Galaxy Tutorial: Bacterial assembly, variant calling and annotation

[nickloman]

This is a lovely tutorial from Torsten Seemann and team that demonstrates the use of GVL’s Galaxy server to do the common steps of bacterial genome analysis: assembly, variant calling and annotation.

The tutorial is here:

http://sepsis-omics.github.io/tutorials/

Before you get started, you need to add the tutorial dataset into your Galaxy instance. Download it from http://sepsis-omics.github.io/tutorials/modules/data-dna/Data.tar.gz and extract it to a local directory.

Use Galaxy to upload the data.

There is also a quick fix you need to do to make Prokka work (will be fixed in next GVL release), so please login to your server with SSH and execute the following two commands:

cd /mnt/gvl
sudo gvl/apps/linuxbrew/bin/* ./galaxy/tools/hmmer/3.1b2/iuc/package_hmmer_3_1b2/2a1881410dc9/bin/

First, if you haven’t already, use the Bryn interface to start your GVL server.

Follow the link to your server to the GVL homepage:

Click the link to Galaxy:

Sign-up for a Galaxy account using any details you wish.

Then you need to make yourself an administrator. Go to the Admin page on your GVL instance and add the email address you signed up with and choose ‘Set admin users’.

Now follow the tutorial over at:

http://sepsis-omics.github.io/tutorials/

[VSpringthorpe]

Having trouble setting myself as an admin for Galaxy. Cant find any ‘Set admin users’ on the GVL admin page…only package descriptions. Am I missing some permissions?

[mattbull]

Having trouble setting myself as an admin for Galaxy. Cant find any ‘Set admin users’ on the GVL admin page…only package descriptions. Am I missing some permissions?

I’m looking into this, and I’ll get you an answer as soon as possible.

[matupton]

I also have not been able to find an option for changing admin settings in GVL. I have also tried to run prokka in galaxy using the fix posted by Nick at the CLIMB opening. Do I need to have admin privilege to make the prokka fix work. Can i cahnge the admin setting from the terminal for galaxy?

many thanks

Garry

[mattbull]

Having trouble setting myself as an admin for Galaxy. Cant find any ‘Set admin users’ on the GVL admin page…only package descriptions. Am I missing some permissions?

I also have not been able to find an option for changing admin settings in GVL. I have also tried to run prokka in galaxy using the fix posted by Nick at the CLIMB opening. Do I need to have admin privilege to make the prokka fix work. Can i cahnge the admin setting from the terminal for galaxy?

many thanks

Garry

Apologies this has taken so long, but we’ve worked out a fix for your issue.

I was a problem we introduced when we removed Nick’s SSH key from new GVL instances. Cloudman (which does the admin for Galaxy) requires at least one to be present to work correctly.

Unfortunately this fix will only affect new GVL instances and not ones that are currently running.

From the GVL dashboard page, you should now be able to click the link to cloudman, sign in with your instance user/password and then click “Admin” in the top right to add yourself as a Galaxy admin.