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rifdock-recipes

Conda recipes for rifdock.

Building

There are two phases of builds that are required: building conda packages and a docker image. First, build the conda packages for rifdock and its rosetta dependency with the following commands:

./docker_build.sh rosetta_omp [CONDA CHANNEL PATH] [GITHUB TOKEN FILE]
./docker_build.sh rifdock [CONDA CHANNEL PATH] [GITHUB TOKEN FILE]

Some notes about the above commands:

  1. [GITHUB TOKEN FILE] is a file containing a GitHub API/Personal access token. The token must be scoped with at least the entire repo scope.

    • The [GITHUB TOKEN FILE] is required since the Rosetta repository is private.

  2. [CONDA CHANNEL PATH] is where docker_build.sh will place the build artifacts.

    • The [CONDA CHANNEL PATH] directory can either be an empty directory or an already-initialized conda channel directory.

Those packages do not need to built again unless there is a compelling upstream update that we'd like to use. That being said, as our workflow evolves, we may wish to capture that in our container by including additional scripts or tools. To build an image with rifdock installed via conda, use the following command:

./create_rifdock_image.sh [CONDA CHANNEL PATH]

Using

Move the exported image to your work machine, and load the image with the following command

docker load < rifdock.latest.tar

then you can get an interactive session in the container with

docker run -it rifdock:latest bin/bash

or run a rif command directly

docker run \
           -v [RIF INPUT DIR]:/home/conda/rif:rw,z \
           -e HOST_USER_ID=$(id -u) \
           rifdock:latest \
           /bin/bash -c "cd /home/conda/rif && rifgen @rifgen.flags"

where the RIF INPUT DIR and the precise command (in quotes) should be adjusted based on your usecase.