[[BR]]
= Description des outils et procédures utiles à la formation LMDZ =

== Installation testée sur une installation Ubuntu 18.04 ==

Before anything, to avoid run commands with "sudo"

sudo bash


== 1. Installations automatiques par apt ==

To start with

{{{
apt update
apt upgrade
}}}

 [[BR]]
Base :
{{{
apt install -y csh ksh keychain ncftp vim vim-gnome xournal nfs-common  # base
}}}

{{{
apt install -y lftp
apt install -y synaptic gdebi                            # install paquets
apt install -y xfig grads imagemagick gv grace           # graphique
apt install -y texlive-base texlive-latex-extra texlive-lang-french latexdiff  texlive-publishers  #LaTeX
apt isntall -y latexmk texlive-science
apt install -y latex2html
apt install -y texlive-extra-utils texlive-font-utils # pdfjam
}}}

{{{
apt install -y inkscape gimp                             # dessin
apt install -y unoconv # conversion associee a libreoffice
apt install -y qpdfview # un visualiseur remplissant mieux les pdf
apt install -y traceroute # aide systeme
}}}

{{{
# Pour compilation dont LMDZ [[BR]]
apt install -y cdo nco netcdf-bin libnetcdf-dev ncview   # netcdf
apt install -y gfortran g++ libblas-dev subversion git   # fortran et svn
apt install -y openmpi-common libopenmpi-dev openmpi-bin # openmpi
apt install -y gifsicle
apt install -y ekiga                                        # conf renater

sudo snap install pdftk # Autre package de concatenation de pdf
apt install -y dos2unix
}}}

== 2. Workspace ==

solution assez desagreable pour revenir vers un environnement de travaill multi-bureau utilisable ...

See : 
{{{
https://linuxconfig.org/how-to-install-gnome-shell-extensions-on-ubuntu-18-04-bionic-beaver-linux
}}}

{{{
sudo apt install gnome-tweak-tool
sudo apt install gnome-shell-extensions
apt install chrome-gnome-shell
}}}

Installer les "workspace grid" depuis un navigateur en suivant les informations sur
{{{
https://addons.mozilla.org/en-US/firefox/addon/gnome-shell-integration/
}}}

go to
{{{
 https://extensions.gnome.org
}}}

search for Gnome extensions you wish to install.
For us : "Workspace Grid"
Flip the ON switch to install the extension

== 3. Disable automatic rotation of the w orkspace ==

Problème Ubuntu sur les portables enseignement : l'orientation du bureau change quand on tourne l'ordinateur.

{{{
https://askubuntu.com/questions/1035209/how-to-turn-off-screen-rotation-in-ubuntu-18-04-lts 
}}}

Try this command to stop and disable
{{{
sudo systemctl stop iio-sensor-proxy.service
sudo systemctl disable iio-sensor-proxy.service
}}}

To completely remove :
{{{
sudo apt-get remove iio-sensor-proxy
}}}

== 4. python ==

Not as root nor su

{{{
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
chmod +x ./Miniconda3-latest-Linux-x86_64.sh
./Miniconda3-latest-Linux-x86_64.sh
}}}

On a new window to reinitiate the environment

{{{
conda install netcdf4 h5py jinja2 pip sqlalchemy basemap matplotlib numpy scipy
conda create --name python2 python=2.7
conda create --name python3 python=3.7
}}}

Jupyter notebooks
{{{
sudo apt install -y python3-notebook jupyter jupyter-core python-ipykernel  
}}}

== 5. ferret install from ferret ==

#https://github.com/NOAA-PMEL/PyFerret/blob/master/README.md


{{{
conda create -n FERRET -c conda-forge pyferret ferret_datasets --yes
}}}

Pour passer en mode pyferret :
cd ~/miniconda3
. bin/activate FERRET


== 6. acroread ==


Installation acrobat reader fournie par [[BR]]
https://linuxconfig.org/how-to-install-adobe-acrobat-reader-on-ubuntu-18-04-bionic-beaver-linux

{{{
sudo  apt install -y libxml2:i386 gdebi-core
wget ftp://ftp.adobe.com/pub/adobe/reader/unix/9.x/9.5.5/enu/AdbeRdr9.5.5-1_i386linux_enu.deb
sudo gdebi AdbeRdr9.5.5-1_i386linux_enu.deb
}}}


== 7. rstudio, for tuning tools ==

{{{
sudo apt install r-base
wget https://download1.rstudio.org/desktop/bionic/amd64/rstudio-1.2.5001-amd64.deb
sudo gdebi rstudio-1.2.5001-amd64.deb

sudo apt install -y r-cran-rgl libx11-dev libglu1-mesa-dev libfreetype6-dev

install.packages(c("ncdf4","rstan","tensor","Hmisc","lhs","fields","rgl","shape","mco","far","DiceKriging","GenSA","mvtnorm","loo"))
}}}