QuagmiR on Biowulf - Gu-Lab-RBL-NCI/QuagmiR GitHub Wiki

Install QuagmiR on Biowulf

Use ssh biowulf.nih.gov to connect from the terminal command line to Biowulf

Installation of QuagmiR on Biowulf

• a. Download repository git clone https://github.com/Gu-Lab-RBL-NCI/QuagmiR
• b. Go to the repository cd QuagmiR/
• c. Activate Anaconda Module module load Anaconda
• d. Activate environment dependencies conda env create -f environment.yml

Pre-run a QuagmiR job on Biowulf

1. Load fastq file on the data folder
2. Load/edit your motif-consensus.fa file
3. (Optional) Edit the config.yaml file if necessary

Run a QuagmiR job on Biowulf

4. Activate and interactive job module sinteractive --mem=20g --cpus-per-task=4 Wait for few minutes to get the resources
5. Activate Anaconda Module module load Anaconda
6. Activate QuagmiR source activate quagmir
7. Unlock snakemake snakemake --unlock
8. Run snakemake snakemake
9. Once the job is done you can leave the interactive module with exit