LEfSe after update on the Galaxy

1

Hello

I was using LEfSe in my analysis, mostly to create LDA and Cladograms. Nowadays, I can not find LEfSe tool after Galaxy update.
Could you help me with this problem?

2

Hi Barbara,
did you find a solution for this problem? I am having the same issue. I am writing an email to the Huttenhower lab asking for help.

3

I did not solved this problem. I did the same as you. If you will get any information from the Huttenhower lab please let me know.

Best regards

Barbara

4

Welcome @barbara_z and @Davide_F
Which Galaxy server are you using?

5

Hello David

I solved this problem. I send you a link under which you will find a previous version of LEfSe when you click on “Metagenomics” on the left panel you will see all the conmmand to create LDA and Cladograms.
http://www.bioinformatics.nl/galaxy

By the way wit new version of Galaxy we can perform many additional analysis which are also veru interesting :slightly_smiling_face:

Best regards
Barbara

6

So you guys are using LEfSe in a custom galaxy server from Wageningen University & Research? May I ask why?

7

When I use part of the data, I can get the result. Actually I was recommended trying to use the command line version, which has no such restrictions (lefse · biobakery/biobakery Wiki · GitHub).

Do you know how to use the command line version?

8

@datle90, which restrictions are you talking about?

About the command line, you’ll need to check their instructions

I still wonder why you guys are using this specific Galaxy for LEfSe, since the Hutlab one works fine.

9

Actually, I am using the Hutlab one too but I got the same error.

10

Folks, I feel this topic is way confusing, so lets try to clear some things, please,

@datle90:

what error are you talking about? I was able to use LEfSe with zero problems
since @barbara_z opened this topic.

@barbara_z:

Any particular reason?

Thank you.