GeneRaxWorkshop
If you have already installed the required software, you can go to the wiki to start the workshop.
If you are working on a workstation of the ITAPHY workshop, you can just open a console and run:
. /usr/local/GeneRaxWorkshop/scripts/setup_environment.sh
git clone https://github.com/BenoitMorel/GeneRaxWorkshop.git
cd GeneRaxWorkshop
and skip the rest of this readme file (go to the wiki)
Otherwise (e.g. if you want to run the practical from your own laptop), you have to go through the rest of this readme.
Requirements
To compile the softare, please first install the following dependencies (you might already have some of them installed):
- git
- cmake
- gcc
- python3
- The ete3 python library
- MPI (optionnal, but we'll use it to parallelize computations)
- Java 1.6 or later
To check if you already have them installed, check that the following commands exist:
git --version
cmake --version
gcc --version
python3 --version
mpiexec --version # checks MPI installation
java -version
On ubuntu, you can install the missing dependencies with:
sudo apt-get install git-all
sudo apt-get install cmake
sudo apt install build-essential # installs gcc
# I am not sure what's the best way to install python3, so I'll let you find out
sudo apt install mpich # installs MPI
sudo pip3 install ete3
We will use the following tools (I provide a script to install them):
To install these tools automatically:
git clone https://github.com/BenoitMorel/GeneRaxWorkshop.git
cd GeneRaxWorkshop
./scripts/install.sh
The installation should take 5 to 10 minutes. Then, if you want to be able to run the tools from anywhere:
source scripts/setup_environment.sh
After this you should be able to run tools such as raxml-ng from anywhere:
raxml-ng --version
Note that this script adds a line to your ~/.bashrc file, in order to set up the environment variables everytime you open a console. Feel free to remove this line from bashrc at the end of the workshop.
You can now start the practical here