No access to online LefSe

Downstream analysis and statistics LEfSe
1

Hi, is the website down? I can’t establish a connection to the server. Thanks!

2

I am having the same issue here. Since when you have had this issue? Few months back it was operating normally,

3

It was working just last week still. Then I tried to access it yesterday and no luck.

4

i am also unabel to access it. is there any way to troubleshoot?

5

Hi all (@chwang.mt, @Shailes_Bhattarai, @KL2003),

First, we apologize for this issue, we are aware that there is currently no access to our Galaxy site (or lab website) and are actively working on getting it back up. However, unfortunately, we do not have an ETA on when it will be accessible again and we apologize for the inconvenience.

In the meantime there are a couple of other options for doing this type of analysis, LEfSe itself has not been under development for quite some time in the lab.

  1. MaAsLin2 is our newer and still under maintenance tool to conduct DA analysis, it is more robust to the data and usually results in far fewer false positive hits from the model, see this manuscript for more information on DA methods or the MaAsLin manuscript for more details about the tool. Additionally, it allows for the incorporation of longitudinal data and allows for many covariates to be adjusted for. Here is a link to the tutorial for that tool.
  2. You can always install and run LEfSe on the command line.

I hope this helps in your analysis needs and again we apologize for this inconvenience.

Best,
Kelsey

6

Hi Kelsey,

Thank you for providing additional options for running LEfSe, since the link still remains down.

You mention that LEfSe can be run on the command line, however, do you have any good links to the functions available within LEfSe on the command line? I can’t find information of how to run it on the command line once it is installed and I would appreciate any help/example script or tutorials.

Thank you!

7

Hi @Kelsey_Thompson,

I am having issues running Picrust2 on galaxy Europe, getting a ‘tool not found’ issue, would this be the cause of that too?

8

Hi @sar ,
Apologies for the inconvenience. Unfortunately, hutlab galaxy is down at the moment causing Picrust2 issues. We are working to get back the galaxy servers as soon as possible.

In the mean time, please feel free to use the command line version of Picrust2 here. We will keep everyone updated on the Hutlab http://galaxy.biobakery.org/ status. Thank you for your patience.

Regards,
Sagun