Question: Are DIY algorithms possible? Any shell?
0
gravatar for dragon28
17 months ago by
dragon2830
dragon2830 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.

ADD COMMENTlink modified 17 months ago • written 17 months ago by dragon2830
5
gravatar for Bjoern Gruening
17 months ago by
Bjoern Gruening5.0k
Germany
Bjoern Gruening5.0k 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 COMMENTlink written 17 months ago by Bjoern Gruening5.0k
0
gravatar for dragon28
17 months ago by
dragon2830
dragon2830 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 COMMENTlink written 17 months ago by dragon2830
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