/sm_test

Snakemake test files

Primary LanguagePython

sm_test

Snakemake test files

Creating the snakefile to conduct the following steps:

  1. Run FastQC
  2. Trim with trimmomatic
  3. 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

Execution Notes

  • Clone from GitHub
  • Copy config-template.yaml to config.yaml and modify to suit your data.
  • Execute with snakemake. On Pearcey, snakemake is in the Python 3.6 and Miniconda3 modules.

Visualising the DAG

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

Optional: Create Python 3.7 Virtual Environment on Pearcey

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