- V2.0 Note. The Docker container has not yet been updated.
- Will do that once we it looks like this new release is stable.
With this release, I am including infrastructure to help those using Docker containers. This may help people who have difficulty building the software from scratch - although you will need to install and configure docker instead docker.
In the distro, there is a Dockerfile which I have used to generate a Docker image that has been pushed to Docker Hub. Retrieve to your local Docker environment via
docker pull ianwatson/lilly_medchem_rules:v1.2
The image is built on a gcc image, then goes to some trouble to
install Ruby, via rvm. Perhaps a better approach might be to start
with a Ruby image and add gcc to that.
The image has a CMD that will consume a smiles file via stdin and output surviving molecules to stdout.
docker run -i -a stdout -a stdin ianwatson/lilly_medchem_rules:v1.2 < file.smi
There is a script in the container run_from_docker_image.sh that will
mount a local file directory containing a smiles file, into the image
and run the rules on that input file. The bad*.smi files and the
log files will be written to that same directory, while the surviving
molecules will be written to stdout. Easy would be to copy that file
to somewhere outside the image and use it there.
I would welcome any feedback on this initial container implementation, since I am no expert. But I do want to provide an alternative for people encountering build difficulties.