Re: [Rdkit-discuss] Docker with (latest) rdkit+jupyter

2017-11-22 Thread JP 
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 

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 
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  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 
>  ---> 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 " 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
>
> ___
>

Re: [Rdkit-discuss] Docker with (latest) rdkit+jupyter

2017-11-21 Thread Markus Sitzmann 
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  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: 
>> sha256:604cda0c0be5d40cc26db31912d8b1b7276840a56544b846abef441b32d987fc
>> Status: Downloaded newer image for continuumio/miniconda3:latest
>>  ---> f700f7f570c7
>> Step 2/7 : MAINTAINER Greg Landrum 
>>  ---> 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 " 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 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

Re: [Rdkit-discuss] Docker with (latest) rdkit+jupyter

2017-11-21 Thread Tim Dudgeon 

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: 
sha256:604cda0c0be5d40cc26db31912d8b1b7276840a56544b846abef441b32d987fc

Status: Downloaded newer image for continuumio/miniconda3:latest
 ---> f700f7f570c7
Step 2/7 : MAINTAINER Greg Landrum >

 ---> 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 " 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 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

[Rdkit-discuss] Docker with (latest) rdkit+jupyter

2017-11-21 Thread JP 
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:
sha256:604cda0c0be5d40cc26db31912d8b1b7276840a56544b846abef441b32d987fc
Status: Downloaded newer image for continuumio/miniconda3:latest
 ---> f700f7f570c7
Step 2/7 : MAINTAINER Greg Landrum 
 ---> 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 " 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 list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss