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Software Requirements
an initial python venv
bonito has a very specific requirement on pytorch 1.10.0, so depending on the base CUDA version we'll look at setting up one of these two:
# CUDA 11.1
pip install torch==1.10.0+cu111 torchvision==0.11.0+cu111 torchaudio==0.10.0 -f https://download.pytorch.org/whl/torch_stable.html
# CUDA 10.2
pip install torch==1.10.0+cu102 torchvision==0.11.0+cu102 torchaudio==0.10.0 -f https://download.pytorch.org/whl/torch_stable.html
since we're wanting to use the A100's I'm assuming that they're running CUDA 11, but just wanted to capture this note
bonito
guppy (I see there is a nightly build of IGV that supports the new modbam tags, so worth testing)
samtools
bedtools
minimap2
nextflow
clair3 (as implemented below)
the specific workflow: nextflow run epi2me-labs/wf-human-snp --help
whatshap
cuteSV
sniffles2
IGV (though this might need some work as it's GUI based)
could look at the web server version