02. Installation and dependencies
Notice that the pipeline requires the "UTF-8" encoding for text files, in order to run both the conda environment building and to allow the reading of configuration tables by the pipeline.
Usually ChIP-seq experiments represent a large amount of data that may be difficult to analyze on a desktop machine, for this reason we strongly recommend the use of a cluster/high-performance computation (HPC) system to run analyses with this pipeline.
In the Example for testing section of this Wiki we provide some insights on CPU and memory usage for a test data set.
To install the pipeline it is required to download this repository and install a conda environment for which we provide a building file.
Follow the steps below for the installation:
- navigate to the directory where the repository should be downloaded by typing, for instance:
cd $HOME - download the GitHub repository with
git clone https://github.com/sebastian-gregoricchio/SPACCa, or click on Code > Download ZIP on the GitHub page - install the conda environment from the .yaml environment file contained in the repository:
conda env create -f $HOME/SPACCa/workflow/envs/SPACCa_conda_env_stable.yaml - activate the conda environment:
conda activate SPACCa(if the env is not activated the pipeline won't work properly)
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