Download and Installation

Author: SeekGene

Time: 2 min

Words: 209 words

Updated: 2026-02-26

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scMethyl + RNA-seq Download

Clone

Clone the repository:

git clone https://github.com/seekgene/SeekSoulMethyl.git
cd SeekSoulMethyl

Create and activate conda environment:

For users in China:

conda env create -n seeksoulmethyl -f conda_dependencies.zh.yml
conda activate seeksoulmethyl

For international users:

conda env create -n seeksoulmethyl -f conda_dependencies.yml
conda activate seeksoulmethyl

Installation

Install the package:

cd dependence
pip install . \
  simpleqc/target/wheels/simpleqc-0.1.0-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl \
  search-pattern/target/wheels/search_pattern-0.1.0-py3-none-manylinux_2_5_x86_64.manylinux1_x86_64.whl
cd ..

We will download our modified versions of Bismark and ALLCools for analysis.

• Bismark adds the CB (error-corrected barcode) tag and the UR (raw UMI) tag to BAM files.
• ALLCools performs UMI deduplication and methylation level calculation based on the UR tag.

# Clone and install custom ALLCools
conda activate seeksoulmethyl
git clone https://github.com/seekgene/ALLCools.git && \
pip install ./ALLCools && \
rm -rf ./ALLCools

# Clone and install custom Bismark
git clone https://github.com/seekgene/Bismark.git && \
bin_path=$(dirname `which python`)
cp -r ./Bismark/* $bin_path/ && \
    chmod +x $bin_path/bismark* && \
    chmod +x $bin_path/deduplicate_bismark && \
    rm -rf ./Bismark