gmod/jbrowse-gff-base repository overview

Still under development.

The goal for this base is to be used in other containers that will have scripts to fetch GFF, process it into NCList (the typical format for GFF in JBrowse 1) and then load it into a AWS S3 bucket. Accordingly, this base has typical Linux tools to fetch and extract data (wget, curl, tar, unzip and gzip), JBrowse to provide flatfile_to_json.pl, and the AWS CLI tools to allow transferring to S3. Note that for security, the AWS keys should be passed in on the command line when executing the container and not encoded in the Dockerfile.

Starting with the 1.1 version of this container, it provides the JBrowse 2 command line interface which makes it easy to sort, bgzip, tabix index and name index GFF files.

It also has tabix/bgzip, samtools, bedtools, bcftools and genometools. Other things could be added on request.

The current home for the encoding Dockerfile for this image is at https://github.com/alliance-genome/agr_jbrowse_container/blob/master/Dockerfile.processenv⁠ but it may find a new home as this gets developed.