MAFFT Runtime Environment home page

MAFFT is a multiple alignment program for amino acid or nucleotide sequences. See http://align.bmr.kyushu-u.ac.jp/mafft/software/ for more information.

Version information

Only this development version currently available.

Interface definition

The runtime environment sets the following environment variables:

• MAFFT_BINARIES points to the MAFFT binary directory
• PATH is set so that MAFFT_BINARIES is included in the path

Example

Here is an example to verify the RE installation. It is taken and adapted from the MAFFT distribution. Download mafft_test.tar.gz.

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

$ wget https://extras.csc.fi/mgrid/mafft_re/mafft_test.tar.gz
$ tar xvfz mafft_test.tar.gz
$ ngsub -d 1 mafft_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. We cannot use make install in this case because we want the binaries installed in a non-default location.

$ wget http://align.bmr.kyushu-u.ac.jp/mafft/software/mafft-6.603-with-extensions-src.tgz
$ tar xvfz mafft-6.603-with-extensions-src.tgz 
$ cd mafft-6.603-with-extensions
$ cd core
$ make clean
$ make
$ cd ..
$ cd extensions/
$ make clean
$ make
$ cd ..
$ mkdir -p /home/opt/mafft-6.603/bin
$ cp binaries/* /home/opt/mafft-6.603/bin/
$ cp scripts/* /home/opt/mafft-6.603/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
#
# MAFFT 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 )
    export MAFFT_BINARIES=$application_base_path/mafft-6.603/bin/
    # include MAFFT binaries in the path
    export PATH=$PATH:$MAFFT_BINARIES
;;

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 MAFFT guru in sequence analysis related questions.