# LEfSe via galaxy

**URL:** <https://forum.biobakery.org/t/lefse-via-galaxy/8122>\
**Category:** Downstream analysis and statistics\
**Created:** [June 9, 2025, 1:56pm UTC](https://forum.biobakery.org/t/lefse-via-galaxy/8122 "2025-06-09T13:56:53Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![Wos](https://avatars.discourse-cdn.com/v4/letter/w/8e7dd6/32.png) [@Wos](https://forum.biobakery.org/u/Wos)\
**Post date:** [June 9, 2025, 1:56pm UTC](https://forum.biobakery.org/t/lefse-via-galaxy/8122/1 "2025-06-09T13:56:53Z")

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Hello,

First time user of LEfSe via galaxy. I organized my dataset according to the input file format guide on the galaxy page. Initially, when I import, it says size is big (paraphrasing), I compressed and uploaded. But when I execute format data for Lefse, it immediately shown error “Traceback (most recent call last):  
File “/galaxy\_venv/bin/lefse\_format\_input.py”, line 33, in   
sys.exit(load\_entry\_point(‘lefse==1.1.2’, ‘console\_scripts’, ‘lefse\_format\_input.py’)())  
File “/galaxy\_venv/bin/lefse\_format\_input.py”, line 25”

To check if it was from my dataset, I downloaded the hmp\_aerobiosis\_small.txt dataset, imported and tried the same. Again the same error as above. Is it a server thing? datatype? Can someone kindly help? please.

Thanks, Wos

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**Author:** ![nearinj](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/nearinj/32/2135_2.png) [@nearinj](https://forum.biobakery.org/u/nearinj)\
**Post date:** [June 16, 2025, 7:15pm UTC](https://forum.biobakery.org/t/lefse-via-galaxy/8122/2 "2025-06-16T19:15:45Z")

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Hi @Wos ,

If your looking to use LEfSe I would recommend checking out the LEfSe R package here:

> **[lefser](https://www.bioconductor.org/packages/release/bioc/html/lefser.html)**
>
> lefser is the R implementation of the popular microbiome biomarker discovery too, LEfSe. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers from two-level classes (and optional sub-classes).

Alternatively you can also run MaAsLin2 on galaxy which is used to answer the same types of analysis that LEfSe was originally designed for.

Cheers,  
Jacob Nearing