Evaluation of MERFISHtools

This Snakemake workflow generates the entire analysis of the forthcoming manuscript "A Bayesian model for single cell transcript expression analysis on MERFISH data".

Requirements

• Any 64-bit Linux installation with GLIBC 2.5 or newer (i.e. any Linux distribution that is newer than CentOS 6).

Setup

Step 1: Setup Snakemake

To run this workflow, you need to setup Snakemake via the Conda package manager. This does not require admin priviledges.

Step 2: Download the workflow

First, create a working directory:

mkdir merfishtools-evaluation
cd merfishtools-evaluation

Then, download the workflow archive from https://doi.org/10.5281/zenodo.752340. Finally, extract the downloaded archive with

tar -xf merfishtools-evaluation.tar.bz2

Step 4: Run the workflow

Then you can perfom a dry-run of the workflow with

snakemake -n

and execute the workflow using, e.g., 24 cores with

snakemake --cores 24 --use-conda

Note that the argument --use-conda is mandatory in such that Snakemake can deploy the software packages delivered together with the workflow. For further possibilities, see

snakemake --help

and http://snakemake.bitbucket.org.

Author

Johannes Köster

License

MIT