ta_dna_snakemake_pbs

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Snakemake workflow for Tetramorium alpestre 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. If you want to run your own custom workflow, check out the insert link here generic workflow.

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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