Dockerfile

FROM cami/interface

# add interface definition
COPY dockermount.conf /dckr/etc/
COPY list-spec.sh /dckr/etc/tasks.d/--list-spec
COPY print_version.sh /dckr/etc/tasks.d/--version

# Folder optionally containing all data uploaded by the user
ENV DCKR_USERREF $DCKR_MNT/userref

# This variable MUST specify the absolute path, inside the container, of a file containing the absolute paths to gzipped FASTQ files.
ENV CONT_FASTQ_FILE_LISTING $DCKR_MNT/input/sample.fq.gz.list

# This variable MUST specify the absolute path, inside the container, of a file containing the absolute paths to gzipped FASTQ files
ENV CONT_PAIRED_FASTQ_FILE_LISTING $DCKR_MNT/input/sample.interleaved.fq.gz.list

# This variable MUST specify the absolute path, inside the container, to a file containing absolute paths to contig FASTA files
ENV CONT_CONTIGS_FILE_LISTING $DCKR_MNT/input/sample.fna.list

# This variable specifies the absolute path of where the files containing the computed binning and/or taxonomic groups must be created
ENV CONT_PROFILING_FILES $DCKR_MNT/output

# folder containig provided reference data(bases)
ENV CONT_DATABASES_DIR $DCKR_MNT/camiref