3. Installation

Linux, Mac OSX and Windows WSL are supported by nASAP. When running nASAP, the following packages are used.

Packages	Env	Modules	Links
fastp=0.22.0	linux	preprocess	https://github.com/OpenGene/fastp
bioawk=1.0	linux	preprocess	https://github.com/lh3/bioawk
flash	linux	preprocess	https://ccb.jhu.edu/software/FLASH/
bowtie2=2.4.5	linux	alignment	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
samtools	linux	alignment	http://www.htslib.org/
bedtools	linux	alignment	https://bedtools.readthedocs.io/en/latest/
pyBigWig=0.3.17	Python	feature assign	https://github.com/deeptools/pyBigWig

3.1 conda install

Create env.yml file.

# env.yml
name: nasap_env
dependencies:
- libcurl=7.87.0
- scipy=1.5.2
- pandas=1.1.5
- hvplot=0.7.3
- pip=21.2.2
- bioconda::deeptools=2.5.7
- bioconda::pybigwig=0.3.17
- bioconda::pysam=0.8.3
- bioconda::bioawk=1.0
- bioconda::bedtools=2.30.0
- bioconda::bowtie2=2.3.5.1
- bioconda::fastp=0.22.0
- bioconda::flash=1.2.11
- bioconda::fastq-pair=1.0
- bioconda::samtools=1.13
- pip:
  - nasap==0.2.9

Create and activate conda env.

conda env create -f ./env.yml
conda activate nasap_env

3.2 docker install

docker pull biodancer/nasap:latest
# test container 
docker run --rm -it -v `pwd`/data:/tmp -w /tmp biodancer/nasap:latest nasap --help

3.3 pip install

pip install nasap

If the installation failed, try running the command below.

pip install python-dev-tools

3.4 source code install

git clone https://github.com/biodancerwangzhi/nasap.git
cd nasap
python setup.py install