Installation¶

There are two different ways to install Atlas:

Install Atlas natively (Recommended).

OR
Clone the Github repository. If you are familiar with git, Atlas can be cloned and the respective folder added to the python path. Further details are below.

Note

Need Help? If you run into any problems with installation, please visit our chat room: https://gitter.im/glucksfall/pleiades

Option 1: Install Atlas natively on your computer¶

The recommended approach is to use system tools, or install them if necessary. To install python packages, you could use pip, or download the package from the python package index.

Install with system tools

With pip, you need to execute and Atlas will be installed on $HOME/.local/lib/python3.6/site-packages folder or similar.
```
pip3 install atlas_rbm --user
```
If you have system rights, you could install Atlas for all users with
```
sudo -H pip3 install atlas_rbm
```
Download from the python package index

Alternatively, you could download the package (useful when pip fails to download the package because of lack of SSL libraries) and then install with pip. For instance:
```
wget https://files.pythonhosted.org/packages/ec/ed/8b94e0a29f69a24ddb18ba4a4e6463d3ecede308576774e86baf6a84b998/atlas_rbm-1.0.2-py3-none-any.whl
pip3 install atlas_rbm-1.0.2-py3-none-any.whl --user
```
Note

Why Python3?: Atlas is intended to be used with >=python3.4 because python2.7 won’t receive further development past 2020, including security updates.

Note

pip, Python, and Anaconda: Be aware which pip you invoque. You could install pip3 with sudo apt-get install python3-pip if you have system rights, or install python3 from source, and adding <python3 path>/bin/pip3 to the path, or linking it in a directory like $HOME/bin which is commonly added to the path at login. Also be aware that, if you installed Anaconda, pip could be linked to the Anaconda specific version of pip, which will install Atlas into Anaconda’s installation folder. Type which pip or which pip3 to find out the source of pip, and type python -m site or python3 -m site to find out where is more likely Atlas will be installed.

Option 2: Clone the Github repository¶

Clone with git

The source code is uploaded and maintained through Github at https://github.com/networkbiolab/atlas. Therefore, you could clone the repository locally, and then add the folder to the PYTHONPATH. Beware that you should install the pysb package (pysb) and others packages by any means, specially the Jupyter Notebook project (https://jupyter.org).
```
path=/opt/atlas
git clone https://github.com/networkbiolab/atlas $path
echo export PYTHONPATH="\$PYTHONPATH:\$path" >> $HOME/.profile
```
Note

Adding the path to $HOME/.profile allows python to find the package installation folder after each user login. Similarly, adding the path to $HOME/.bashrc allows python to find the package after each terminal invocation. Other options include setting the PYTHONPATH environmental variable in a sh file (see the example folder) or invoke python3 setup.py clean build install to install Atlas as it was downloaded from the PyPI server.