Thanks Markus -- great pointer.
This kind of works for me now (just as you suggested -- install python 3.5
and everything in that environment).
FROM continuumio/miniconda3
MAINTAINER Greg Landrum <greg.land...@gmail.com>
ENV LANG C
# install and activate python 3.5 -- this is a requirement below
RUN conda create -n py35 python=3.5
ENV PATH /opt/conda/envs/py35/bin:$PATH
# install the RDKit:
RUN conda config --add channels https://conda.anaconda.org/rdkit
# note including jupyter in this brings in rather a lot of extra stuff
RUN conda install --name py35 -y nomkl rdkit pandas cairo cairocffi jupyter
RUN mkdir /notebooks
CMD jupyter-notebook --ip="*" --no-browser --allow-root
--notebook-dir=/notebooks
On 21 November 2017 at 18:51, Markus Sitzmann <markus.sitzm...@gmail.com>
wrote:
> Hi JP,
>
> From the Docker log you posted it is obvious that the build starts from
> the latest miniconda version which than will use python 3.6 as default,
> however one of the python packages still relies python 3.5.
>
> One thing you can try is to tell the conda install command in the docker
> script to go back to python 3.5 or create a python 3.5 based environment.
> Unfortunately I just don’t remember out of my head which option you have to
> use for this but you fill find it in the conda documentation.
>
> And as much I like the idea of conda, it is unfortunately one of the
> biggest troublemakers in my personal projects.
>
> Another point is, if you look for one of the recent post from Greg here on
> the list, there is another problem with the latest conda version you might
> run into.
>
>
> Markus
>
>
> -------------------------------------
> | Markus Sitzmann
> | markus.sitzm...@gmail.com
>
> On 21. Nov 2017, at 16:53, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
>
> I've got some dockerfiles that might be worth a look.
> https://github.com/InformaticsMatters/docker_jupyter
>
> Not sure if they will help.
>
> Tim
>
>
>
> On 21/11/2017 15:25, JP wrote:
>
> Yo RDKitters,
>
> I am running a CADD workshop for a group of MSc students and would like to
> show them some some RDKit awesomeness.
>
> I thought the best way to do this is to use an rdkit enabled docker image
> + jupyter notebooks (they are comfortable with python).
>
> In preparation, I tried building the docker image from the docker file at
> https://github.com/rdkit/rdkit_containers/tree/master/docker/run_conda3
> but this fails on Ubuntu 16.04.3 LTS with the following error:
>
> $ docker build -t run_rdkit_conda https://raw.githubusercontent.
> com/rdkit/rdkit_containers/master/docker/run_conda3/Dockerfile
> Downloading build context from remote url: https://raw.githubusercontent.
> com/rdkit/rdkit_containers/master/docker/run_conda3/Dockerfile 357B
> Sending build context to Docker daemon 2.048kB
> Step 1/7 : FROM continuumio/miniconda3
> latest: Pulling from continuumio/miniconda3
> 85b1f47fba49: Pull complete
> 6b3cb0c49789: Pull complete
> fecb432dacf0: Pull complete
> f461f7e3890d: Pull complete
> Digest: sha256:604cda0c0be5d40cc26db31912d8b1
> b7276840a56544b846abef441b32d987fc
> Status: Downloaded newer image for continuumio/miniconda3:latest
> ---> f700f7f570c7
> Step 2/7 : MAINTAINER Greg Landrum <greg.land...@gmail.com>
> ---> Running in ad6a648c18ba
> ---> 18e6d6093d5b
> Removing intermediate container ad6a648c18ba
> Step 3/7 : ENV PATH /opt/conda/bin:$PATH
> ---> Running in e21cf8e5332f
> ---> ddef65292068
> Removing intermediate container e21cf8e5332f
> Step 4/7 : ENV LANG C
> ---> Running in efa12ef17f37
> ---> 137d7e20350d
> Removing intermediate container efa12ef17f37
> Step 5/7 : RUN conda config --add channels https://conda.anaconda.org/
> rdkit
> ---> Running in 79566bf4b6e9
> ---> 032965875391
> Removing intermediate container 79566bf4b6e9
> Step 6/7 : RUN conda install -y nomkl rdkit pandas cairo cairocffi jupyter
> ---> Running in c5aa6417a63a
> Fetching package metadata .............
> Solving package specifications: .
>
> UnsatisfiableError: The following specifications were found to be in
> conflict:
> - cairocffi -> python 3.5* -> xz 5.0.5
> - python 3.6*
> Use "conda info <package>" to see the dependencies for each package.
>
> The command '/bin/sh -c conda install -y nomkl rdkit pandas cairo
> cairocffi jupyter' returned a non-zero code: 1
>
> Any ideas?
> JP
>
>
> ------------------------------------------------------------------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
>
>
> _______________________________________________
> Rdkit-discuss mailing
> listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
