Installation¶

System requirements¶

The reference files can be downloaded from zenodo.

We recommend to create an independent conda environment for SCRIP. If users do not have conda, please install Miniconda first:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

git clone git@github.com:wanglabtongji/SCRIP.git
cd SCRIP
python setup.py install

pip install scrip

SCRIP fast searching is based on GIGGLE. Please install GIGGLE manually first.

Simply you can use SCRIP install_giggle to install GIGGLE.

Or try manually installation:

git clone git@github.com:ryanlayer/giggle.git
cd giggle
make
export PATH=$PATH:`pwd` # or cp bin/giggle to your environment
cd ..

Next, validate the installation:

giggle

It should return:

giggle, v0.6.3
usage:   giggle <command> [options]
   index     Create an index
   search    Search an index