Class materials for the NIH HPC snakemake class
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00container exercises 05 and 06 Feb 7, 2018
exercise00 bug fixes Feb 7, 2018
exercise01 fixed some formatting Feb 7, 2018
exercise02 bug fixes Feb 7, 2018
exercise03 bug fixes Feb 7, 2018
exercise04 exercises 05 and 06 Feb 7, 2018
exercise05 fixed some formatting Feb 7, 2018
exercise06 wrong module name in readme Feb 21, 2018
.gitignore bug fixes Feb 7, 2018
LICENSE work on exercise 2 and simplifly setup procedure Feb 6, 2018
README.md wrong module name in readme Feb 21, 2018
Snakefile more missing files in 00ref Feb 7, 2018
setup.sh fixing bugs in setup Feb 7, 2018

README.md

https://www.singularity-hub.org/static/img/hosted-singularity--hub-%23e32929.svg

Setup - please complete before class

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.