Quick installation using pip¶
The following assumes you have pip
on your system (this comes standard with new Macs for instance), that you have made a virtualenv or a conda environment and that you’re connected to the internet.
The key steps for the minimal install are:
Install numpy
$ pip install numpy
Use pip to download, build and install PyCogent.
$ pip install cogent
If the above fails to download PyCogent you can download an archive to your hard drive and then do.
$ pip install path/to/pycogent-master.zip
Optional installs¶
To use the Ensembl querying code¶
$ pip install cogent[mysql]
To use the parallel capabilities¶
$ pip install cogent[mpi]
To install all dependencies¶
$ pip install cogent[all]
This will install all the above and matplotlib for drawing
To use the development version of PyCogent¶
Just replace the first line of the requirements file with git+https://github.com/pycogent/pycogent.git
.