The Shell

Monday

###Why you should care

Demo a workflow pipeline

Commit all data files for Problem 2 using:

  python multi_svn.py add areas*
  python multi_svn.py commit "Adding data files for hotspot analysis."

Shortcuts

Up and down arrows
Tab

Version Control

svn checkout
svn update
svn add
svn commit

Wednesday

Shebangs

A shebang is a special code at the beginning of a script to tell the shell to run it as a scripot for a particular language.

Comes from Sharp(#) + Bang(!)

Syntax

#!/path/to/interpreter
#!/bin/bash
#!/usr/bin/python

Portability

Above commands work on Linux and Mac. To allow use on Windows:

#!/usr/bin/env bash
#!/usr/bin/env python

This looks for the interpreter in the PATH

Shell from inside Python

Everything you can do in the shell you can do using Python. The two key modules for doing so are:

os, which is easy import os os.system(“ls -l -a”)

subprocess, which is “best”

  import subprocess
  subprocess.call(["ls"])
  subprocess.call(["ls", "-l"])
  directory_list = subprocess.check_output(["ls", "-l"])
  directory_list = subprocess.os.listdir('.')

Data Carpentry for Biologists

Notes