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HighlanderLab / tree_seq_pipeline

Pipeline to infer tree sequences with different datasets
MIT License
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Add step-by-step instructions on how to get this going into README #33

Closed gregorgorjanc closed 1 year ago

gregorgorjanc commented 1 year ago

Here are my notes

Add this to your ~/.bash_profile or equivalent file

export DRMAA_LIBRARY_PATH=/exports/applications/gridengine/ge-8.6.5/lib/lx-amd64/libdrmaa.so

Then on Eddie

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 &