8 months ago by
United States
Hello,
The tool was recently upgraded at Galaxy Main https://usegalaxy.org. So, make sure that you are using the most current version. For data uploads, Upload/FTP, in general, has been a bit slower but we are working to improve that near-term.
A Galaxy Training Network (GTN) tutorial includes this tool with example usage in combination with the Mothur tools: https://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.html
For more usage help, the tool also has a wiki and google group: https://galaxyproject.org/learn/visualization/custom/lefse/
There are no known current issues with the LEfSe version hosted at Galaxy Main, but if there are any new ones discovered, that you cannot figure out what might be going wrong based on the help above, we can help (including determining if this is a usage versus tool/server problem. If you have problems at Galaxy Main, or can reproduce the problem there, a bug report can be sent in for review. If the problem occurs at job submission, and no error dataset is produced, a shared history link can be sent in. Be sure to note the datasets involved, the tool settings with inputs filled in (screenshots would be good), so we can reproduce the problem. A link to this Biostars post should be included.
How-to is explained in this prior post (I see your comment there). https://biostar.usegalaxy.org/p/23815/. And this is the direct link to the Support FAQ with the same details: https://galaxyproject.org/support/#unexpected-results
If you are working at a different public Galaxy server, the administrators of that server can be contacted to find out if this is an input or server-side/tool problem. Contact information is generally on the home page of the server. Some public Galaxy servers also post contact information here: https://galaxyproject.org/public-galaxy-servers/
Thanks! Jen, Galaxy team
