abalter abalter - 6 months ago 57
Bash Question

How to access shell variable in ipython

Using the

magic I can access
type environment variables, but not ones defined in my terminal, or

$:/<path>/balter/chip-seq-analysis/chipseq$ echo $hg38
balter@exalab3:/<path>/balter/chip-seq-analysis/chipseq$ ipython
Python 2.7.12 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:42:40)
Type "copyright", "credits" or "license" for more information.

IPython 5.1.0 -- An enhanced Interactive Python.
? -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help -> Python's own help system.
object? -> Details about 'object', use 'object??' for extra details.

In [1]: !echo $hg38

In [2]: !echo $SHELL

In [3]:


if your variables are not exported, no subprocess can access them, python or not.


is only seen by the current process (here: bash)

but if you do (in your .bashrc):

export foo

or set & export:

export foo=value

then the variable becomes visible by subprocesses. That's your fix.

BTW, to get an env. variable in python, the real python way is:

import os