Question: Galaxy vs Linux Command Line
1
gravatar for fininros
3.0 years ago by
fininros10
fininros10 wrote:

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.

linux galaxy bioinformatics • 1.8k views
ADD COMMENTlink modified 2.9 years ago by Jennifer Hillman Jackson370 • written 3.0 years ago by fininros10
4

see Why Should I Use Galaxy ?

ADD REPLYlink written 3.0 years ago by Pierre Lindenbaum118k
3

3.8 years ago, and still a good question ;)

ADD REPLYlink written 3.0 years ago by John12k
4
gravatar for John
3.0 years ago by
John12k
Germany
John12k wrote:

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.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by John12k
2
gravatar for Jennifer Hillman Jackson
2.9 years ago by
Bay Area, CA
Jennifer Hillman Jackson370 wrote:

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 galaxy-dev@lists.galaxyproject.org 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.

ADD COMMENTlink written 2.9 years ago by Jennifer Hillman Jackson370
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