Using PHYLIP on Quarry at IU

Note: Following a system-wide upgrade in December 2012, Quarry now runs Red Hat Enterprise Linux version 6 (RHEL 6) and uses the Modules package (instead of SoftEnv) for manipulating user environments. For more, see Information about the 2012 upgrade to Quarry at IU. If you encounter any problems or have questions, email the High Performance Systems group.

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

Below is information about using PHYLIP on the Quarry cluster at Indiana University.

Programs in PHYLIP were designed to be run interactively, but if you run them from the command line on Quarry, the programs are limited to 20 minutes of processor time. For longer runs, you need to submit your program as a batch job. It will wait its turn to run, and when it finishes, you'll receive mail announcing that your job has finished. Following are instructions for passing options to PHYLIP programs when you run them interactively, and how to submit jobs that run PHYLIP programs.

Configuring your account on Quarry

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:

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

To make permanent changes to your environment, edit your ~/.modules file. For more, see In Modules, how do I save my environment with a .modules file?

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:

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 :

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:

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:

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 On Quarry at IU, how do I use the serialjob script to submit jobs?

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: