Re: Status of rsat?

[Jacques van Helden <Jacques.van-Helden@univ-amu.fr>]

Hi Andreas

Thanks a lot for your enthusiasm and constant help !

I think the reason why I still use pip is historical: initially I had a single script to install the python libraries on Mac OS X and Unix. 

However, I imagine that currently the best is to use as much as possible the OS-dependent package managers (apt-get, brew), so I will be pleased to replace this by apt-get and brew packages (in separate files).

Would this be OK ? 

Cheers

Jacques

Aix-Marseille Université (AMU). 
Lab. Theory and Approaches of Genomic Complexity (TAGC)
INSERM Unit UMR_S 1090, 163, Avenue de Luminy, 13288 MARSEILLE cedex 09. France
Office: INSERM building, block 6
Tel: +33 4 91 82 87 49
Fax: +33 4 91 82 87 01

Jacques.van-Helden@univ-amu.fr
https://orcid.org/0000-0002-8799-8584

On 21 Nov 2019, at 18:37, Andreas Tille <andreas@an3as.eu> wrote:

Hi Jacques,

On Thu, Nov 21, 2019 at 05:13:15PM +0100, Jacques van Helden wrote:

https://github.com/RSAT-doc/installing-RSAT <https://github.com/RSAT-doc/installing-RSAT>

Ubuntu procedure
https://rsat-doc.github.io/installing-RSAT/installing_RSAT_procedure.html <https://rsat-doc.github.io/installing-RSAT/installing_RSAT_procedure.html>


The bash file sin the installer folder contain the lists of dependencies.

I had a **quick** look at the script

  bash_install_scripts/installer/02_python_packages.bash

which is doing:

sudo pip install numpy
sudo pip install scipy
sudo pip install matplotlib
sudo pip install suds
sudo pip install soappy
sudo pip install fisher
sudo pip install httplib2
## pip install pygraphviz ## OSError: Error locating graphviz.


With the exception of soappy (which is currently only available for
Python2 - see #938180) and fisher (which really needs to be packaged)
the first chunk of manually installed packages could be taken from the
Debian package pool.  Before I start to tackle things like fisher (or
help fixing bug #938180) could you explain your motivation why these are
installed via pip instead of apt?

Even python3-pygraphviz is available (and has no bug that would indicate
any loading problem).

Kind regards

     Andreas.

--
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