Snakemake test files
Creating the snakefile to conduct the following steps:
- Run FastQC
- Trim with trimmomatic
- align to reference and estimate abundance with Trinity - TBD 5 (?). Normalise FKPM and TPM - TBD
Additionals: 6. Map to ERCC reference in Bowtie2 - TBD 7. de-novo assembly with Trinity
- Clone from GitHub
- Copy
config-template.yaml
toconfig.yaml
and modify to suit your data. - Execute with
snakemake
. On Pearcey, snakemake is in the Python 3.6 and Miniconda3 modules.
On CSIRO clusters, you need to load the imagemagick module to get the display
command. Once done, this will work:
snakemake --dag | dot -Tpng | display
This is a workaround for the fact that the Python 3.7 module does not contain snakemake, and the version installed in Python 3.6 is old.
Load the Python 3.7 module and create a Python virtual environment:
module load git python/3.7.2
git clone git@github.com:EPLeyne/sm_test.git
cd sm_test
source /apps/python/3.7.2/bin/virtualenvwrapper_lazy.sh
mkvirtualenv -a . snakemake
workon snakemake
pip install snakemake
From that point on you will need to activate the virtual Python environment each time:
module load git python/3.7.2
source /apps/python/3.7.2/bin/virtualenvwrapper_lazy.sh
workon snakemake