Problem to install the package BCBio from biopython - not available?

Marcela Uliano · 04-08-2016, 08:23 AM

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/

maubp · 04-10-2016, 06:29 AM

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.

maubp · 04-10-2016, 11:34 AM

For Brad's GFF code, you need https://github.com/chapmanb/bcbb/tree/master/gff

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04-08-2016, 08:23 AM	#1
Marcela Uliano Member Location: Berlin, Germany Join Date: Apr 2012 Posts: 18	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/

04-10-2016, 06:29 AM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	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.

04-10-2016, 11:34 AM	#3
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	For Brad's GFF code, you need https://github.com/chapmanb/bcbb/tree/master/gff