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 Python3.5 and Python3.7 from this page
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¶
BuildPython.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.
There are three scripts availble for other Python versions BulidPython27.py, BuildPython35 and BuildPython37.py. Choose your Python version
and run the compilation as follow:
You should find your compiled version in
bin/pybioshell.so. If you have any problems with compilation, please do not hesitate to contact us.