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 [email protected] https://orcid.org/0000-0002-8799-8584 > On 21 Nov 2019, at 18:37, Andreas Tille <[email protected]> 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. > > -- > http://fam-tille.de
