VSEARCH 2.4.0

Basic information

Tested on (Requirements)

  • OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 6.6 (Rocks 6.2)
  • Dependencies:
    • g++ >= 4.9.4

Installation

  1. Download the desired version of the software (Source code - tar.gz)

    cd /home/mgomezzul/apps/vsearch/gcc
wget https://github.com/torognes/vsearch/archive/v2.4.0.tar.gz
tar -zxvf v2.4.0.tar.gz

  2. Do the following steps fpr the compilation:

    module load gcc/4.9.4
cd vsearch-2.4.0
./autogen.sh
./configure --prefix=/share/apps/vsearch/2.4.0/gcc/4.9.4 --build=x86_64-redhat-linux
make

  3. After compiling vshare, continue with the following steps:

    sudo mkdir -p /share/apps/vsearch/2.4.0/gcc/4.9.4
sudo chown -R mgomezzul.apolo /share/apps/vsearch/2.4.0/gcc/4.9.4
make install
sudo chown -R root.root /share/apps/vsearch/2.4.0/gcc/4.9.4

Module

#%Module1.0#####################################################################
##
## module vsearch/2.4.0_gcc-4.9.4
##
## /share/apps/modules/vsearch/2.4.0_gcc-4.9.4     Written by Mateo Gomez-Zuluaga
##

proc ModulesHelp { } {
    puts stderr "\tvsearch/2.4.0_gcc-4.9.4 - sets the Environment for VSEARCH 2.4.0 in \
    \n\tthe share directory /share/apps/vsearch/2.4.0/gcc/4.9.4\n"
}

module-whatis "\n\n\tSets the environment for using VSEARCH 2.4.0 \
            \n\tbuilded with GNU GCC 4.9.4\n"

# for Tcl script use only
set       topdir     /share/apps/vsearch/2.4.0/gcc/4.9.4
set       version    2.4.0
set       sys        x86_64-redhat-linux

module load gcc/4.9.4

prepend-path PATH    $topdir/bin
prepend-path MANPATH $topdir/share/man

Use

Slurm template

#!/bin/bash
 #SBATCH --partition=longjobs
 #SBATCH --nodes=1
 #SBATCH --ntasks-per-node=32
 #SBATCH --time=1:00:00
 #SBATCH --job-name=vsearch
 #SBATCH -o result_%N_%j.out
 #SBATCH -e result_%N_%j.err

 export SBATCH_EXPORT=NONE
 export OMP_NUM_THREADS=???

 module load vsearch/2.4.0

 vsearch --usearch_global queries.fsa --db database.fsa --id 0.9 --alnout alnout.txt

Author

  • Mateo Gómez Zuluaga