Galaxy vs Linux Command Line

Question

[fininros]

Both Linux and Galaxy command lines allow for workflows to be built up, I'm just wondering what are the main similarities and differences between these two systems in regards to how they;

(i) store input data
(ii) record users history
(iii) the assembly tools they use; and
(iv) sharing/publishing results?

I'm trying to understand which would be better for user-friendly development of a bioinformatic workflow. Thanks in advance.

[Pierre Lindenbaum]

see Why Should I Use Galaxy ?

[John]

3.8 years ago, and still a good question ;)

Answer 1

[John]

From the point of view of a workflow developer, the difference is who your target audience are. If you want to write a workflow for people who don't have access to anything other than Galaxy - choose Galaxy. If you want a workflow that is a bit specific to an unusual problem and the only people who will use it will be competent to semi-competent users, go with a Linux/OSX command line workflow.

I mean, this is just generic advice - we could give better advice if we knew what the workflow is for, what tools it uses, who uses it, and where it's going to be run.

Answer 2

[Jennifer Hillman Jackson]

Hello,

Galaxy will do all of these items as built-in functionality whereas in a custom line-command workflow each would need to be engineered in. Galaxy includes API access for high-through-put analysis (working through the web interface is not the only method). BioBlend is a popular choice for this type of use case.

• (i) store input data
• (ii) record users history
• (iv) sharing/publishing results

For this item, if the tool that you wish to use is not wrapped for Galaxy yet, it could be. Check the Galaxy Tool Shed for currently wrapped tools. To wrap another, start here.

• (iii) the assembly tools they use

Take care, Jen, Galaxy team

Ps: If you need Galaxy specific help at any point that is not covered in the documentation, please feel free to write to this mailing list [e-mail] and/or post to the Galaxy Biostars forum. There is also a development community IRC channel: #galaxyproject. Or perform a search to view prior Q&A. Details.