PyBioShell is a set of Python bindings to BioShell library. It allows use of BioShell classes like any other Python modules. The closest tool similar by functionality is Biopython, which however is partially written in Python.
The easiest option to get PyBioShell on your machine is to download precombiled library, available for the following Python versions. Click on an appropriate link below:
or type this command in your terminal:
curl -O http://bioshell.pl/downloads/bioshell/Python37/pybioshell.so
Remember to add path with
pybioshell.so to your shell variables e.g.
or add this variable to your
echo 'export PYTHONPATH="$PYTHONPATH:$HOME/bioshell/bin" ' >> ~/.bashrc
Remember also to add
data/ directory to your shell variables. Look here for details.
Another way is to compile it from sources, following the steps given below. The procedure assumes your
bioshell repository is located in
src.git/binder/; these paths are arbitrary but the commands must be adjusted accordingly.
In order to compile
binder, you need to have
Ninja building tool (website) and cmake. You will also need python headers,
python-dev package or similar (e.g.
python3.5-dev). On Ubuntu Linux you can install them with
sudo apt-get install ninja-build cmake python-dev
The use of
clang compiler is advised. Try to get
clang-6.0 or newer (see this link)
1. Clone and compile
To clone binder from its github repository:
git clone https://github.com/RosettaCommons/binder cd binder python3 ./build.py -j 4
where the last command actually builds binder using four CPU cores for that. Note, that binder uses more than 1GB of disc space and its compilation may take a few hours.
2. Build PyBioShell¶
scripts/build_pybioshell.py file and edit variables, adapting it to your system. In particular, you most likely have to fix
clang++ version (
LINKER_CMD variable) as well as the path where the
binder executable is located (
Make a directory
build_bindings in the main BioShell directory, i.e in the directory where
pybioshell.config is located.
Choose your Python version and run the compilation as follow:
python3 build_pybioshell.py -v 3.5
You should find your compiled version in
bin/pybioshell.so. If you have any problems with compilation, please do not hesitate to contact us.