jelber2/README.md

## README.md

      
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              README.md
            
          
    MethPhaser installation

Install micromamba or mamba or conda
# Install micromamba
"${SHELL}" <(curl -L micro.mamba.pm/install.sh)
You will then see something like this in a BASH shell (parts with "(type....)" are added for instructions
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  3069  100  3069    0     0  13059      0 --:--:-- --:--:-- --:--:-- 13059
Micromamba binary folder? [~/.local/bin]  (hit enter)
Init shell (bash)? [Y/n] y (type y)
Configure conda-forge? [Y/n] y (type y)
Prefix location? [~/micromamba] (type y)
Modifying RC file "/home/jelber43/.bashrc"
Generating config for root prefix "/home/jelber43/micromamba"
Setting mamba executable to: "/home/jelber43/.local/bin/micromamba"
Adding (or replacing) the following in your "/home/jelber43/.bashrc" file

# >>> mamba initialize >>>
# !! Contents within this block are managed by 'mamba init' !!
export MAMBA_EXE='/home/jelber43/.local/bin/micromamba';
export MAMBA_ROOT_PREFIX='/home/jelber43/micromamba';
__mamba_setup="$("$MAMBA_EXE" shell hook --shell bash --root-prefix "$MAMBA_ROOT_PREFIX" 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__mamba_setup"
else
    alias micromamba="$MAMBA_EXE"  # Fallback on help from mamba activate
fi
unset __mamba_setup
# <<< mamba initialize <<<

Please restart your shell to activate micromamba or run the following:\n
  source ~/.bashrc (or ~/.zshrc, ~/.xonshrc, ~/.config/fish/config.fish, ...)
Source your .bashrc file to enable micromamba
source ~/.bashrc
Make a micromamba environment with Python3.11, pip, openssl, and ca-certificates
micromamba create -n methphaser -c bioconda -c conda-forge python=3.11 pip ca-certificates openssl -y
Activate the micromamba environment
micromamba activate methphaser
Use pip to install remaining python packages
pip3 install pysam tqdm pandas scipy matplotlib certifi seaborn
Get methphaser python scripts
git clone https://github.com/treangenlab/methphaser
Add the scripts to your PATH (your directory might be different of course)
export PATH="/home/jelber43/sandbox/methphaser/methphaser:$PATH"
Get example data to test installation
wget 'https://zenodo.org/api/records/8360845/files-archive' -O test_data.zip
Make an test_data directory, then unzip the zip file contents there.
mkdir -p test_data
unzip test_data.zip -d test_data/.
Run MethPhaser Step1 (takes < 5 min)
./methphaser/meth_phaser_parallel -b test_data/HLA.R10.haplotagged.bam -r test_data/GCA_000001405.15_GRCh38_no_alt_analysis_set.chr6.fna -g test_data/LSK.filtered.gtf -vc test_data/HLA.R10.phased.vcf.gz  -o test_data/work 

/home/jelber43/sandbox/methphaser/methphaser/methphasing:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  from pkg_resources import require
# ignore these two previous lines
Run MethPhaser Step2 (< 1 min)
./methphaser/meth_phaser_post_processing -ib test_data/HLA.R10.haplotagged.bam -if test_data/work/ -ov test_data/output.vcf -ob test_data/output -vc test_data/HLA.R10.phased.vcf.gz