Running breseq on TACC

Installing breseq on stampede for mac

Open a new terminal window and use the following commands:

  1. ssh into stampede and set up folder structures and modules:
    • ssh <username>@stampede.tacc.utexas.edu
    • mkdir local
    • mkdir $WORK/src
    • module load R
    • module load perl
    • module load bowtie/2.2.5
    • module load launcher
    • module load autotools
    • module save
  2. Download the breseq repository from github and install it on stampede
  3. Use the "find" function in the terminal window (command f) to look for the word "check" searching from the bottom of the window to the top of the window. You should see multiple instances of "passed check" and a few other random "checks" thrown in. Stop searching once you start seeing left aligned "checking" from the previous command. Assuming you do not see any messages of "failed check" you have successfully installed breseq.
  4. Add breseq to your path
    • cdh
    • IF YOU DO NOT HAVE A .bashrc file, you must first run the following command: /usr/local/startup_scripts/install_default_scripts
    • nano .bashrc
      • in section 2 add the following line exactly as it is written to modify your path to include breseq's installation location then save and exit the text editor:
        • export PATH=$HOME/local/bin:$PATH
        • If you see a blank file, go back to the previous step and run the command to generate a .bashrc file
    • logout
    • ssh <username>@stampede.tacc.utexas.edu
    • which breseq
If all has gone well, you should get "~/local/bin/breseq" as a response. If you don't, troubleshoot.

Updating breseq on stampede for mac

Do this anytime you know there is a new version of breseq, anytime breseq is not working, or anytime you have not used breseq in a while.
  1. cd $WORK/src/breseq
  2. make clean
  3. git pull
  • If output sates that anything is changed do the following, otherwise skip to next section.
    1. ./bootstrap.sh
    2. ./configure --prefix=$HOME/local
    3. make
    4. make install
    5. make test
    6. Use the "find" function in the terminal window (command f) to look for the word "check" searching from the bottom of the window to the top of the window. You should see multiple instances of "passed check" and a few other random "checks" thrown in. Stop searching once you start seeing left aligned "checking" from the previous command. Assuming you do not see any messages of "failed check" you have successfully installed breseq.

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Topic revision: r3 - 30 Mar 2016 - 20:44:25 - Main.DanielDeatherage
 
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