[galaxy-dev] Multifactor RNA-Seq Analysis and interaction terms

[Lance Parsons]

One of the labs I work with regularly uses Galaxy for their RNA-Seq 
analysis. They have been doing very simple analyses up to this point, 
using DESeq2. However, they are moving toward more complicated 
experimental designs that will include additional factors, some of which 
(genotype for example) will be interaction terms 
. 
I have a few questions:


1.

   I know Marius van den Beek  added group
   tags  in 18.09,
   which seem like they are at least one way to use multiple factors
   along with collections. Is there any primer/tutorial on using these?
   It’s not quite clear to me just yet.

2.

   Does anyone have any thoughts or suggestions as to how one could add
   interaction terms (/e.g./ |condition:genotype|) to the DESeq2
   wrapper? Does this functionality exist in a different Galaxy tool?

Thanks in advance.

​

--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 136
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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[galaxy-dev] Adding the Ilifu cloud to launch.usegalaxy.org

[Peter van Heusden]

Hi there

While I will continue to work on getting a Cloudlaunch server running
locally, could the Ilifu cloud (http://www.ilifu.ac.za/) be added as an
option on https://launch.usegalaxy.org/catalog ? What details would be
required?

And then - what are the requirements for adding appliances to the appliance
catalogue?

Thanks,
Peter
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Re: [galaxy-dev] Running Cloudlaunch against a new OpenStack cloud

[Peter van Heusden]

Hi there

I've got a bit further, but now I've got a problem - how do you access the
admin panel when you have the complete site set up?

1) If Debug = False (as it is for a production setup), Django doesn't load
static files (e.g. CSS).

2) When going via the nginx proxy, I can't figure out what URL will direct
me to the admin page.

Peter
P.S. I'm doing some work on the ansible to get this all set up - I'll do a
PR once everything seems to be working.

On Fri, 19 Oct 2018 at 01:25, Alexandru Mahmoud  wrote:

> Hello!
>
> I am new to the team, so this will be a brief response to only one of your
> questions while waiting for someone else to get to the email (and I am not
> replying all so that people don’t dismiss it as answered):
>
> For 3 specifically, you can access the admin panel at http://127.0.0.1(or
> localhost):8000/admin, where you should be able to login with the user
> created with the ‘createsuperuser’ command. Under “Appliances” or
> “Applications” (depending on the version of cloudlaunch) you’ll be able to
> see and change/add configurations for apps.
> If you want to see in more detail how the appliances are being set up and
> how the launch config is used in code, look for the "Backend component
> name", then find the corresponding backend plugin in the cloudlaunch repo.
> I hope that is a helpful start, and feel free to email me if nobody
> responds in a reasonable amount of time to your other questions, as I can
> get more answers in person and relay them to you.
>
> Best,
> Alex Mahmoud
>
>
> On Oct 18, 2018, at 3:45 PM, Peter van Heusden  wrote:
>
> Hi there
>
> I'd like to set up cloudlaunch to be able to set up on-demand Galaxy
> servers and associated clusters on the new Ilifu OpenStack cloud. From
> looking around the repositories it looks like Cloudlaunch is at least 2
> components:
>
> 1. The cloudlaunch server
> 2. The UI - either cloudlaunch-ui or cloudlaunch-cli
>
> I'm trying to get cloudlaunch server installed on a Ubuntu 18.04 VM. The
> only requirement seems to be python3-pip. For postgresql support I
> installed the python3-psycopg2 module, the postgresql-10 server and create
> a user and db (both named cloud). Then I installed the server with `pip3
> install cloudlaunch-server` and ran commands:
>
> cloudlaunch-server django migrate
> cloudlaunch-server django createsuperuser
> cloudlaunch-server django runserver
>
> The next step (https://github.com/galaxyproject/cloudlaunch) refers to
> redis-server. Installing this package seemed to satisfy that requirement,
> running it manually didn't work so I just ran the celery command as
> illustrated. And finally relaunched the django server.
>
> Then nodejs and npm were installed, the cloudlaunch-ui cloned from github,
> the various npm package specified installed and finally npm start brings up
> the cloudlaunch user interface.
>
> So far so good but:
>
> 1. Is there more extensive documentation anywhere? Specifically
> documentation about running this in production.
>
> 2. Is there a docker container that can be used instead of all this manual
> installation?
>
> 3. How are appliances configured and added to the Appliance Catalogue?
>
> Thanks!
> Peter
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