How To Add Hg16 Index Into The Built-In Index / Reference Genome List In Galaxy?

Question

[sachit.adhikari]

How do I add hg16 into the build-in index in Galaxy framework?

[Chris Miller]

Pardon me for asking, but why would you need hg16? That's almost 10 years old.

Answer 1

[Matt Shirley]

Take a look at the documentation. This works in a straightforward way if you have access to the computer Galaxy is running on. If you don't, you'll have to have "admin" rights (add yourself to the admin_users field in the config file) and add enable_beta_job_managers = True to the "beta" section of the config file. Then you can use the new "manage local data" feature.

[sachit.adhikari]

I can't find enablebetajobmanagers = True in universewsgi.ini file.

[Matt Shirley]

You have to add it. This is an option that is not included in the configuration file, and so if you want to use the local data management features you must put it on a line in the "beta" section.

[sachit.adhikari]

I added under # -- Beta features without # and with # restart the server but I can't see Manage Local Data.

[Matt Shirley]

Are you an admin user? You will have to log in as a user with admin permissions and then check under the "admin" menu in the top toolbar.

[sachit.adhikari]

Of course I am an admin user. I tried this but didn't work.

[Matt Shirley]

Are you running a recent version of Galaxy? There is a galaxy-dist and galaxy-central branch. They both should have the code for this feature, and if you take a look at the news brief that announced this feature you will notice it's been there since July. I've used this successfully, so you should take a step back and ask if you've missed any steps. Here is a link to my config file with the relevant bit in it. Note that I'm running on a PBS cluster, so most of the other configuration values will not affect you.

[sachit.adhikari]

Apparently, I was using the old version of Galaxy. I update the Galaxy today and it's working now. Thanks mate!

Answer 2

[sachit.adhikari]

I added under # -- Beta features without # and with # restart the server but I can't see Manage Local Data.