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Question: Tools not running on local Galaxy
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gravatar for mazelazowska
2.0 years ago by
mazelazowska • 10
mazelazowska • 10 wrote:

Hi,

I am trying to run tools that require Biopython or Python. I installed "package_python_3_4" but it is not working. It seems that "zlib version 1.2.8" package is installed but does not work. I tried to install/uninstall it couple of times, but it has no effect.

What should I do?

Thank you Monika
galaxy • 635 views
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modified 2.0 years ago by Wolfgang Maier • 600 • written 2.0 years ago by mazelazowska • 10
1
gravatar for Wolfgang Maier
2.0 years ago by
Wolfgang Maier • 600
Germany
Wolfgang Maier • 600 wrote:

Hi Monika,

which tools are you trying to use? Are they declaring their requirement like this (in the tool wrapper .xml files): <requirement type="package" version="3.4">python3</requirement>

?

In addition, I just checked the toolshed recipe for the package_python_3_4 installation and I think it does not automatically make the installed zlib available at runtime. So maybe a tool using zlib-dependent functionality of python3 should also include the requirement declaration: <requirement type="package" version="1.2.8">zlib</requirement>

You could try adding this line to the requirements section of the tool wrappers and just see what happens.
ADD COMMENT • link written 2.0 years ago by Wolfgang Maier • 600
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