Not seeing any tools in local galaxy setup

Question: Not seeing any tools in local galaxy setup

3.8 years ago by

binni • 20

Sweden

binni • 20 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 • 1.0k views

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modified 3.8 years ago by Dannon Baker ♦ 3.7k • written 3.8 years ago by binni • 20

3.8 years ago by

Dannon Baker ♦ 3.7k

United States

Dannon Baker ♦ 3.7k 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 COMMENT • link written 3.8 years ago by Dannon Baker ♦ 3.7k

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

ADD REPLY • link written 3.8 years ago by binni • 20

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 REPLY • link modified 3.8 years ago • written 3.8 years ago by Dannon Baker ♦ 3.7k

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

ADD REPLY • link written 3.8 years ago by binni • 20

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