snakemake --forceall --dag | dot -Tpng > dag.png
Make sure that [Miniconda 3] is installed. When prompted, answer yes to add conda to the PATH environment variable.
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
Download bisread-sra pipeline
git clone https://github.com/hdinhdp/bisread-sra.git
Go to the bisread-sra directory
cd bisread-sra
Use the yaml file to install all required software into an isolated Conda environment with the name bisread-sra
conda env create --name bisread-sra --file environment.yml
Activate the environment
source activate bisread-sra
Note: to exit the environment, just execute the following command. Don't do this until you are done working.
source deactivate
Make the samples.json file with all the SRA ids.
The current config.yml
file may not be compatible with the library type. Make sure to modify this file using a text editor to your specific
library parameters if this is not a WGBS data.
It is possible to speedup the process by allowing snakemake to spawn multiple jobs in parallel whenever possible by specifying the job number.
snakemake --jobs 4