Download and Installation

Author: SeekGene

Time: 2 min

Words: 387 words

Updated: 2026-05-28

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scMethyl + RNA-seq Download

Clone the Repository

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

Create the 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

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 ..

Install Modified Dependencies

SeekSoul™ Methyl Tools relies on customized versions of Bismark and ALLCools:

• Bismark: adds CB and UR tags to BAM records
• ALLCools: supports UR-based UMI correction and methylation quantification

conda activate seeksoulmethyl

# Install custom ALLCools
git clone https://github.com/seekgene/ALLCools.git
pip install ./ALLCools
rm -rf ./ALLCools

# 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

Download the Reference Database

Prebuilt reference archives are available for common species:

# Human reference genome (GRCh38)
wget -dc -O human-reference-GRCh38.tar.gz "https://seekgene-public.oss-cn-beijing.aliyuncs.com/methy_demo/methy_exp/v1.1/human-reference-GRCh38.tar.gz"
wget -dc -O human-reference-GRCh38.tar.gz.md5 "https://seekgene-public.oss-cn-beijing.aliyuncs.com/methy_demo/methy_exp/v1.1/human-reference-GRCh38.tar.gz.md5"

# Mouse reference genome (GRCm39)
wget -dc -O mouse-reference-GRCm39.tar.gz "https://seekgene-public.oss-cn-beijing.aliyuncs.com/methy_demo/methy_exp/v1.1/mouse-reference-GRCm39.tar.gz"
wget -dc -O mouse-reference-GRCm39.tar.gz.md5 "https://seekgene-public.oss-cn-beijing.aliyuncs.com/methy_demo/methy_exp/v1.1/mouse-reference-GRCm39.tar.gz.md5"

# Extract archives
tar -xzf human-reference-GRCh38.tar.gz
tar -xzf mouse-reference-GRCm39.tar.gz

If you need to build a custom reference database, see:

• Reference genome database guide
• Full build tutorial

Download Test Data

For downloading demo data, please refer to the Datasets document.

Demo Resources

For complete demo datasets and downloadable result bundles, see the supplementary documents:

• Cell line demo datasets