Computational Techniques for Life Sciences

Testing an Application

We installed Tophat, now it is time to test it to make sure it is working. Revisting the Tophat website, we find that they give instructions on how to test the code.

First, we will create a suitable place to test.

$ cd /work/03439/wallen/lonestar/apps/
$ mkdir tophat-test
$ cd tophat-test

Download and unpack the testing resources as described on the Tophat webiste:

$ wget https://ccb.jhu.edu/software/tophat/downloads/test_data.tar.gz
$ tar -xvzf test_data.tar.gz
$ cd test_data
$ ls -l

Since it is against policy to run applications on the login nodes, we must gain access to a compute node. The TACC tool idev is used to start an interactive session on a Lonestar5 compute node. Interactive sessions are helpful to test code, debug code, and practice small jobs before submitting large jobs:

$ idev --help
$ idev -p normal -m 180 --reservation=CTLS2017

Check your environment to make sure you have the correct modules loaded still:

$ module list
Currently Loaded Modules:
  1) intel/16.0.1   2) cray_mpich/7.3.0   3) TACC/1.0   4) perl/5.22.1   5) bowtie/2.2.6   6) boost/1.59

We also have to put Tophat in our path. There is no module for Tophat yet, so we need to do it manually.

$ echo $PATH        
$ which tophat      # no tophat yet
$ export PATH=$PATH:/work/03439/wallen/lonestar/apps/tophat/2.1.1/bin
$ echo $PATH
$ which tophat      # tophat now in path

Finally, we will test Tophat interactively using the command provided on the tophat website:

$ tophat -r 20 test_ref reads_1.fq reads_2.fq

Carefully read the output to screen to make sure there are no errors. If everything worked, you should get output similar to the following:

$ cat tophat_out/align_summary.txt
Left reads:
          Input     :       100
           Mapped   :        72 (72.0% of input)
Right reads:
          Input     :       100
           Mapped   :        70 (70.0% of input)
71.0% overall read mapping rate.
 
Aligned pairs:        50
50.0% concordant pair alignment rate.