How to access shell variable in ipython

Question

Using the ! magic I can access env type environment variables, but not ones defined in my terminal, or .bashrc.

$:/<path>/balter/chip-seq-analysis/chipseq$ echo $hg38
/<path>/genomes/hg38/release-85/Homo_sapiens.GRCh38.dna.primary_assembly.fa
balter@exalab3:/<path>/balter/chip-seq-analysis/chipseq$ 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
/usr/bin/bash

In [3]:

if your variables are not exported, no subprocess can access them, pyhton or not. — Jean-François Fabre
– Jean-François Fabre ♦, Commented Nov 21, 2016 at 20:29
So, in my .bashrc I need to have export hg38=.... with the export? I'll try that. — abalter
– abalter, Commented Nov 21, 2016 at 21:40
@Jean-FrançoisFabre please make it an answer so I can accept! — abalter
– abalter, Commented Nov 21, 2016 at 22:01

Jean-François Fabre · Accepted Answer · 2016-11-21 22:37:40Z

2

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

foo=value

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
print(os.getenv("foo"))

answered Nov 21, 2016 at 22:37

Jean-François Fabre♦

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