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.
On this page:
- 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
Research computing resources at Indiana University (Big Red II, Quarry, Mason, and Rockhopper) use the Modules environment management package, which allows you to dynamically customize your software environment on each system.
To see which versions of PHYLIP are currently available on Quarry,
module avail command; at the command line (e.g.,
dvader@q0142 ~]$ enter:
To load the PHYLIP module, at the command line, enter:[dvader@q0142 ~]$ module load phylip
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?
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 WildWest
q0148) instead. To
- 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 . . .
- Load the
phylipmodule: [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
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:
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
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
command. The options presented above for DNADIST can be passed as:
Here, each option is separated from the next by
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 script submits the rest of the command
line as a job. The quotes prevent your shell from
interpreting the redirection symbols (
| ), 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
- If you have system-specific questions about Big Red II, Quarry,
Mason, or the Research Database Complex (RDC), email the High
Performance Systems team.
- If you have questions about compilers, programming, scientific and
numerical libraries, or debuggers on a research computing system, email Scientific
Applications and Performance Tuning team.
- If you have questions about statistical and mathematical software
on any of the research computing systems, email the
Research Analytics group.
- If you have questions about shared scratch space on the Data
Capacitor, email the High
Performance File Systems team.
- If you have questions about the Research File System (RFS) or Scholarly Data Archive (SDA), email the Research Storage team.
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Last modified on November 04, 2013.