Installing multible tools at ones

Question: Installing multible tools at ones

3.6 years ago by

Denmark

I might be missing the obvious. I am setting up a fresh Galaxy server for some first-year bioinformatics students to use. The basic Galaxy server has very few tools bundled with it, and the rest must be installed via toolsheds. Which is fine if you are only missing 1-2 tools, but when starting from scratch I am missing closer to 50-100.

Is there such a thing as tool-bundles?

I have been using https://usegalaxy.org as a tool reference and installed/categorized my servers tools in much the same way.

For example it would be very handy if I could click 'Install "NGS: SAM Tools"' in the admin interface, and Galaxy would install all 14 tools categorized under NGS: SAM Tools.

Kind regards

Anders

toolbundle • 983 views

ADD COMMENT • link •

modified 3.6 years ago • written 3.6 years ago by anders.dannesboe • 0

3.6 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi Anders,

such tool-bundles exists and we call it suites. For example this one: https://toolshed.g2.bx.psu.edu/view/devteam/suite_bamtools_2_3_0 These suites can be created by everyone and it's up to the community to bundle nice tools together.

To solve your underlying problem, have a look at the Galaxy API (e.g. http://bioblend.readthedocs.org/). You can use the API to install tools and put them into categories. All what you need to do is to write a small script, like we did in our Galaxy Docker flavors. For example see the Dockerfile here: https://github.com/bgruening/docker-galaxy-genome-annotation

Hope this helps,

Bjoern

ADD COMMENT • link written 3.6 years ago by Bjoern Gruening ♦ 5.1k

In your Genome Annotation Docker example, you are creating a new Docker container with the tools already installed. If you already have created a Docker Galaxy container and want to add the tools, would you be forced to create a new Container? I intended to use the base Galaxy Docker container, and have the tools automatically downloaded and installed after/while the Container is started; is that type of setup not supported?

ADD REPLY • link written 2.2 years ago by steve • 30

You can just use your Galaxy instance and install all tools from a specific flavor during runtime of your container. I hope this helps.

ADD REPLY • link written 2.2 years ago by Bjoern Gruening ♦ 5.1k

Thanks I think I understand now (also as per our comments here). My intention is to keep the tool installation separate from both the container configuration and from the /export/ mounted location. This way I would be able to start any Galaxy Docker container, mount my previous /export/ directory with user & tools databases, etc., and then run a script that can install any of my desired tools if they are not already present. Is this not the typical practice? One of my concerns is that mounting my previous /export/ dir with a new Galaxy Docker flavor might cause problem (is this the case?) OR that damage to my /export/ dir might cause the loss of all the tools I had installed manually (already had something like this happen, my mistake). Mostly I'm trying to keep the various aspects of Galaxy Docker separated from one another (container config, tool install lists, /export/ data) so that a change or problem in one doesn't affect the others. I am still new with Galaxy though so maybe these are non-issues. EDIT: Looks like Ansible is set up for this exact purpose.

ADD REPLY • link modified 2.2 years ago • written 2.2 years ago by steve • 30

Uh, these are many questions for a comment. Can you open a new question or contact me via mail? In general /export/ is meant to stay and be reusable over many releases. And the tool installation from within the container is based on the ansible tools role.

ADD REPLY • link written 2.2 years ago by Bjoern Gruening ♦ 5.1k

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