configure mafft location

[bruceamurphy]

Hi, I get this error when trying to use UPP: "PASTA ERROR: PASTA is exiting because of an error: '/rds/general/user/userid/home/anaconda3/lib/python2.7/site-packages/PASTA-1.7.8-py2.7.egg/bin/mafft' not found. Please install 'mafft' and/or configure its location correctly in '/rds/general/user/userid/home/.pasta/pasta_tool_paths.cfg' " I have mafft installed but it doesn't seem to be seeing it. The file called "pasta_tool_paths.cfg" doesn't exist yet at the specified location. If I create it how do I configure the location of mafft? Thanks.

[smirarab]

Did you install PASTA using the instructions from PASTA? It seems there is a problem with PASTA installation. Can you try installing PASTA again and monitor the logs for errors?

[lizzyjoyce]

Hi there, I'm having the same issue with PASTA looking for mafft in the wrong directory, even after reinstalling PASTA according to the instructions. The only workaround I have found is PASTA_TOOLS_DEVDIR=$CONDA_PREFIX/bin/. Any idea what the issue might be or how to resolve it? Many thanks.

[smirarab]

Thanks for the reports and sorry for the long delay in responding.

Just to be clear, you have installed PASTA separately? And also, when installing PASTA, did you notice that somewhat unorthodoxly, it asks you to run

sudo python setup.py develop

instead of the usual

sudo python setup.py

If you have run without develop, I think that is the issue. If you have run with the develop command and still get the error, please let me know and I will look into it.

Regards Siavash

On Wed, Jun 17, 2020 at 9:08 PM lizzyjoyce [email protected] wrote:

Hi there, I'm having the same issue with PASTA looking for mafft in the wrong directory, even after reinstalling PASTA according to the instructions. The only workaround I have found is PASTA_TOOLS_DEVDIR=$CONDA_PREFIX/bin/. Any idea what the issue might be or how to resolve it? Many thanks.

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-- Siavash Mirarab