Question: Combine multiple files in Galaxy
0
gravatar for ando.kelli
18 months ago by
ando.kelli0
ando.kelli0 wrote:

Hi all,

I have over 300 fasta files that I need to combine into a single fine.

I don't have command line experience, so want to do this in Galaxy.

I have tried using the concatenate datasets tool under text manipulation, however this won't work with so many files. This tool only seems useful for combining a few files at a time into one.

I thought this would be relatively straight forward. However, it's doing my head in a bit, and any advice would be greatly appreciated.

ADD COMMENTlink modified 18 months ago by Jennifer Hillman Jackson23k • written 18 months ago by ando.kelli0

Are you using a usegalaxy.org? There is a different cat tool that will help you!

ADD REPLYlink written 18 months ago by Bjoern Gruening4.8k

Hi Bjoern,

No I'm using an Australian site (University of Queensland).

*ended up watching some Linux tutorials on YouTube and managed to use 'cat' to combine the files.

A few years back I was using the main usegalaxy.org, and at the time it had the BLAST2GO tool which I now need. I'll need to find another way to use that tool now.

Thanks for your help!

ADD REPLYlink written 18 months ago by ando.kelli0

Try to contact your Galaxy admins and ask them to install the tools. Otherwise you can use two Galaxy instances :)

ADD REPLYlink written 18 months ago by Bjoern Gruening4.8k

Yeah I had the same thought. I couldn't easily find the tool in another public instance, and realised that I'll probably keep running into the same problem over and over.

I ended up biting the bullet and installing Galaxy and then several tools. I also had someone who's fluent in Linux sit with me and install a bunch of things to use directly through the command line. Such a big learning curve but will be worth it.

Thanks for your help!

ADD REPLYlink written 18 months ago by ando.kelli0
0
gravatar for Jennifer Hillman Jackson
18 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Galaxy is probably not the best choice for this manipulation. The Concatenate tool was not designed to process 300+ datasets except when used through the API. Using "cat" on the command line is simpler/quicker than writing an API script unless this is something that you need/expect to do repeatedly, with a reproducible history, and plan to use other Galaxy tools downstream.

Perhaps someone in your work/lab group can help you?

Jen, Galaxy team

ADD COMMENTlink written 18 months ago by Jennifer Hillman Jackson23k

Hi Jen,

Thanks for your help. I ended up doing some YouTube tutorials and did it using Linux.

Kel

ADD REPLYlink written 18 months ago by ando.kelli0
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