Bam File IGV Not Working

[ilan-gold]

• Specific code commit:
• Version of the web browser and OS: Any and Mac
• Environment where the error occurred (Vagrant VM and site conf mode or AWS instance):
  AWS

Steps to reproduce

This could potentially be related to #2718 but it is unclear at the moment.

Login as admin and navigate to https://hsci.stemcellcommons.org/data_sets/e3bee913-4b0c-4e61-961e-022086a42619/#/files/

Then launch an IGV on one of the .bam files available.

Observed behavior

This log error seems suspicious

No Data

Expected behavior

No error

[ilan-gold]

there are two parts as to why this likely is not working:

1. Rewrite generate_bam_index() #2718 is problematic in so far as the index file is inaccessible to anything
2. igv appears to need an indexURL parameter for indexed files needed for certain visualizations in igv-js (https://github.com/igvteam/igv.js/wiki/Tracks-2.0)

i am investigating/working on both

[ilan-gold]

testing has completed and have confirmed this to be working - once #3471 and #3475 are resolved i will make the pull request against this and #2718 (as well as a pull request in the https://github.com/refinery-platform/docker_igv_js repo to handle the extra file). i was unable to reproduce the issue seen in the log, and am unsure if it is even a problem (although when talking to geoff/using the viz, it didn't actually affect the launch of the visualization).

[hackdna]

See also #2713