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Question: How to update the Python version in Galaxy
1
gravatar for asif.karim.csedu
2.7 years ago by
asif.karim.csedu • 10
asif.karim.csedu • 10 wrote:

Hi,

I am a very new user of Galaxy. I have been trying to develop some tools to be integrated into the Galaxy server with Python 3.5. However, I got to know that the galaxy server itself was written with Python 2.6/2.7.

Therefore, I am getting several errors since the Galaxy is not compatible with my source code.

Can someone let me know how to update the python version in the Galaxy server?

Reza
update version galaxy python • 1.2k views
ADD COMMENT • link •
modified 2.7 years ago by Martin Čech ♦♦ 4.9k • written 2.7 years ago by asif.karim.csedu • 10
1
gravatar for Martin Čech
2.7 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

Galaxy will not run on Python3 so you need to make your tool dependent on a specific Python package from the Tool Shed. I would recommend using one of these:

https://toolshed.g2.bx.psu.edu/view/iuc/package_python_3_4/aca5076020ea https://toolshed.g2.bx.psu.edu/view/tiagoantao/package_python_3_5/7e89e85c8b19

With that, when your tool is installed, Galaxy will also install the requested Python and will run your tool with that python in PATH. Please see the following tool that depends specifically on Python 2.7: https://github.com/galaxyproject/tools-iuc/blob/master/tools/gff3_rebase/macros.xml
ADD COMMENT • link written 2.7 years ago by Martin Čech ♦♦ 4.9k
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