LEfSe on local Galaxy instance

[maleysso...@gmail.com]

Hi,

I recently installed Galaxy and among other tools I would like to have LEfSe on my local instance.
I get it from the galaxy tool shed, and I also installed the requirements packages and R libraries :
Packages :
   python-rpy2
   python-numpy
   python-matplotlib
   python-matplotlib-data
   python-mpltoolkits.basemap
   python-mpltoolkits.basemap-data
   python-argparse
R libraries :
   splines
   stats4
   survival
   mvtnorm
   modeltools
   coin
   MASS

I have a problem with the first tool, "A) Format Data for LEfSe". Although my file is correct (I can run it on Huttenhower-lab), the box "Select which row to use as class" remains saying "No options available". I didn't see any message on the list mentioning this problem, so I think I'm missing some basic manipulation, I'm new to both Galaxy and LEfSe.
So, my question is, is it a Galaxy or LEfSe related issue? If it's LEfSe, any piece of advice?

Thanks in advance.

PS : The only clue I have : checking the LEfSe files of this tool, format_input.xml and format_input_selector.py, I see that this is is related to a dynamic option. And looking into the Galaxy tutorial for installing tool shed, I found
"tools that include dynamically generated selected lists whose options depend upon entries in the tool_data_table_conf.xml file along with references to index files (i.e., tool-data/xxx.loc files) [...] However, index files must still be made available to tools that require them" with no further explanation.

[George Weingart]

Hi Romain,

Can you try to run it with the sample file provided in the Lefse Galaxy screen? ( http://www.huttenhower.org/webfm_send/73)

When you use your file,  can you verify the File-Type for your file that you uploaded is "Tabular"?

When you get the error, can you send me a screen print?

Would you mind sending me your file so I try it?

Thanks and best regards,

George Weingart, PhD

Huttenhower Lab

[Romain Maleysson]

Thanks for your fast reply!

Same problem with the example file.

I set the file format to tabular too.

You can find attached a screen capture of my galaxy instance when running "A) Format Data for LEfSe". I don't get any mistake (could have been helpful), it's just the parameter box for meta-data that remains empty, "No option available".

I also attached a part of my file if you would like to see.

Galaxy is running on Debian (don't know if it's important).

Regards

[Cesar Arze]

I can also confirm that I am having the same issues using the latest release of Galaxy and the LEfSe tool installed from the main toolshed. I've been prodding around in the code and I'm not sure if the format_input_selector.py file is every being invoked, I know that the Galaxy dev's have said they are going to deprecate the <code> tags in favor of something else but looking at the Galaxy source it still seems like it should consume any file provided in <code> tags.

[maleysso...@gmail.com]

We are looking for a solution with George Weingart and Nicola Segata, I'll send the result as soon as this issue is solved.

[maleysso...@gmail.com]

I'm finally back with something, even if it's not really a solution. I mailed the Galaxy dev list but I got no answer so this is the only way I could find to have LEfSe working on a local Galaxy instance.

I remove the Galaxy version that was installed following the tutorial (using git clone command) and installed a previous version found on this page :
https://github.com/galaxyproject/galaxy/releases
The v14.02 makes LEfSe run correctly. Maybe more recent versions also work, I had to go back to this one because of openSSLv3 errors during install of others Galaxy versions, which are due to the Debian environment I'm using.
To install, just decompress the archive and run galaxy-14.02/run.sh
Also, it seems that trying to keep the tools previously installed in a more recent Galaxy isn't working. I got errors testing them, which were solved when I made a fresh install from the tool shed.

Hope this could help someone.

[Matthew Wipperman]

Hello,

I am having the same issue with running LEfSe on Galaxy locally--the upload format of my file (and the sample file) are Tabular, I can successfully format the data, however the actual LEfSe analysis does not run properly. Perhaps the LEfSe scripts need to be updated for a newer version of OS X? Thanks.

--Matt