INSTALL

To install pydpiper, both the current source and most stable release can be downloaded from github:

https://github.com/Mouse-Imaging-Centre/pydpiper

Using the Downloads button, access the .tar.gz or .zip file.
Unzip and untar and change into the source directory (e.g. cd pydpiper)
Run: python setup.py install 

System dependencies:

minc-toolkit v2 - https://github.com/BIC-MNI/minc-toolkit-v2
minc-stuffs - https://github.com/Mouse-Imaging-Centre/minc-stuffs
graphviz - http://www.graphviz.org/ (optional)

Various Python libraries are also required (see `setup.py` for details); these should
be installed automatically by setuptools when the above command is run.

We use [`qbatch`](https://github.com/pipitone/qbatch) for submitting jobs to compute grid queues.  Installing Pydpiper will install the `qbatch` binary as well, but you must ensure this (and a somewhat recent version of GNU Parallel) is in your path. To configure Pydpiper for your queue, you may configure qbatch directly using `QBATCH_*` environment variables to whatever extent you desire and further specify or override whatever you choose using Pydpiper flags (or a config file or environment vars; see the README); however, the default is currently local execution so you must tell Pydpiper what `--queue-type` you intend.  (We also have a "headless" mode developed for "capacity" queues such as Compute Canada's SciNet grid; this mode uses `qsub` directly and only works with TORQUE/PBS queues at the moment but will soon use `qbatch` as well.)