Work with Python

Python 2 and Python 3 are both available via python2 and python3. The command python is an alias for python2. We recommend to be explicit about which version you want to use, also when using the default Python 2, i.e. use python2 when you know your script requires Python 2 and python3 when you know it requires Python 3.

The below examples uses Python 2, but it works analogously in Python 3, i.e. just replace python2 with python3.

Installing Python packages

The standard way to install Python packages is by using the pip package management system. You often find installation instructions online such as:

$ pip install HTSeq

It will not work. If you attempt to run this as-is on the cluster, you get lots of errors complaining about lack of write permissions etc., which is because it tries to install the package in the system-wide Python package folder (to which only sysadms have write permission). You might also see instructions saying you should use sudo ... - that will also not work for the same reason.

There are two ways for non-privileged users to install Python packages using the ‘pip’ module:

  1. Install globally to your home directory (typically ~/.local/lib/python2.7/site-packages/) using python2 -m pip install --user ...

  2. Install locally to a project-specific folder (e.g. ~/my_project/) using python2 -m pip install ... in a self-contained Python virtual environment

Both are done from the terminal. Which one you choose depends on your needs; for some projects you may want to use the virtual environment approach whereas for your everyday work you might want to work toward your global Python package stack. Installing globally is the easiest, because you don’t have to remember to activate a virtual environment and if you need the Python package in different places, you only have to install it once. However, if you are concerned about reproducibility, or being able to coming back to an old project of yours, you most likely want to use a virtual environment for that project so that its Python packages are not updated when you update or install Python packages globally. This is also true if you collaborate with others in a shared project folder.

1. Installing globally (aka “user-site”)

First of all, if an online installation instructions says pip install ..., replace that with python2 -m pip install .... Second, to install globally to your home directory, remember to always specify the --user option. For example,

[alice@dev3 ~]$ python2 -m pip install --user HTSeq
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won t be maintained after that date. A future version of pip will drop support for Python 2.7. More details about Python 2 support in pip, can be found at
Collecting HTSeq
  Cache entry deserialization failed, entry ignored
  Downloading (1.0MB)
    100% |████████████████████████████████| 1.0MB 685kB/s 
Requirement already satisfied (use --upgrade to upgrade): numpy in /usr/lib64/python2.7/site-packages (from HTSeq)
Collecting pysam>=0.9.0 (from HTSeq)
  Cache entry deserialization failed, entry ignored
  Using cached
Installing collected packages: pysam, HTSeq
  Running install for pysam ... done
Successfully installed HTSeq-0.11.2 pysam-0.15.3
You are using pip version 8.1.2, however version 19.3.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

[alice@dev3 ~]$

To see all Python packages that you have installed globally, use python2 -m pip list --user. To also see packages installed site wide on the cluster, use python2 -m pip list. Packages installed with python2 -m pip list --user are typically installed to your ~/.local/lib/python2.7/site-packages/ folder. If CLI executables are installed with one of those packages, they are often installed to ~/.local/bin/.

2. Installing to a virtual environment (aka “virtualenv”)

An alternative to install globally to your home directory, is to install to a local folder using a, so called, Python virtual environment. A virtual environment is a self-contained folder that contains the Python executable and any Python packages you install. When you activate a virtual environment, environment variables like PATH is updated such that you will use the Python executable and the packages in the virtual environment and not the globally installed ones.

Below is an example on how to set up a virtual environment and install the HTSeq package and all of its dependencies into it.

2.1 Install required tools (once per account)

In order to use virtual environments, we need the virtualenv tool. Following the above instructions, you can install it to your global stack as:

[alice@dev3 ~]$ python2 -m pip install --user virtualenv
Collecting virtualenv
  Downloading (3.4MB)
     |████████████████████████████████| 3.4MB 16.4MB/s 
Installing collected packages: virtualenv
Successfully installed virtualenv-16.7.7
[alice@dev3 ~]$ which virtualenv
[alice@dev3 ~]$ virtualenv --version

2.2 Create a virtual environment (once per project)

Start by creating a folder specific to the project you are currently working on. Each project folder will have its own unique set of installed packages. For a project that requires Python 2, do the following (once):

[alice@dev3 ~]$ virtualenv -p $(which python2) my_project
Running virtualenv with interpreter /usr/bin/python2
Already using interpreter /usr/bin/python2
  No LICENSE.txt / LICENSE found in source
New python executable in /wynton/home/boblab/alice/my_project/bin/python2
Also creating executable in /wynton/home/boblab/alice/my_project/bin/python
Installing setuptools, pip, wheel...

2.3 Activate virtual environment (each time you use project)

Now, each time you want to work on your project, go to its folder and active the virtual environment:

[alice@dev3 ~]$ cd my_project
[alice@dev3 my_project]$ . bin/activate   ## IMPORTANT! Note period in front
(my_project) [alice@dev3 my_project]$

Note how (my_project) is prepended to the shell prompt when the virtual environment my_project is activate. This tells you that you run in a customized Python environment. Specifically, python2 now points to a local, frozen version:

(my_project) [alice@dev3 my_project]$ which python2

Similarly, python points to:

(my_project) [alice@dev3 my_project]$ which python

(my_project) [alice@dev3 my_project]$ ls -l $(which python)
lrwxrwxrwx. 1 alice boblab 7 Nov 18 14:04 ./bin/python -> python2

Note how this local python command points to the local python2 command. What is interesting, and important to notice, is that if we set up a Python 3 virtual environment, then the local python command will point to the local python3 command. In other words, when we use virtual environments, the python command will be using either Python 2 or Python3 at our choice.

To see what Python packages are installed in the virtual environment, use:

(my_project) [alice@dev3 my_project]$ python2 -m pip list
Package    Version
---------- -------
mpi4py     1.3.1  
pip        19.3.1 
setuptools 41.6.0 
wheel      0.33.6
(my_project) [alice@dev3 my_project]$ 

2.4 Installing packages (once per package)

Now you can install Python packages to the project folder using python2 -m pip install ... without specifying --user. For instance,

(my_project) [alice@dev3 my_project]$ python2 -m pip install HTSeq
Collecting HTSeq
  Using cached
Collecting numpy
  Downloading (17.0MB)
     |████████████████████████████████| 17.0MB 14.4MB/s 
Collecting pysam>=0.9.0
  Using cached
Building wheels for collected packages: pysam
  Building wheel for pysam ( ... done
  Created wheel for pysam: filename=pysam-0.15.3-cp27-cp27mu-linux_x86_64.whl size=8425720 sha256=110af7ad99aed0212c41e609a30ee9a707faf15ecc53928955c187b35869b8b5
  Stored in directory: /wynton/home/boblab/alice/.cache/pip/wheels/85/ab/84/86ca6dda37a6fc85687b67be7345b735cd82f6584bea56f327
Successfully built pysam
Installing collected packages: numpy, pysam, HTSeq
Successfully installed HTSeq-0.11.2 numpy-1.16.5 pysam-0.15.3

To see which packages are now installed in the virtual environment (the “project folder”) and what their versions are, do:

(my_project) [alice@dev3 my_project]$ python2 -m pip list
Package    Version
---------- -------
HTSeq      0.11.2 
mpi4py     1.3.1  
numpy      1.16.5 
pip        19.3.1 
pysam      0.15.3 
setuptools 41.6.0 
wheel      0.33.6

2.5 Returning to a project

Whenever you open a new terminal, make sure to activate the virtual environment (“project folder”), otherwise it will not find the packages you’ve installed. Pay attention to the shell prompt:

[alice@dev3 ~]$ cd my_project
[alice@dev3 my_project]$ . bin/activate    ## ACTIVATE!
(my_project) [alice@dev3 my_project]$ pip2 show HTSeq
Name: HTSeq
Version: 0.11.2
Summary: A framework to process and analyze data from high-throughput sequencing (HTS) assays
Author: Simon Anders
License: GPL3
Location: /wynton/home/boblab/alice/my_project/lib/python2.7/site-packages
Requires: numpy, pysam

[alice@dev3 my_project]$ 

To deactivate a Python virtual environment, either open a fresh terminal (e.g. log out and back in), or use:

(my_project) [alice@dev3 ~]$ deactivate
[alice@dev3 ~]$ deactivate

Note how prefix (my_project) was dropped from the shell prompt and python2 now points to the system-wide installation;

[alice@dev3 ~]$ which python2


Upgrading pip

You will at times get warnings that you are running an old version of ‘pip’:

You are using pip version 8.1.2, however version 19.3.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

Don’t use the suggested command call in that message. Instead, use:

[alice@dev3 ~]$ python2 -m pip install --user --upgrade pip
Cache entry deserialization failed, entry ignored
Collecting pip
  Downloading (1.4MB)
    100% |████████████████████████████████| 1.4MB 590kB/s 
Installing collected packages: pip
Successfully installed pip-19.3.1

To check the installed version of the ‘pip’ module, use:

[alice@dev3 ~]$ python2 -m pip --version
pip 19.3.1 from /wynton/home/boblab/alice/.local/lib/python2.7/site-packages/pip (python 2.7)