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:
- 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.