Installation

Panopticon can be installed from pypi using:

pip install panopticon-single-cell

Or you can install panopticon on the command line by cloning this git repository. Because this package is in active development, I recommend installing with the --editable flag.

git clone https://github.com/scyrusm/panopticon.git
cd panopticon
pip install --editable .

For some functions you will also need to run (release subject to change)

pyensembl install --release 75 --species homo_sapiens

Now try exploring the exciting panopticon programming with

panopticon --help

If you would like autocompletion of panopticon commands (though I don’t do this myself), put the following line in your .bashrc

eval "$(_PANOPTICON_COMPLETE=source panopticon)"

File locking

I strongly recommend using file locking, to ensure that you do not accidentally open a .loom file outside of a ‘with’ context in two place concurrently. If you do this, your .loom file may become corrupted.

To ensure that file locking is used, set the following environmental variable, e.g. in your .bashrc

export HDF5_USE_FILE_LOCKING=TRUE