I am developing a wrapper for a bioinformatics tool writen in python3.

The native Galaxy-project runs on python2.7.

How can I the tool that requires python3 in a galaxy-project instance?


1 Answer 1


Each Galaxy tool uses its own (typically conda-based) environment, which will normally not use the same python as Galaxy itself (note that Galaxy can run under python 3). An example of this is deepTools, which is python 3 only but will happily run under a python 2 Galaxy since conda is being used to create a python 3 environment for it. It's best to distribute your tool via bioconda and then Galaxy will be easily able to install it.

  • $\begingroup$ I hope I did it the right way: 1- conda create ..., 2-conda install ..., etc... $\endgroup$
    – aerijman
    Apr 4, 2020 at 22:28
  • $\begingroup$ Yes, though it's best to allow galaxy to make the env for you and put a copy of the wrapper in the toolshed. $\endgroup$
    – Devon Ryan
    Apr 4, 2020 at 22:30

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