Citing Galaxy EU

usegalaxy.eu support
#1

Hi,

I would like to cite galaxy EU correctly. Regarding the information on this website Citing Galaxy one is supposed to additionally use the first publication of a public instance used. Which publication (additionally to the general primary publication) should be used to especially cite Galaxy EU with the public server in Freiburg?

Thanks a lot!

Rose

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#2

Hi,

we have a small section about Acknowledgments here: Galaxy Europe
If you could cite the main Galaxy paper and acknowledge the EU server we would be super happy :slight_smile:

Thanks,
Bjoern

#3

Perfect! Thanks you so much for the fast response!

#4

Hi Bjoern,

may I ask you one other question regarding this matter.

There are some tools I used on Galaxy, where I cannot exactly find the owner and look for a paper to be cited, as for example in the case of " Filter data on any column using simple expressions (Galaxy Version 1.1.1)" or " Select lines that match an expression (Galaxy Version 1.0.1)". Does this mean the tool is owned by Galaxy and one does not need to cite another source?
In the case of bcftools norm the initial paper of samtools is quoted on usegalaxy.eu when looking at the tool and so I guessed that this should be also cited, when using it, right?
( bcftools norm Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows (Galaxy Version 1.9+galaxy2); Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16):2078–2079. 2009., https://doi.org/10.1093/bioinformatics/btp352)

Thank you so much again!

#5

Hi @roselucia,

this is all correct :slight_smile:
The Filter and Select tools are developed by the Galaxy community so citing Galaxy here should be enough and bcftools also seems to be the correct citation.

Thanks,
Bjoern

1 Like
#6

Hi @bjoern.gruening ,

thanks again for your help- I really would like to make sure that your work is cited properly and your work is sufficiently acknowledged.

I have one last question about a tool:
Replace Text (Galaxy Version 1.1.3)
I cited your galaxy wrapper as written below and I am wondering, if the tool itself again is Galaxy property (equally to the Filter and the select tool), so that Galaxy itself should be cited also?

Gruening BA. Galaxy wrapper [software]. GitHub; 2014 [cited 2021 Mar 7]. Available from: GitHub - bgruening/galaxytools: Galaxy Tool wrappers

I am really grateful for your help :smiley: !

#7

I think you can skip this tool. You probably can not cite a GitHub repo. It’s fine to not cite it from my point of view :slight_smile: Thanks for being so careful and good luck with your submission.

1 Like
#8

Ok, thank you. So this tool as well belongs to GitHub in general, equally to Filter and Select, right? :slight_smile:

#9

Yes, you can cout it as Galaxy core tool :slight_smile:

1 Like
#10

@bjoern.gruening said:

If you could cite the main Galaxy paper and acknowledge the EU server we would be super happy :slight_smile:

Super-duper happy. @roselucia thanks for taking the time to both cite and ask questions.

2 Likes
#11

Thanks for your great tools :smiley: and great advice!