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immcantation / presto

pRESTO is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq). pRESTO is a bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
https://presto.readthedocs.io
GNU Affero General Public License v3.0
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Verify installation using setup.py works in Windows #38

Closed ssnn-airr closed 8 years ago

ssnn-airr commented 8 years ago

Original report by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

This error:

AttributeError: module '__main__' has no attribute '__spec__'

Has popped up for a couple Windows users running FilterSeq under Anaconda. I've been unable to reproduce the error in Windows 7 or 10, with or without Anaconda.

One user solved the issue with a reinstall of presto via pip:

pip install --no-cache-dir --upgrade --force-reinstall presto

So it may be due to a broken install of Biopython, caused by not having Visual Studio 2015 Community installed before attempting the first installation. However, I need to check that there isn't something funny going on with setup.py installs in Anaconda. I know this works with a standard install of Python.

ssnn-airr commented 8 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

I was able to replicate the issue by uninstalling presto and installing using "python setup.py install" on the source distribution. But, the error doesn't appear if you install via pip.

For some reason setup.py doesn't properly install for Windows... Gah. No clue what could be causing it though. Everything is missing from site-packages/presto when installed via setup.py, but is there when installed via pip.

ssnn-airr commented 8 years ago

Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).

All right, (a) it'll take me forever to figure out why Windows is being a weirdo, (b) there is no compelling to use setup.py instead of pip, and (c) we might want to switch to wheels anyway. So, I'm not going to fix this in favor of simply updating the documentation to tell people to install via pip install presto-x.y.z.tar.gz, which works fine.