Bacterial Genomics

This repository includes example scripts that model possible steps in a genomics workflow, designed to be implemented on virtual machines available through XSEDE's Jetstream environment.

To access your cloud instance, you will use the following software:

• Windows: GitBash
• Mac: Terminal

Log on to your instance using secure shell:

• From your shell, log on to the cloud instance using:
  • ssh USERNAME@IP.ADDRESS
  • USERNAME is hertweck for all cloud instances in this class
  • IP.ADDRESS has been included in an individual email to you personally
• The first time you log in, you will be asked Are you sure you want to continue connecting (yes/no)?; you should type "yes" then hit enter.
• You will be prompted for your password, which was also included in an email from your instructor. Remember that you will not see anything appear on the screen as you type your password (this is ok!).

Running project scripts:

• Obtain the scripts from GitHub using:
  • git clone https://github.com/k8hertweck/bacterialGenomics.git
• You should now see a bacterialGenomics directory
• Change your working directory to bacterialGenomics prior to executing all scripts, which should be run in the following order:
  • projectSetup.sh
  • bacterialAssembly.sh
  • bacterialReadMapping.sh
• Each script includes specific USAGE information that tells you how to execute it
• Please look through the comments in each script carefully to discern the processes being implemented. You should also consult the project documentation and rubric on Canvas for more information on tasks to be completed.

Transferring data from Jetstream to your local computer:

• Start in a shell on your local computer
• Use secure copy (scp) to transfer files to home directory of cloud instance:
  • scp USERNAME@IP.ADDRESS:PATH/TO/FILENAME .
  • USERNAME and IP.ADDRESS are the same as used for login
  • PATH/TO/FILENAME is the location and filename for what you would like to download
• If you don't know where the file is located, go to the directory in the cloud instance and type pwd
• You will be required to enter your password each time you execute an scp command
• If you are attempting to download an entire directory, it is recommended to archive and compress the directory as follows:
  • tar -cvzf DIRECTORY.tar.gz DIRECTORY/
  • DIRECTORY is the name of the directory you want to compress

Other notes:

• There are a few hidden files/directories in this project (e.g., .git/ and .gitignore; you do not need to work with them.
• To log out of your cloud instance, type exit or simply close the shell window.
• You can create and edit text files in the shell using nano by typing nano FILENAME (and use control + q to exit). More information on nano can be found here. Remember that nano will work on the cloud instances and locally on Macs, but is not currently available in GitBash.
• You can have multiple bash shells open at once; it is common to have one open for your cloud instance and another to access your local computer
• If you accidentally execute a command and do not want it to run to completion, use control + c (but if a script has partially executed, files may still be affected)
• If the network connection (e.g., internet) stalls out while you are connected to your cloud instance and running a script, you may need to log back in and rerun the script
• If you execute a script multiple times, you may receive minor error messages (e.g., mkdir: cannot create directory), but the script should still run to completion
• If you encounter difficulty and would like to start over completely, execute the following commands:
  • cd
  • rm -rf bacterialGenomics/ Trimmomatic-0.36.zip Trimmomatic-0.36/
  • Then you should be able to start fresh with the git clone command described above