Question: Obtaining .nomapping file from GMAP on Galaxy server
gravatar for lrutter0306
4 weeks ago by
lrutter03060 wrote:


I am trying to determine which reads to do not map to a reference genome using GMAP. The only output I need is the .nomapping file. I am having difficulty running this on my personal laptop due to lack of space and wanted to run it on the Galaxy server.

It seems GMAP/GSNAP is not available by default on Galaxy (At least under the NGS:Mapping section, it lists things like BWA, Bowtie2, etc.)

When I type "gmap" into, I do find two instances available. However, when I click on either of these cases, I receive a warning: "Repository installation is not possible due to an invalid Galaxy URL: None. You may need to enable third-party cookies in your browser."

I tried multiple browsers (Chrome and Safari) and tried to enable third-party cookies, but still no luck. I came across similar problem posted here earlier ( There, answers suggest to tweak the universe_wsgi.ini file and to follow instructions on setting up an admin user at, which suggests adding the user's Galaxy email to the config/galaxy.yml file. I am unsure how to even access either of these files (universe_wsgi.ini and config/galaxy.yml). Where are these files located, on the online Galaxy GUI or something I am supposed to download to my own laptop?

Basically, my main questions are: 1) Is it possible for me to run GMAP on Galaxy server (especially being able to create .nomapping file)? 2) If it is possible, is the only way to install the GMAP file from tool shed? 3) If so, how can I remove this warning about third-party cookies in my browser, and if it requires tweaking the aforementioned files, where can I find them?

Sorry for so many questions. I just think if question 1 is not possible, then asking 2 and and 3 are not necessary, so I wanted to list them by hierarchy :)

I greatly appreciate any advice anyone can provide on this!

gmap galaxy nomapping gsnap • 80 views
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