MUSCLE Runtime Environment home page

MUSCLE is public domain multiple alignment software for protein and nucleotide sequences. MUSCLE stands for multiple sequence comparison by log-expectation. See http://www.drive5.com/muscle/ for more information.

Version information

Only this development version currently available.

Interface definition

The runtime environment sets the following environment variables:

• PATH is set so that MUSCLE is included in the path

Example

Here is an example to run a smoke test on the RE installation. Download muscle_test.tar.gz.

To run the example, just untar in an empty directory and submit.

$ wget https://extras.csc.fi/mgrid/muscle_re/muscle_test.tar.gz
$ tar xvfz muscle_test.tar.gz
$ ngsub -d 1 muscle_test.xrsl

System administrator guide for installing the RE

Installing the binaries

Here is an example session for installing the software. /home/opt is a shared directory visible to the compute nodes. The whole compilation produces only one static binary called 'muscle' which is then copied to the installation directory.

$ wget http://www.drive5.com/muscle/downloads3.7/muscle3.7_src.tar.gz
$ mkdir muscle-3.7
$ cd muscle-3.7
$ tar xvfz ../muscle3.7_src.tar.gz 
$ make
$ cp muscle /home/opt/muscle-3.7/bin/

Installing the RE scripts

Below is an example RE script. The shared application installation directory is assumed to be /home/opt in this case also.

#!/bin/bash
#
# MUSCLE runtime environment script for Nordugrid ARC.
#
# Runtime environment scripts are called (bash source)
#   from NorduGrid ARC with argument 0, 1 or 2.
# First call with argument "0" is made before the the batch
#   job submission script is written.
# Second call is made with argument "1" just prior to execution of the
#   user specified executable.
# Third "clean-up" call is made with argument "2" after the user
#   specified executable has returned.
#
# author: Olli Tourunen <olli.tourunen@csc.fi>
#

# shared directory for application installation 
application_base_path=/home/opt/

case "$1" in
0 )
    # nothing on the frontend
;;

1 )
    # include MUSCLE binaries in the path
    export PATH=$PATH:$application_base_path/muscle-3.7/bin/
;;

2 )
    # Nothing here
;;

* )
    # Now, calling argument is wrong or missing.
    # If call was made from NorduGrid ARC, it is considered
    # an error. If this script is to be used also to initialize
    # MPI environment for local jobs in cluster, raising error here
    # could be improper.
    return 1
;;
esac

Contact information

Contact olli.tourunen@csc.fi if you have any grid use specific questions. Contact your local ClustalW guru in sequence analysis related questions.