bash snakeflow-enviroment-setup.sh

# Step1: activate snakemake
source activate snakeflow

# Step2: clone this repo

# Step3: copy all your fastq files into fastq dir
find . -name "*fastq.gz" | while read id; do cp $id fastq/; done;

# Step4: modify config.yml with your own paramter
# Note: put config.yml in the same dir with your snakefile.
vim  config.yml

# Step5: run snakemake with -np option. this test your ``commands`` runs without any errors.
snakemake -s salmon-tximport-deseq2-v0.2.snakefile -np

# Step6: export workflow charts
snakemake -s salmon-tximport-deseq2-v0.2.snakefile --dag | dot -Tpdf > dag.pdf

# Step7: or using the default snakemake environment you've created above.
snakemake -s salmon-tximport-deseq2-v0.1.snakefile -p -j 8