Setup

Cloning from github

The INNFER repository can be directly cloned from github with the following command

git clone https://github.com/gputtley/INNFER.git

Installing conda and the environment

Running on the code relies on multiple python packages which are installed using a conda environment. Firstly, conda needs to set up. To install this you can run the following command. You may need to click enter and yes through all prompts. If you already have conda installed, this initial command may not be needed.

source setup.sh conda

Next, you will need to set up the environment, with the following command.

source setup.sh env

Setup SnakeMake

The framework is set up to work with the SnakeMake workflow manager. Firstly, this needs to be setup for the local batch service. To do this for HTCondor run through the following steps.

source setup.sh snakemake_condor

You should call the profile htcondor and if you wish to looks at the condor submission logs then set this directory to somewhere accessible. Note, this is only setup for use on HTCondor batch systems.

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Next: Running INNFER.