Bisread-sra

View the pipeline

snakemake --forceall --dag | dot -Tpng > dag.png

Preliminary steps

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

Generating samples.json and configuring config.yml

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.

Run the snakemake

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