Installation

There are three ways to install ANNOgesic. Please refer to the following sections. ANNOgesic can only work when the requirements are installed properly. If you install ANNOgesic through source code or pip3, please install the pre-required tools by yourself.

Github

All the source code including a run script (contains all the commands which are presented in tutorial) of ANNOgesic can be retrieve from our Git repository. Using the following commands can clone the source code easily.

$ git clone https://github.com/Sung-Huan/ANNOgesic.git

or

$ git clone git@github.com:Sung-Huan/ANNOgesic.git

In order to make ANNOgesic runnable, we should create a soft link of annogesiclib in bin.

$ cd ANNOgesic/bin
$ ln -s ../annogesiclib .

Docker

Some modules of ANNOgesic need third-party tools. In order to avoid all the possible issue caused by the dependencies, a Docker image is provided. For the details of Docker image, please check here.

For using Docker image, please use one of the following commands:

  1. You can simply pull the Docker image as following
$ docker pull silasysh/annogesic

2. Alternatively, you can build the image via Dockerfile. Please Download the Dockerfile from our Git repository. Then switch to the folder which Dockerfile are located. For the following commands, please refer to here.

If you want to check other commands of Docker, please refer to here.

Singularity

Singularity is another way to install ANNOgesic via Docker image without root permission.

$ singularity build \
    annogesic.img \
    docker://silasysh/annogesic:latest

After building Singularity image of ANNOgesic, the user just needs to put the following line before the command that needs to be executed.

singularity exec -B $STORAGE_PATH annogesic.img

Please put the storage path of your home directory to $STORAGE_PATH. df can be used to check the storage system.

pip3

ANNOgesic is also hosted in PyPI server. Thus, it can be simply installed via pip3.

$ pip3 install ANNOgesic
$ pip3 install ANNOgesic --upgrade

You can also install ANNOgesic without root permission.

$ pip3 install --user ANNOgesic
$ pip3 install ANNOgesic --user --upgrade

Install Dependencies

If the user want to install ANNOgesic via source code, get_package_database.sh can provide a way to install tools and download database automatically. The required versions of the tools will be shown on the screen as well.