yixf-self / install_gistic

Install GISTIC2 by one line code

Install GISTIC2 by one line code

I have written two Chinese blogs for telling readers how to install GISTIC 2.0 (a famous software for copy number analysis) step by step. Recently I realize the installation steps can be implemented automatically, so I write this program.

Update:

• 2020-03-08: add system check

Install from script

1. Download GISTIC 2.0 from ftp://ftp.broadinstitute.org/pub/GISTIC2.0
2. Download this repository.

git clone https://github.com/ShixiangWang/install_GISTIC
cd install_GISTIC
chmod u+x install_GISTIC2.sh

3. Run script.

This program is a pure bash script and can be run in the following way.

./install_GISTIC2.sh args1 args2

# args1: the path to GISTIC_x_x_xx.tar.gz file
# args2: the install directory, must be absolute path, not relative path

Install from docker

Two ways:

Just pull from Docker hub https://hub.docker.com/r/shixiangwang/gistic.

docker pull shixiangwang/gistic

Build the image by yourself.

git clone https://github.com/ShixiangWang/install_GISTIC
cd install_GISTIC
sudo docker build -t gistic:latest .

Run docker image

sudo docker run -it gistic /bin/bash

The installed GISTIC is located at /opt/GISTIC.

Note

unset DISPLAY is recommendly added to run script for avoiding X11 related errors.

This program is tested and currently only support GISTIC 2.0.23, any suggestion or pull request is welcome.

LICENSE

MIT © 2019-2020 Shixiang Wang