Difference between revisions of "Using virtualenv"

From mn/bio/cees-bioinf
Jump to: navigation, search
(Created page with "virtualenv is a tool to create isolated Python environments. See [https://virtualenv.pypa.io/en/latest/index.html https://virtualenv.pypa.io/en/latest/index.html] === Setting...")
 
Line 2: Line 2:
  
 
=== Setting up virtualenv on the cod-nodes/abel ===
 
=== Setting up virtualenv on the cod-nodes/abel ===
 
+
<pre>module load python2
module load python2 virtualenv my_python_dir
+
virtualenv my_python_dir</pre>
 
 
 
will create locally a python tree.
 
will create locally a python tree.
  
 
Then you can run
 
Then you can run
 
+
<pre>cd my_python_dir
cd my_python_dir ./bin/activate
+
./bin/activate</pre>
 
+
And you're ready to go.<br/>This will help to set paths properly:
And you're ready to go. Thsi will help to set paths properly:
+
<pre>export PYTHONPATH=$PYTHONPATH:$PWD/lib/python2.7/site-packages/</pre>
 
 
export PYTHONPATH=$PYTHONPATH:$PWD/lib/python2.7/site-packages/
 
 
 
 
==== When using setup.py scripts ====
 
==== When using setup.py scripts ====
 
+
<pre>python setup.py install --prefix=/path/to/my_python_dir</pre>
python setup.py install --prefix=/path/to/my_python_dir
+
Then to install a package not already in the python2 module do:
 
+
<pre>pip install package_name</pre>
<br/>Then to install a package not already in the python2 module do:
+
This package (if found by pip) will be installed locally and reachable via the paths previously set up.
 
 
pip install package_name
 
 
 
this package (if found by pip) will be installed locally and reachable via the paths previously set up.
 

Revision as of 12:00, 26 January 2015

virtualenv is a tool to create isolated Python environments. See https://virtualenv.pypa.io/en/latest/index.html

Setting up virtualenv on the cod-nodes/abel

module load python2
virtualenv my_python_dir

will create locally a python tree.

Then you can run

cd my_python_dir
./bin/activate

And you're ready to go.
This will help to set paths properly:

export PYTHONPATH=$PYTHONPATH:$PWD/lib/python2.7/site-packages/

When using setup.py scripts

python setup.py install --prefix=/path/to/my_python_dir

Then to install a package not already in the python2 module do:

pip install package_name

This package (if found by pip) will be installed locally and reachable via the paths previously set up.