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camibase

camibase is a Docker image which serves as basis for building user-specific containers.

Usage

  1. Pull container using docker pull cami/base
  2. Add/install software in your container (refer to the manual for building an application container)
  3. Add a file with the commands to run using the defined variables (refer to the manual for building an application container)
  4. Save you container as a named image (refer to the manual for building an application container)
  5. Run the resulting docker container using docker run [docker options] myimage mytask

Variables for use in container

Please only use the following environment variables in your scripts and applications. Do not use absolute paths except for mounting the host volumes to the container (this is a limitation of the docker commmand). To see the actual content of these variables, etc. for mounting, see the output of docker run cami/base --list-mount. To see an exhaustive list of defined variables, see the output of docker run cami/base --list-var.

$DCKR_INFILE: single input FASTA file

$DCKR_OUTFILE: single output file

$DCKR_CAMIREF: folder containig provided reference data(bases)

$DCKR_CACHE: folder to save data which is persistent between consecutive container executions

$DCKR_USERREF: folder containing all data uploaded/provided by the user

$DCKR_THREADS: number of threads to be used by processes running in the container

$DCKR_USER: optional non-root user to be used in the container (Dockerfile statement USER)

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cami
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