schimar/smk_generic

Generic snakemake workflow

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Snakemake workflow for DNA analysis (on the mach2 HPC cluster with the PBS-torque batch job submission system). This repository was initially based on the Snakemake Cluster Tutorial and the Software Carpentry lesson repository.

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conda and other dependencies

create environment from yaml file (in envs/):

# run these two once, to create the environment:
conda init bash

module load Anaconda3/2021.04/miniconda-base-2021.04 
source $UIBK_CONDA_PROFILE 

mamba env create -f envs/s6.yaml

# with this, you can activate the environment with all [dependencies](https://github.com/schimar/ta_dna_snakemake_pbs/blob/main/envs/s21.yaml):
conda activate smk6

# (also, when ssh'ing onto mach2, you can activate the env and then do a dry-run of your workflow) 


# if you've added new software to install to the conda environment, then you can update:
conda env update --name ta --file envs/s6.yaml

NOTE: the update command didn't quite work in my case, but I had to either mamba remove env smk6 and create the env anew, or use the mamba env create coimmand again. Do whatever works for you, I suppose...

Submit the main snakemake job:

qsub code/clusterSnakemake.pbs