fusetester (DNAnexus Platform App)

Testing 'mounting' of file(s) using FUSE

This is the source code for an app that runs on the DNAnexus Platform. For more information about how to run or modify it, see https://wiki.dnanexus.com/.

You may just want to look at resources/opt/lldxfuse.py as an example of interacting with DNAnexus using fuse. This script could also be run on a local computer (provided you have python-llfuse and the DNAnexus SDK installed) to allow files on DNAnexus to appear to be local. This might be useful for visualization using your favorite genome browser.

I have not really looked into optimizing the number of threads or buffer size, that is left as an exercise to the reader...

This test applet does not do much-- it just loops through each provided BAM file and calls samtools to determine how many reads from chromosome 22 are in each file. Since the index is used, it does not have to read the whole file!

Inputs

• Input BAM files bamfiles: array:file
• Indices for BAM files baifiles: array:file

the corresponding bamfiles and baifiles have to be provided in the same order

Outputs

• There are no outputs-- look at the log. If everything worked, the number of reads for each bamfile from chromosome 22 will be reported.