ARCHIVED: Using PHYLIP on Quarry at IU

The Phylogeny Inference Package (PHYLIP) is a set of programs for inferring phylogenies (evolutionary trees). For more, see the PHYLIP home page.

On Quarry at Indiana University, you can run PHYLIP programs interactively from the command line on the login nodes, or in batch mode, using a TORQUE script to submit a job to the compute nodes. If your interactive session will require more than 20 minutes of processor time, you must run it on one of Quarry's interactive nodes.

• Setting up your user environment
• Running PHYLIP programs interactively
• Passing options to PHYLIP programs
• Running PHYLIP programs as batch jobs
• Getting help

Setting up your user environment

To see which versions of PHYLIP are currently available on Quarry, use the module avail command; at the command line (e.g., dvader@q0142 ~]$ enter:

   [dvader@q0142 ~]$ module avail phylip

   ------- /N/soft/rhel6/modules/quarry/LIFE-SCIENCES ------
   phylip/3.69

To load the PHYLIP module, at the command line, enter:

   [dvader@q0142 ~]$ module load phylip

Running PHYLIP programs interactively

To run PHYLIP programs interactively on Quarry, you can load the phylip module, and then launch programs from the command line on a login node.

However, if your session will require more than 20 minutes of processor time, you must use one of Quarry's interactive nodes (q0145 - q0148) instead. To do so:

1. SSH to an interactive node:

     [jajbinks@q0142 ~]$ ssh q0148
     jajbinks@q0148's password:
     Last login: Mon Jan 7 13:52:58 2013 from q0144.quarry.hps.iu.edu
     . . .

2. Load the phylip module:

     [jajbinks@q0148 ~]$ module load phylip

Passing options to PHYLIP programs

You can pass options to PHYLIP programs in two ways: create a file that contains the options you want to pass, or echo options to the program when it runs. This section describes both methods. These methods can be used both when running PHYLIP programs from the command line and when submitting batch jobs to run them.

A file that contains options for PHYLIP programs should be a plain text file that contains one entry per line. Each entry is a response to a menu or query that you would enter when running PHYLIP interactively. For example, if you wanted to use the default options, all you would do in the program is press y and Return. The option file for such a run would be a single line containing the letter Y. A more sophisticated run might be a file with the contents:

  D
  G
  I
  T
  15
  2
  Y

PHYLIP accepts options on its standard input; to pass them from a file, use Unix redirection, using either of the following commands:

  dnadist < my_option_file

  cat my_option_file | dnadist

The second way of passing options to PHYLIP programs from the command line is to use echo to pipe them to the program's standard input. If you want to use default options with a program, all you need to echo is y:

  echo y | dnaml

To pass a series of options, echo must output each option on a separate line. You can do this by enclosing the options in quotes, separating them with a \n that will be expanded into new-line characters, and by explicitly requesting /bin/echo rather than using the built-in echo command. The options presented above for DNADIST can be passed as:

  /bin/echo "D\nG\nI\nT\n15\n2\nY" | dnadist

Here, each option is separated from the next by \n.

Running PHYLIP programs as batch jobs

PHYLIP programs can be submitted to run as batch jobs by prefixing the command line with the word serialjob and by quoting redirection symbols. The following commands can be used to run the previous examples as batch jobs:

  serialjob dnadist "<" my_option_file

  serialjob /bin/echo "D\nG\nI\nT\n15\n2\nY" "|" dnadist

The serialjob script submits the rest of the command line as a job. The quotes prevent your shell from interpreting the redirection symbols (< and |), keeping them part of the job that is submitted. For more about serialjob, see its manual page. Also, see ARCHIVED: At IU, how do I use the serialjob script to submit batch jobs on Quarry?

The script will print a message indicating that your job has been submitted. To check the status of your job on Quarry, use the checkjob command:

  checkjob your_job_id

Getting help