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Bioinformatics - ClustalW-MPI
Instructions on how to run (and, if needed, install a customized version of) ClustalW-MPI
ClustalW-MPI is a parallel implementation of Clustal-W, based on MPI.
1. Running ClustalW-MPI on Thunder
Example: Conduct a multiple alignment on a set of sequences
Location: /mmfs1/thunder/projects/ccastest/training/examples/ClustalW_MPI_example
File list
· clustalw-mpi_job.pbs: job submission script
· 16s.fasta: a set of sequences in fasta format
Steps
· copy example directory to your SCRATCH directory
o “cp -r /mmfs1/thunder/projects/ccastest/training/examples/ClustalW_MPI_example $SCRATCH”
· Go to the copied directory
o “cd ./ClustalW_MPI_example”
· Edit the job submission script as needed, then submit the job
o “clustalw-mpi_job.pbs”
2. Install Customized ClustalW-MPI on Thunder
Warning: This part is intended ONLY for those who want to install and test their own version in their HOME directory.
Summary
· Google sparsehash is recommended for building.
· MPI (Message Passing Interface) is needed for building the MPI-enabled version of the ABySS (available via “module load openmpi” or “module load mpich”)
Details
In the following pages, we assume that you want to install the software in a directory named “SOFTWARE” inside your HOME directory on the CCAST’s Thunder cluster. “USERNAME” is your username on Thunder.
(a) Install
· Go to SOFTWARE inside your home directory – create if it does not exist:
o "cd /mmfs1/home/USERNAME/SOFTWARE"
· Download ClustalW-MPI, unzip and go to the unzipped directory:
o "wget http://www.bii.a-star.edu.sg/docs/software/clustalw-mpi-0.13.tar.gz"
o "tar -xzvf clustalw-mpi-0.13.tar.gz"
o "cd clustalw-mpi-0.13"
· Load mpich:
o "module load mpich"
· Build:
o "make"
(b) Test
· Make a test directory and go into it:
o "cd /mmfs1/thunder/scratch/USERNAME"
o "mkdir clustalw-mpi_example"
o "cd clustalw-mpi_example"
· Download a sample of test data to the current location:
o "wget https://github.com/mmatschiner/tutorials/raw/master/multiple_sequence_alignment/data/16s.fasta"
· Write and submit the job
o "qsub clustalw-mpi_job.pbs"
------------------------------------------- file clustalw-mpi_job.pbs -------------------------------------------
#!/bin/bash
#PBS -q default
#PBS -N ClustalW-MPI_test
#PBS -l select=1:mem=10gb:ncpus=4
#PBS -l walltime=02:00:00
#PBS -W group_list=x-ccast-prj-[your project group name here]
cd $PBS_O_WORKDIR
#Set the path to your executable location
export MY_CLUSTALW_MPI=/mmfs1/home/USERNAME/SOFTWARE/clustalw-mpi-0.13
module load mpich
mpirun -np $NCPUS $MY_CLUSTALW_MPI/clustalw-mpi -infile=16s.fasta
exit 0