Easy Installation

This guide helps you install PSAIA with basic features. We recommend building PSAIA with Docker to avoid dependency issues. We recommend compiling PSAIA(and possibly its requirements) from the source code using the latest compiler for the best performace. You can also deploy PSAIA without building by Docker . Please note that PSAIA only supports Linux; for Windows users, please consider using WSL or docker.

Prerequisites

This program needs Naccess, And it is currently not open source and needs to be downloaded from http://www.bioinf.manchester.ac.uk/naccess/ .
This program needs Qcontacts, And it is currently open source and can be downloaded from https://github.com/brunoV/qcons.

Requirements

Some of these packages can be installed with popular package management system, such as apt and yum:

sudo apt update && apt install -y --no-install-recommends \
    g++ lib32z1 csh git ca-certificates sudo vim bc

If your system is already able to run the software at this point, there is no need to continue running further. However, if it is not working yet, you will need to follow the steps below to configure the necessary environment for the software.

Due to the requirement of libgfortran3 by PSAIA, we need to install the g++ -6 that it requires. Meanwhile, g++ -6 also requires the prerequisite software gnupg2, you can follow these steps below to download them:

sudo echo "deb http://dk.archive.ubuntu.com/ubuntu/ bionic main universe" >> /etc/apt/sources.list
sudo apt install -y gnupg2
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 3B4FE6ACC0B21F32
sudo apt update
sudo apt-get install -y --no-install-recommends g++-6
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-6 6
sudo apt-get install libgfortran3 

Please refer to our guide on requirements.

Get PSAIA source code

Of course a copy of PSAIA source code is required, which can be obtained via one of the following choices:

Clone the whole repo with git: git clone https://github.com/RUC-MIALAB/PSAIA.git
Clone the minimum required part of repo: git clone https://github.com/RUC-MIALAB/PSAIA.git --depth=1
Get the source code of a latest version from here

Update to latest release

Please check the release page for the release note of a new version.

It is OK to download the new source code from beginning following the previous step.

To update your cloned git repo in-place:

git remote -v
# Check if the output contains the line below
# origin https://github.com/RUC-MIALAB/PSAIA.git (fetch)
# The remote name is marked as "origin" if you clone the repo from your own fork.

git fetch origin
git checkout v0.0.1 # Replace the tag with the latest version
git describe --tags # Verify if the tag has been successfully checked out

Container Deployment

We’ve built a ready-for-use version of PSAIA with docker. For a quick start: pull the image, prepare the data, run container. Instructions on using the image can be accessed in Dockerfile.