genialis/docker-bio-linux8-resolwe

Name: docker-bio-linux8-resolwe

Owner: Genialis

Description: Containerized version of Bio-Linux 8 tailored for Resolwe.

Created: 2016-01-22 14:15:18.0

Updated: 2016-11-02 09:59:55.0

Pushed: 2017-08-08 11:36:43.0

Homepage: null

Size: 60

Language: Shell

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README

docker-bio-linux8-resolwe

Containerized version of Bio-Linux 8 tailored for Resolwe.

Usage

To start an interactive session in the container, use:

er run -it resolwe/bio-linux8-resolwe

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

er 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.:

er 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:

cker run -it --rm -v $PWD/data_dir:/home/biolinux/data resolwe/bio-linux8-resolwe \
uch /home/biolinux/data/foo
h: 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:

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