.h /usr/local/include && \ cd .. && rm -rf libdeflate && \ - git clone https://github.com/samtools/htslib && \ - cd htslib && git checkout 1.10 && autoheader && autoconf && \ - ./configure --enable-libcurl --with-libdeflate && \ + git clone --recursive https://github.com/samtools/htslib && \ + cd htslib && git checkout 1.13 && autoheader && autoconf && \ + ./configure --disable-libcurl --with-libdeflate && \ cd .. && make -j4 CFLAGS="-fPIC -O3" -C htslib install && \ - echo "/usr/local/lib" >> etc/ld.so.conf && \ - ldconfig + git clone https://github.com/samtools/bcftools && \ + cd bcftools && git checkout 1.13 && autoheader && autoconf && \ + ./configure --disable-libcurl --with-libdeflate --disable-bcftools-plugins && \ + cd .. && make -j4 PLUGINS_ENABLED=no CFLAGS="-O3" -C bcftools install && \ + echo "/usr/local/lib" >> etc/ld.so.conf RUN cd / \ - && wget --progress=dot:giga https://github.com/nim-lang/nightlies/releases/download/2020-12-22-devel-297c8e403d110dd872e070563328f4e0c734cd01/nim-1.5.1-linux_x64.tar.xz \ + && wget --no-check-certificate --progress=dot:giga https://github.com/nim-lang/nightlies/releases/download/2020-12-22-devel-297c8e403d110dd872e070563328f4e0c734cd01/nim-1.5.1-linux_x64.tar.xz \ && tar Jxf nim-1.5.1-linux_x64.tar.xz \ && rm -f nim-1.5.1-linux_x64.tar.xz \ && mv nim-1.5.1 nim && \ @@ -42,7 +46,8 @@ RUN cd / \ echo 'PATH=/nim/bin:/root/.nimble/bin:$PATH' >> ~/.bash_profile -RUN cd / && \ +RUN cd / && \ + ldconfig && \ source scl_source enable devtoolset-2 && \ export PATH=/nim/bin:$PATH && \ git clone https://github.com/iffy/nim-argparse && cd nim-argparse && git checkout v0.10.1 && nimble install -y && \ @@ -50,7 +55,7 @@ RUN cd / && \ git clone --depth 1 git://github.com/brentp/slivar.git && \ cd slivar && \ sed -i 's/-no-pie//' nim.cfg && \ - nimble install -y && \ + nimble install -y && \ nim c -d:release -d:danger -o:/usr/bin/slivar src/slivar && \ mkdir -p /opt/slivar/ && cp js/slivar-functions.js /opt/slivar/ && \ rm -rf /slivar /duktape-nim && slivar expr -h