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We have already installed breseq in $BI/bin, so you should be ready to go! Skip this section.

Download breseq from Google code

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Info
titleInfo for installing breseq on TACC

You do not need to install a compiler (GCC/ICC), bowtie2, or R on TACC as they are available via the module system.

Code Block
module load R

module load GCC
module load bowtie/2.1.0

You could add these commands to your  $HOME/.profile_user if you wanted them available by default.

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Because this data set is relatively small (roughly 100x coverage of a 48,000 bp genome), a breseq run will take < 5 minutes. Submit this command to the TACC development queue.

Code Block
breseq -j 12 -r lambda.gbk lambda_mixed_population.fastq > log.txt

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Expand
Need some help?
Need some help?

If you use scp then you will need to run it in a terminal that is on your desktop and not on the remote TACC system. It can be tricky to figure out where the files are on the remote TACC system, because your desktop won't understand what $HOME, $WORK, $SCRATCH mean (they are only defined on TACC).

To figure out the full path to your file, you can use the pwd command in your terminal on TACC:

Code Block
login1$ pwd

Then try a command like this on your desktop (if on a Linux machine or MacOS X):

Code Block
desktop1$ scp -r username@lonestar.tacc.utexas.edu:/the/directory/returned/by/pwd/output .

It would be even better practice to archive and gzip the output directory before copying it using tar -cvzf to archive. Then copying that file and using tar -xvzf to unarchive it.

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