qlogin -l h_vmem=32G
module load anaconda/5.3.1
conda deactivate # you might need to run this multiple times! there should be no (env) in your prompt!
# assuming that conda is properly setup - usually you do this
#
# conda init bash
# conda config --add envs_dirs /exports/cmvm/eddie/eb/groups/HighlanderLab/anaconda/envs
#
# which will give you these envs and pkgs entries in ~/.condarc
#
# cat ~/.condarc
# envs_dirs:
# - /exports/cmvm/eddie/eb/groups/HighlanderLab/anaconda/envs
# pkgs_dirs:
# - /exports/cmvm/eddie/eb/groups/HighlanderLab/anaconda/pkgs
conda activate HLab_tsinfer
# Go to your workplace
cd XYZ
git clone https://github.com/HighlanderLab/tree_seq_pipeline.git
cd tree_seq_pipeline
# edit Snakemake/config/tsinfer_Eddie.yaml, particularly
# workdir
# vcfDir
# meta
# ancestralAllele
cd Snakemake/workflow
# Interactive use
snakemake
snakemake -j 1 --use-conda -n # dry run
snakemake -j 1 --use-conda # actual run
snakemake -j 1 --use-conda -F # force rerun
# Submit to cluster
snakemake -j 32 --use-conda --drmaa " -l h_vmem=32G" --jobscript jobscript.sh &
snakemake -j 32 --use-conda --drmaa " -l h_vmem=32G" --jobscript jobscript.sh -F &
Here are my notes
Add this to your
~/.bash_profile
or equivalent fileThen on Eddie