CIF-parsers/container.def at master · cod-developers/CIF-parsers · GitHub

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Bootstrap: docker
From: debian:unstable

%files
    patches /usr/local/CIF-parsers/patches
    downloads /usr/local/CIF-parsers/downloads

%post
    apt-get update

    apt-get install --yes cif-linguist cod-tools gemmi groovy libciftools-java libcifxom-java make openbabel patch python3-ase python3-pycifrw python3-pymatgen wget

    # cif2cif
    apt-get install --yes csh gfortran ncompress
    (
        mkdir --parents /usr/local/install/cif2cif && cd /usr/local/install/cif2cif
        for PKG in ciftbx cif2cif
        do
            wget http://www.bernstein-plus-sons.com/cgi-bin/yaya/decomp.cgi/NDB/mmcif/software/ciftbx_4.1.0/$PKG.cshar
            csh $PKG.cshar
            ( cd $PKG.src && make )
        done
        cd /usr/local/bin
        ln -s /usr/local/install/cif2cif/cif2cif.src/cif2cif
    )

    # crystcif-parse
    apt-get install --yes npm
    (
        mkdir --parents /usr/local/install/crystcif-parse && cd /usr/local/install/crystcif-parse
        npm install crystcif-parse
        cd /usr/local/bin
        ln -s /usr/local/install/crystcif-parse/node_modules/crystcif-parse/bin/validate.js
    )

    # STAR::Parser is installed from the IUCr website
    apt-get install --yes cpanminus
    (
        DOWNLOAD_DIR="/usr/local/CIF-parsers/downloads"
        mkdir --parents /tmp/starparser && cd /tmp/starparser
        if ! [ -f "${DOWNLOAD_DIR}"/STAR-Parser-0.59.tar.gz ]
        then
                wget https://www.iucr.org/__data/iucr/cif/software/starparser/STAR-Parser-0.59.tar.gz
        else
                cp -av "${DOWNLOAD_DIR}"/STAR-Parser-0.59.tar.gz /tmp/starparser
        fi
        cpanm STAR-Parser-0.59.tar.gz
        tar -xf STAR-Parser-0.59.tar.gz
        cp STAR-Parser-0.59/bin/parse.pl /usr/local/bin/star-parse
        sed -i 's/\/usr\/local\/bin\/perl/\/usr\/bin\/perl/' /usr/local/bin/star-parse
        rm -rf /tmp/starparser
    )

    # vcif
    (
        DOWNLOAD_DIR="/usr/local/CIF-parsers/downloads"
        mkdir --parents /usr/local/install/vcif && cd /usr/local/install/vcif
        if ! [ -f "${DOWNLOAD_DIR}"/vcif-1.2.2.tar.gz ]
        then
                wget https://www.iucr.org/resources/cif/software/archived/vcif-1.2/vcif-1.2.2.tar.gz
        else
                cp -av "${DOWNLOAD_DIR}"/vcif-1.2.2.tar.gz /usr/local/install/vcif
        fi
        tar -xf vcif-1.2.2.tar.gz && rm vcif-1.2.2.tar.gz
        cd vcif-1.2.2
        make
        cd /usr/local/bin
        ln -s /usr/local/install/vcif/vcif-1.2.2/vcif
    )

    # zinc
    apt-get install --yes bison gcc
    (
        DOWNLOAD_DIR="/usr/local/CIF-parsers/downloads"
        mkdir --parents /usr/local/install/zinc && cd /usr/local/install/zinc
        if ! [ -f "${DOWNLOAD_DIR}"/zinc.tar.Z ]
        then
                wget https://www.iucr.org/__data/iucr/cif/software/zinc/zinc.tar.Z
        else
                cp -av "${DOWNLOAD_DIR}"/zinc.tar.Z /usr/local/install/zinc
        fi
        tar -xf zinc.tar.Z && rm zinc.tar.Z
        patch Makefile < /usr/local/CIF-parsers/patches/zinc.diff
        make CFLAGS='-Wno-implicit-int -Wno-implicit-function-declaration -Wno-return-mismatch'
        cd /usr/local/bin
        ln -s /usr/local/install/zinc/cifZinc
    )