After cloning this repository, a number of steps (downloading the singularity
container and data, ...) have to be carried out to complete before starting
class. This requires that singularity and snakemake are on the path
for the setup. Here is an overview of the complete setup:
On the NIH HPC systems start an interactive session and clone the repository:
user@headnode> sinteractive --cpus-per-task=12 --mem=24g --gres=lscratch:20
...
user@cn1234> module load singularity snakemake hisat
user@cn1234> cd /data/$USER # or whereever you'd like the class directory to be
user@cn1234> git clone https://github.com/NIH-HPC/snakemake-class.git
user@cn1234> cd snakemake-class
Then run the setup
user@cn1234> ./setup.sh
...
+------------------------------------------------------------------------------+
| |
| Class materials have been set up successfully |
| |
+------------------------------------------------------------------------------+
The Snakefile in the root directory of the repo takes care of all the setup
required for class. It also serves as another example for a Snakemake workflow.