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Old 04-08-2016, 07:23 AM   #1
Marcela Uliano
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Location: Berlin, Germany

Join Date: Apr 2012
Posts: 18
Default Problem to install the package BCBio from biopython - not available?

Hey guys!

I have a exonarate gff result and I'm trying to covert it to gb format, so I can train ausgustus!

The thing is I've found this script https://github.com/robsyme/nextflow-...ter/bin/gff2gb but I'm having a dependency with the BCBio from Biopython.

I've been trying to install biopython (and such dependency) in a virtual machine on the cluster where I work, but I find Biopython webpage to be offline!!

Can someone help me to get this file so I can install it?

Thank you so much!


This post is also here: https://www.biostars.org/p/185764/
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Old 04-10-2016, 05:29 AM   #2
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

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Unfortunately the Biopython website went down on Friday, see http://mailman.open-bio.org/pipermai...il/015909.html

We're working on it, and there's a possible migration in progress, see http://mailman.open-bio.org/pipermai...il/015910.html - you can view this already at http://biopython.github.io/wiki/Biopython (very plain at the time of writing).

In the meantime the official *.tar.gz source releases of Biopython are available from PyPI via https://pypi.python.org/pypi/biopython to things like "pip install biopython" should continue to work as usual.
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Old 04-10-2016, 10:34 AM   #3
maubp
Peter (Biopython etc)
 
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For Brad's GFF code, you need https://github.com/chapmanb/bcbb/tree/master/gff
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