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.
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
On the research supercomputers at Indiana University, the Modules environment management system provides a convenient method for dynamically customizing your software 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:
- 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
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
Research computing support at IU is provided by the Research Technologies division of UITS. To ask a question or get help regarding Research Technologies services, including IU's research supercomputers and research storage systems, and the scientific, statistical, and mathematical applications available on those systems, contact UITS Research Technologies. For service-specific support contact information, see Research computing support at IU.
This is document awwd in the Knowledge Base.
Last modified on 2023-04-21 16:58:59.