Use case scenario:

A user has uploaded or created a BAM file with RNA-Seq data. They would like to create a bedgraph file representing a scaled RNA-Seq coverage graph. However, for the bedgraph to be useful, the file needs to be sorted, compressed, and tabix-indexed. Currently, we have a BioViz CyVerse app that creates a bedgraph file using a tool from the deepTools suite, but the bedgraph file is not compressed or tabix-indexed. Rather than just create the "plain" bedgraph file, let's also create the bedgraph file and then sort, compress, and tabix-index it. This will be much more useful to a user than simply the plain-text, uncompressed, unindexed file.

This will probably require created a docker image where the docker "run" command is actually running a script that we write that does all of the above. Note that you can potentially obtain the original docker image with deepTools and use that to further provision it with tabix/samtools. Also, be sure to save the docker provisioning file (the docker file).

Create a Cyverse analyses app that does two things:

• creates a scaled coverage graph using bamCoverage (from the deepTools suite)
• sorts and tabix-indexes the resulting bedgraph file (the output from bamCoverage)

References:

bamCoverage documentation
How to index a bedgraph
tabix and bgzip in Samtools
Deploying apps in CyVerse
Tool integration in DE

Some examples of scripts that do all of the above can be found in our code repositories in various places. Remind [~aloraine] to provide links to the most relevant repositories and scripts.