We are setting up a Galaxy instance (Cloudman, EC2) to teach an RNA-Seq class and would love to include Sailfish or Salmon (in addition to STAR). But, have run into installation errors with both.
We were able to get further with Sailfish, and currently have the following successfully installed from the main toolshed: (1) package_sailfish_0_7_6 (04996d8b8587, iuc) & (2) sailfish (85d0d479f05b, bgruening)
However, Sailfish is not showing up in the Tools list! And we think it might be because the sailfish installation has "sailfish.xml" listed under "Invalid tools."
Any advice on how to fix the above issue with Sailfish or on getting Salmon successfully installed will be much appreciated! Please let me know if I can provide any more information from our end.