There are two different ways to install Atlas:
Install Atlas natively (Recommended).
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.
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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-packagesfolder 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
Why Python3?: Atlas is intended to be used with >=python3.4 because python2.7 won’t receive further development past 2020, including security updates.
pip, Python, and Anaconda: Be aware which pip you invoque. You could install pip3 with
sudo apt-get install python3-pipif you have system rights, or install python3 from source, and adding
<python3 path>/bin/pip3to the path, or linking it in a directory like
$HOME/binwhich 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 pip3to find out the source of pip, and type
python -m siteor
python3 -m siteto 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
Adding the path to
$HOME/.profileallows python to find the package installation folder after each user login. Similarly, adding the path to
$HOME/.bashrcallows python to find the package after each terminal invocation. Other options include setting the
PYTHONPATHenvironmental variable in a sh file (see the example folder) or invoke
python3 setup.py clean build installto install Atlas as it was downloaded from the PyPI server.