Installing Connor

Connor requires python 2.7 or later and has been tested with:

Connor does not work in Windows OS because it depends on the python library pysam, which is not supported on Windows.

Connor runs in a single process and typical runs consume less than 2Gb mem.

Prerequisites

Python (2.7 or later) and pip. See https://www.python.org/downloads/ for more details on downloading a recent version of Python 2/3.

Note

Pip installs all required libraries; see [Installing] below.

The simplest way to install Connor is through PyPI:

$ pip install connor
You can also install Connor via the conda envirionment/package manager using the bioconda channel:

$ conda install -c bioconda connor
If you don't have root permissions, you can install connor locally:

$ pip install connor --user

Following a --user install, you may need to adjust your path settings to include $HOME/.local/bin.
You can also install directly from source from github:

$ pip install git+https://github.com/umich-brcf-bioinf/Connor

$ pip uninstall connor

If you already have prerequisite modules installed, you can also clone from github and run directly from the source like so:

$ git clone https://github.com/umich-brcf-bioinf/Connor

$ connor/connor-runner.py input.bam output.bam

For running automated tests, Connor also requires: