BSviz

Setup

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --add channels https://conda.anaconda.org/biocore

conda env create --file environment.yaml
conda activate BSviz

Launch

flask run -p 5000 -h 0.0.0.0

Access http://127.0.0.1:5000/

Export enviromnent.yaml (Only for developers)

Linux

conda create -n BSviz python=3.7 anaconda
conda activate BSviz
conda install -c https://conda.anaconda.org/biocore scikit-bio
conda install -c bioconda bismark pybedtools
# pip install pybedtools
conda install openblas
conda list --export | grep -v "pyqt" > environment.linux.yaml

Mac OS

conda create -n BSviz python=3.7 anaconda
conda activate BSviz
conda install -c https://conda.anaconda.org/biocore scikit-bio
conda install -c bioconda bismark
pip install pybedtools
conda install openblas
conda list --export | grep -v "pyqt" > environment.macos.yaml

build bismark index

mkdir -p ~/reference/bismark/Gencode_v34/fasta
cd ~/reference/bismark/Gencode_v34/fasta
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.p13.genome.fa.gz
bismark_genome_preparation --parallel 40 ~/reference/bismark/Gencode_v34/fasta

mkdir -p ~/reference/bismark/Gencode_M25/fasta
cd ~/reference/bismark/Gencode_M25/fasta
wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/GRCm38.p6.genome.fa.gz
bismark_genome_preparation --parallel 40 ~/reference/bismark/Gencode_M25/fasta

download reference

wget http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gff3.gz
wget http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/gencode.vM25.annotation.gff3.gz

Developpers

Yoshiaki Yasumizu, Yasunari Matsumoto

Licence

This software is freely available for academic users. Usage for commercial purposes is not allowed. Please refer to the LICENCE page.

yyoshiaki/BSviz