Dockerfile.tabix

#Note that for the upload command to work, the AWS access key and the AWS
# secret key must be args in the docker run command as environment vaiables, 
# along with the WB release and species with bioproject, as below.
# Example invocation:

#     docker build --no-cache -f Dockerfile -t test-gff . 
#     docker run --rm  \
#                -e "WB_RELEASE=280" \
#                -e "WB_SPECIES=c_nigoni_PRJNA384657" \
#                -e "AWS_ACCESS_KEY=<access_key>" \
#                -e "AWS_SECRET_KEY=<secret key>" \
#                 test-wb-gff

# The script "single_species_build.sh" is currently hard coded to do the
# processing and assumes that the target S3 bucket is the one used for AGR's
# main JBrowse instance, agrjbrowse, and the path is /mod-jbrowses/test (but
# this will change with the next WB release),  

# Also note that this image only processes GFF files into NCList json and does
# not deal with processing FASTA data (since it changes relatively infrequently,
# that is the sort of thing that ought to be done "by hand").  It also doesn't
# deal with any other file times like BigWig or VCF.

#FROM gmod/jbrowse-gff-base:latest 
FROM jbrowse_processor_base

LABEL maintainer="scott@scottcain.net"

WORKDIR /

RUN git clone --single-branch --branch main https://github.com/WormBase/website-jbrowse-protein.git
#RUN git clone --single-branch --branch master https://github.com/alliance-genome/agr_jbrowse_config.git

RUN cp  /website-jbrowse-protein/build_with_tabix.sh / 


VOLUME /data
#ENTRYPOINT ["/bin/sh", "/docker-wrapper.sh"]

CMD ["/bin/bash", "/build_with_tabix.sh"]