Question: Installing Sailfish or Salmon
0
gravatar for rkhetani
20 months ago by
rkhetani0
Boston, MA
rkhetani0 wrote:

Hi everyone,

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.

Thanks!!

rna-seq salmon sailfish • 694 views
ADD COMMENTlink modified 20 months ago by Martin Čech ♦♦ 4.6k • written 20 months ago by rkhetani0

Do you know if you installed Sailfish dependency using Conda or Tool Shed?

ADD REPLYlink written 20 months ago by Martin Čech ♦♦ 4.6k

Martin, we installed it using Tool Shed.

ADD REPLYlink written 20 months ago by rkhetani0
1
gravatar for Martin Čech
20 months ago by
Martin Čech ♦♦ 4.6k
United States
Martin Čech ♦♦ 4.6k wrote:

I installed sailfish locally and I am unable to reproduce your 'invalid tool' error. Did you restart your Galaxy after the installation?

ADD COMMENTlink written 20 months ago by Martin Čech ♦♦ 4.6k

No, we did not restart. Doing it right now, will post back after. Sorry, I did not realize we had to restart; thanks for the suggestion!

ADD REPLYlink written 20 months ago by rkhetani0

Restarted Galaxy, but unfortunately nothing has changed. Sailfish is not in the tools menu even though it is installed, and "sailfish.xml" is still registering as an "Invalid tool".

Let me know if you think it's cleaner to install with Conda (I have no experience with it on AWS, but can give it a shot). Thanks!

ADD REPLYlink modified 20 months ago • written 20 months ago by rkhetani0

I would try uninstalling and installing again (including the packages). Invalid tool error should not happen inconsistently for a tool. :/

Try watching the Galaxy logs during the installation to see whether there is some issue shown there.

ADD REPLYlink written 20 months ago by Martin Čech ♦♦ 4.6k

Okay, I will try uninstalling both and reinstalling. Will post the results here; fingers are crossed!

Thanks Martin!

ADD REPLYlink written 20 months ago by rkhetani0
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