The %my_run command execute a script in IPython as %run does but searching the file in the user path in addition to the python path.

custom_run.py

# =======================================================================================
# Startup file with magic functions: %my_run, %add_custom_path, %clean_custom_path and 
# %show_custom_path, which runs stuff in the python path as well as user specified paths.
#
# The %my_run command executes a script as %run does but searching the script in 
# the user path in addition to python path.
#
# ---------------------------------------------------------------------------------------
# This is a modification of the code done by Gaute Hope <gaute.hope@nersc.no> due to 
# IPython issue 101
#
# References:
#   - https://github.com/ipython/ipython/issues/101
#   - http://ipython.org/ipython-doc/dev/config/custommagics.html
#   - https://gist.github.com/gauteh/2f8f49f082f1d09b3db0
# =======================================================================================

import os, sys
from IPython import get_ipython
from IPython.core.magic import register_line_magic
from IPython.utils.path import filefind

_my_custom_paths = []

def find_in_pythonpath (filename):
    global _my_custom_paths

    try:
        path_dirs = ['.'] + _my_custom_paths + os.environ['PYTHONPATH'].split(':')
    except:
        path_dirs = ['.'] + _my_custom_paths
    
    return filefind(filename, path_dirs)

def find_in_syspath(filename):
    return filefind(filename, sys.path)

@register_line_magic
def my_run (line):
    ip = get_ipython()
    ip.magics_manager.magics['line']['run'](line, file_finder=find_in_pythonpath)
del my_run

@register_line_magic
def add_custom_path (line):
    global _my_custom_paths  
    if os.path.isabs(line) == False:
        path = os.path.abspath(line)
    else:
        path = line
    if path not in _my_custom_paths:
        _my_custom_paths.append(path)
del add_custom_path

@register_line_magic
def clean_custom_path (line):
    global _my_custom_paths 
    _my_custom_paths = []
del clean_custom_path

@register_line_magic
def show_custom_path (line):
    global _my_custom_paths
    for path in _my_custom_paths:
        print path
del show_custom_path

# =======================================================================================