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Last active September 5, 2022 19:24
installing groopm2

###a.) first create env with most dependencies:

conda create -n groomp2 python=2.7 matplotlib scipy bamm cython pillow pytables tempdir diamond hmmer pplacer mfqe orfm

###b.) obtain pip3 and use it to install singlem globally (while currently in the base environment OR any python3 environment)

sudo apt update
sudo apt install python3-pip
conda deactivate

conda deactivate # deactivate not only conda environment but also conda entirely (until you don't even see the base einvironment)

# This script calculates the depth of coverage and breadth of coverage for a given bam.
# Outputs a dictionary containing the contig/chromosome names and the depth and breadth of coverage for each
# and for the entire genome.
# If you optionally specify the name of the mitochondrial chromosome (e.g. mtDNA, chrM, chrMT)
# The script will also generate breadth and depth of coverage for the nuclear genome AND the ratio
# of mtDNA:nuclearDNA; which can act as a proxy in some cases for mitochondrial count within an individual.
# Author: Daniel E. Cook