Are DIY algorithms possible? Any shell?

Question: Are DIY algorithms possible? Any shell?

2.0 years ago by

dragon28 • 30

dragon28 • 30 wrote:

Hi Biostars, Is there any way (bash/python/C/etc.) to implement algorithms on my data in usegalaxy.org?

For example, I import a fastq file, then do a QC on it and find some justification to trim it a bit.

Currently, it seems it is only possible to do this manually on usegalaxy.org.

In, fact it seems that there is no way to even log into a shell on usegalaxy.org.

Any advise appreciated.

Thanks in advance.

rna-seq notebook jupyter galaxy ipython • 473 views

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modified 24 months ago • written 2.0 years ago by dragon28 • 30

2.0 years ago by

Bjoern Gruening ♦ 5.1k

Germany

Bjoern Gruening ♦ 5.1k wrote:

Hi,

what do you mean with

Currently, it seems it is only possible to do this manually on usegalaxy.org.

If you need to trim your FASTQ files you can use a trimmer like TrimGalore or similar. Not sure why you need a shell here. Keep in mind that giving everyone shell access on a public server comes with some security implications and a loss of reproducibility at some point. However, we have also covered your use-case and have integrated Jupyter/IPython in Galaxy:

Is this what you are looking for? Please keep in mind that this is only meant for the final steps, not for the data-reduction step, this you probably want to do with real Galaxy tools.

Cheers, Bjoern

ADD COMMENT • link written 2.0 years ago by Bjoern Gruening ♦ 5.1k

24 months ago by

dragon28 • 30

dragon28 • 30 wrote:

Hi Bjoern, Yes, what I meant by that statement was that all operations in usegalaxy.org are done manually by making selections manually, making decisions about results and manually taking action. Thanks for the quick pointer and tutorial on jupyter/ipython! Thanks again, Mike

ADD COMMENT • link written 24 months ago by dragon28 • 30

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