Commit 8ea3e4e5 authored by VIGNET Pierre's avatar VIGNET Pierre
Browse files

Update doc with virtualenvs

parent 1e1449cd
...@@ -2,7 +2,7 @@ CADBIOM (Computer Aided Design of Biological Models) is an open source modelling ...@@ -2,7 +2,7 @@ CADBIOM (Computer Aided Design of Biological Models) is an open source modelling
Based on Guarded transition semantic, it gives a formal framework to help the modelling of Based on Guarded transition semantic, it gives a formal framework to help the modelling of
biological systems such as cell signaling network. biological systems such as cell signaling network.
Official website: [](http://cadbiom.genouest.org/) Official website: [link](http://cadbiom.genouest.org/)
# Installation # Installation
...@@ -48,24 +48,60 @@ will be installed from pypi repository: ...@@ -48,24 +48,60 @@ will be installed from pypi repository:
* numpy * numpy
* pycryptosat * pycryptosat
### Virtual environment
This is not a mandatory step but it is a good practice to use virtual environments
to separate projects from each other.
* Install virtualenvwrapper:
pip install virtualenvwrapper
* Edit your .bashrc or .zshrc file to source the virtualenvwrapper.sh script with these lines:
export WORKON_HOME=~/.virtualenvs
mkdir -p $WORKON_HOME
source /usr/bin/virtualenvwrapper.sh
The location of this script may vary depending on your Linux distro
* Restart your terminal or run:
source /usr/bin/virtualenvwrapper.sh
* Create your virtualenv:
mkvirtualenv cadbiom -p /usr/bin/python2.7
* Later if you want to reactivate the virtualenv:
workon cadbiom
### SAT solver ### SAT solver
Note: Cadbiom software requires a SAT solver which is Cadbiom software requires a SAT solver which is
proposed as a Python wrapper by an independant library (pycryptosat). proposed as a Python wrapper by an independant library (pycryptosat).
For now, pycryptosat is not on pypi; so we use a fork from *For now, pycryptosat is not on pypi; so we use a fork from
[Cryptominisat repository](https://github.com/msoos/cryptominisat/tree/5.0.1) [Cryptominisat repository](https://github.com/msoos/cryptominisat/tree/5.0.1)*
Here you will find the installation of pycryptosat package: Here you will find the installation commands of the pycryptosat package:
git clone https://gitlab.irisa.fr/0000B8EG/pycryptosat/tree/5.0.1_cmake_dev git clone https://gitlab.irisa.fr/0000B8EG/pycryptosat/tree/5.0.1_cmake_dev
mkdir build mkdir build
cd build && cmake ../ cd build && cmake ../
make python_interface_install make python_interface_install
### Cadbiom ### Cadbiom
If you want to install the library with its GUI, and command line, If you want to install the library with its GUI, and command line in one command,
after the git clone step, just do: after the git clone step, just do:
make install make install
......
...@@ -2,7 +2,7 @@ CADBIOM (Computer Aided Design of Biological Models) is an open source modelling ...@@ -2,7 +2,7 @@ CADBIOM (Computer Aided Design of Biological Models) is an open source modelling
Based on Guarded transition semantic, it gives a formal framework to help the modelling of Based on Guarded transition semantic, it gives a formal framework to help the modelling of
biological systems such as cell signaling network. biological systems such as cell signaling network.
Official website: [](http://cadbiom.genouest.org/) Official website: [link](http://cadbiom.genouest.org/)
# Installation # Installation
...@@ -48,24 +48,60 @@ will be installed from pypi repository: ...@@ -48,24 +48,60 @@ will be installed from pypi repository:
* numpy * numpy
* pycryptosat * pycryptosat
### Virtual environment
This is not a mandatory step but it is a good practice to use virtual environments
to separate projects from each other.
* Install virtualenvwrapper:
pip install virtualenvwrapper
* Edit your .bashrc or .zshrc file to source the virtualenvwrapper.sh script with these lines:
export WORKON_HOME=~/.virtualenvs
mkdir -p $WORKON_HOME
source /usr/bin/virtualenvwrapper.sh
The location of this script may vary depending on your Linux distro
* Restart your terminal or run:
source /usr/bin/virtualenvwrapper.sh
* Create your virtualenv:
mkvirtualenv cadbiom -p /usr/bin/python2.7
* Later if you want to reactivate the virtualenv:
workon cadbiom
### SAT solver ### SAT solver
Note: Cadbiom software requires a SAT solver which is Cadbiom software requires a SAT solver which is
proposed as a Python wrapper by an independant library (pycryptosat). proposed as a Python wrapper by an independant library (pycryptosat).
For now, pycryptosat is not on pypi; so we use a fork from *For now, pycryptosat is not on pypi; so we use a fork from
[Cryptominisat repository](https://github.com/msoos/cryptominisat/tree/5.0.1) [Cryptominisat repository](https://github.com/msoos/cryptominisat/tree/5.0.1)*
Here you will find the installation of pycryptosat package: Here you will find the installation commands of the pycryptosat package:
git clone https://gitlab.irisa.fr/0000B8EG/pycryptosat/tree/5.0.1_cmake_dev git clone https://gitlab.irisa.fr/0000B8EG/pycryptosat/tree/5.0.1_cmake_dev
mkdir build mkdir build
cd build && cmake ../ cd build && cmake ../
make python_interface_install make python_interface_install
### Cadbiom ### Cadbiom
If you want to install the library with its GUI, and command line, If you want to install the library with its GUI, and command line in one command,
after the git clone step, just do: after the git clone step, just do:
make install make install
......
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