Re: [Open Babel] Python Docker image
On 2nd thought maybe just apk-installing libxrender: https://pkgs.alpinelinux.org/package/v3.4/main/x86/libxrender will do the trick. When something on linux says #!/bin/sh and doesn't work when sh is not bash, it's about par for the course. Same as linux C code that works on both kinds of C: GNU C and GNU libc. Dima ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Python Docker image
On 4/6/2019 3:04 AM, moritz.be...@gmail.com wrote: Thanks for the hint to use conda. However, maybe alpine-glibc is the wrong base image? You snuck a /bin/bash in there and when I change that to /bin/sh or /bin/ash I get a lot of errors upon importing pybel. That image is for a service sitting behind uwsgi so there is no GUI, looks like that's the main problem. I don't think conda will work without glibc, but I'm not sure it takes to pull the GUI subsystem in alpine. So maybe try starting from one of the debian or centos conda images instead? Dima ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Python Docker image
Thanks for the hint to use conda. However, maybe alpine-glibc is the wrong base image? You snuck a /bin/bash in there and when I change that to /bin/sh or /bin/ash I get a lot of errors upon importing pybel. >>> import pybel == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/stlformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/pngformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/pubchem.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/APIInterface.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/MCDLformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/gulpformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/pwscfformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/MNAformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/acrformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/mopacformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/bgfformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/acesformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/boxformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/cdxmlformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/reportformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/opendxformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/orcaformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/dlpolyformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/amberformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/inchiformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/crkformat.so did not load properly. Error: libXrender.so.1: cannot open shared object file: No such file or directory == *** Open Babel Error in openLib /opt/anaconda/lib/openbabel/2.4.1/rsmiformat.so did not load pr
Re: [Open Babel] Python Docker image
On 4/2/19 7:42 PM, Dimitri Maziuk via OpenBabel-discuss wrote: sorry, too much trimming: > FROM frolvlad/alpine-glibc > RUN echo 'export PATH=/opt/anaconda/bin:$PATH' > > /etc/profile.d/anaconda.sh && \ > wget --quiet \ > https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \ > -O ~/anaconda.sh && \ > /bin/bash ~/anaconda.sh -b -p /opt/anaconda && \ > rm ~/anaconda.sh > ENV PATH /opt/anaconda/bin:$PATH RUN conda install -y -c openbabel openbabel -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Python Docker image
On 4/2/19 6:45 PM, moritz.be...@gmail.com wrote: > Hi all, > > I'm building Docker images for openbabel with Python bindings for > Python versions 3.6 - 3.8 from source. Don't. FROM frolvlad/alpine-glibc RUN echo 'export PATH=/opt/anaconda/bin:$PATH' > /etc/profile.d/anaconda.sh && \ wget --quiet \ https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh \ -O ~/anaconda.sh && \ /bin/bash ~/anaconda.sh -b -p /opt/anaconda && \ rm ~/anaconda.sh ENV PATH /opt/anaconda/bin:$PATH RUN conda install -y -c rdkit rdkit -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
