index.txt

A Quick Guide to Getting Started with Shell and BLAST 
=========================================================

Written by Jia Liu, Paul Villanueva, and Adina Howe.

This is material for a workshop hosted on 11/17/2020 by the GERMS lab. The goal of the workshop is to get someone with no experience with the command line completing doing basic BLAST commands in a few hours.

In order to complete this workshop, you'll need:

1. A shell client. If you're using a Mac, you can use the built-in Terminal program. If you're using Windows, you'll need to download a program like `Gitbash <https://git-scm.com/downloads>`_ or `PuTTY <https://www.putty.org/>`_. 
2. The materials for the workshop. The materials for the workshop are available at `the Github repo <https://github.com/germs-lab/blast_crash_course>`_. You can download them to your computer by typing ``git clone https://github.com/germs-lab/blast_crash_course.git`` in your shell program.

.. note::
	If you're attending the workshop on 11/17/2020 by VI Escuela Regional de Microbiología, you will have a different set up for this and there is no need for you to follow these directions.


.. toctree::
   :maxdepth: 2
   :caption: Contents:
   :numbered:

   materials/shell-tutorial/docs/file_nav
   materials/shell-tutorial/docs/working_with_files
   materials/shell-tutorial/docs/searching_files.txt
   ncbi/index

Acknowledgement:

This work was supported by the National Science Foundation Directorate of Biological Sciences under awards DEB 1737758 and DEB 1737765.