Unable to access the Galaxy module of lefse

I can´t access the http://galaxy.biobakery.org

Proxy Error

The proxy server received an invalid response from an upstream server.
The proxy server could not handle the request GET /.

Reason: Error reading from remote server


Apache/2.4.10 (Debian) Server at galaxy.biobakery.org Port 80

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Hi all - apologies for the inconvenience we are aware that the Galaxy site is down again. We are working with our IT to resolve this issue, but it requires some new hardware, and last we heard, it will not be available until next week at the earliest. We will monitor this issue and let you know if this timeline is pushed any further. Again, we apologize for the inconvenience, please see my post from a few months ago for alternatives to using LEfSe on galaxy.

Best,
Kelsey

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It is January 2024 and there is still no access.

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I tried to access their galaxy server today, and the server is back!
Thank you for all the efforts from everyone in Huttenhower Lab!

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Indeed, thanks to all the Huttenhower team for bringing galaxy back! (and thanks @lingvv for letting us know is running again ;)).

I tried to use lefse and got this message:
error
An error occurred with this dataset:
Traceback (most recent call last):
File “/usr/bin/lefse_format_input.py”, line 7, in
from lefsebiom.ConstantsBreadCrumbs import *
ModuleNotFoundError: No module named ‘lefsebiom’

Anyone else gets the error message too? I tried with a dataset I analysed in the past and it was also not working, making me think is a server problem…?

Thanks team for the effort!
Cheers,
Núria

I have the same error.
Anyone could fix it, please?

Hi @nuriaeliasmasiques and @ChM,

Thank you for the heads up. Some of the lefse dependencies seems to be out of date and we are currently working on fixing the lefse issue. We will resolve it asap and let you know.

Regards,
Sagun

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raceback (most recent call last):
File “/usr/bin/lefse_format_input.py”, line 7, in
from lefsebiom.ConstantsBreadCrumbs import *
ModuleNotFoundError: No module named ‘lefsebiom’

Today, the Galaxy website can be logged in normally, but the following error still occurs during lefse analysis. May I ask when it can be restored?

Hi bioBakery team,

There seems to be a different error now (below). I am unsure if it’s a problem on my side or the module itself. Thank you!

Traceback (most recent call last):
File “/usr/bin/lefse_format_input.py”, line 10, in
from importlib.metadata import distribution
ModuleNotFoundError: No module named ‘importlib.metadata’

Dear bioBakery Team,

I tried to use LefSe and got this message (which I think is different from the rest of the error messages shown in this topic):

Number of significantly discriminative features: 2 ( 2 ) before internal wilcoxon
Traceback (most recent call last):
File “/galaxy_venv/bin/lefse_run.py”, line 33, in
sys.exit(load_entry_point(‘lefse==1.1.2’, ‘console_scripts’, 'lefse_run.

I got this message with a dataset I analysed in the past.

Many thanks for your work and effort. Your tools are very useful and helpful!
Best,
J.Ignacio