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This repository has been archived by the owner on Dec 13, 2018. It is now read-only.

Containerized version of Bio-Linux 8 tailored for Resolwe.

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genialis/docker-bio-linux8-resolwe

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docker-bio-linux8-resolwe

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UPDATE (2018-12-13)

This Docker image and its corresponding Docker Hub images, resolwe/bio-linux8, resolwe/bio-linux8-resolwe, resolwe/bio-linux8-resolwe-preview, resolwe/bio-linux8-ugly, have been superseeded by Resolwe's and Resolwe Bioinformatics' Docker Hub repositories which contain a set of smaller, modular Docker images.

Therefore, this repository along with its Docker Hub images will be deleted on Mar 13, 2019.

Containerized version of Bio-Linux 8 tailored for Resolwe.

Usage

To start an interactive session in the container, use:

docker run -it resolwe/bio-linux8-resolwe

To instruct Docker to automatically remove the container when it exits, pass the --rm option to the command:

docker run -it --rm resolwe/bio-linux8-resolwe

To mount a local directory inside the container, pass the -v <host-path>:<container-path> option to the command, e.g.:

docker run -it --rm -v $PWD/data_dir:/home/biolinux/data resolwe/bio-linux8-resolwe

NOTE: Use absolute paths to specify <host-path> and <container-path>.

However, if the user and group IDs of the user on the host don't match the user and group IDs of the biolinux user used inside the container, this won't work:

$ docker run -it --rm -v $PWD/data_dir:/home/biolinux/data resolwe/bio-linux8-resolwe \
  touch /home/biolinux/data/foo
touch: cannot touch '/home/biolinux/data/foo': Permission denied

To solve this problem, pass the host user's user and group IDs to the container as HOST_UID and HOST_GID environment variables and the image's entrypoint script will change the biolinux user's user and group IDs automatically:

$ docker run -it --rm -v $PWD/data_dir:/home/biolinux/data \
  -e HOST_UID=$(id -u) -e HOST_GID=$(id -g) resolwe/bio-linux8-resolwe \
  touch /home/biolinux/data/foo
$ ls data_dir | grep foo
foo

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Containerized version of Bio-Linux 8 tailored for Resolwe.

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