Question: Not seeing any tools in local galaxy setup
1
gravatar for binni
3.0 years ago by
binni20
Sweden
binni20 wrote:

Hi.

I have cloned the galaxy-dist repo to a cluster I have access to. On that cluster we have login nodes that users share when logging in, and then we have nodes we reserve through slurm. Our system also uses a module system to load different bioinformatics software / different versions.

My goal is to start galaxy on the login node when I do analysis and have it submit the steps in the workflow to the slurm system. Now, after a fresh clone of the repo, I wanted to test running a simple samtools command to see if galaxy is working. However even if i have loaded samtools before I start galaxy, I dont find it in the web ui, and I really don't find anything except some basic text manipulation.

I tried install from toolshed a samtools package but still no cigar.

How can I make galaxy aware of my local bioinformatics tools that I load from our module system?

 

galaxy • 734 views
ADD COMMENTlink modified 3.0 years ago by Dannon Baker3.7k • written 3.0 years ago by binni20
1
gravatar for Dannon Baker
3.0 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k wrote:

What exactly did you install from the toolshed?  It's possible you installed dependencies and not the 'wrappers' that actually represent the galaxy tools.

ADD COMMENTlink written 3.0 years ago by Dannon Baker3.7k

Might have. Not at the pc at the moment, will check tonight. How do I install a tool rather than deps?

ADD REPLYlink written 3.0 years ago by binni20

The dependencies are listed as 'package_samtools' or the like in the toolshed, like this:

https://toolshed.g2.bx.psu.edu/view/iuc/package_samtools_1_1

What you want is either the 'suite', which references a whole bunch of tools (and their dependencies), like:

https://toolshed.g2.bx.psu.edu/view/devteam/suite_samtools_0_1_19

Or an individual tool repository like:

https://toolshed.g2.bx.psu.edu/view/jjohnson/samtools_filter

 

Either way, when you go to install, the description of the package will indicate what's actually contained within -- which galaxy tools, dependencies, etc.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Dannon Baker3.7k

Thanks a lot! I have then been struggling to get the deps installed instead of the package! Will inform how it goes.

ADD REPLYlink written 3.0 years ago by binni20
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