BLAST 2.6.0

Basic information

Tested on (Requirements)

  • OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 6.6 (Rocks 6.2)
  • Dependencies:
    • python >= 2.7.11
    • libm (by default)

Installation

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

    cd /home/mgomezzul/apps/vsearch/gcc
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz
tar -zxvf ncbi-blast-2.6.0+-x64-linux.tar.gz

  2. After unpacking blast, continue with the following steps to finish the installation:

    cd ncbi-blast-2.6.0+
rm ChangeLog LICENSE ncbi_package_info README
sudo mkdir -p /share/apps/ncbi-blast/2.6.0
sudo mv bin /share/apps/ncbi-blast/2.6.0/

Module

#%Module1.0#####################################################################
##
## modules ncbi-blast+/2.6.0
##
## /share/apps/modules/ncbi-blast+/2.6.0_x86_64  Written by Mateo Gomez-Zuluaga
##

proc ModulesHelp { } {
    puts stderr "\n\tThe NCBI Basic Local Alignment Search Tool (BLAST) finds \
            \n\tregions of local similarity between sequences in the \
        \n\tshare directory /share/apps/ncbi-blast+/2.6.0\n"
}

module-whatis "\n\tSets the Environment for NCBI-BLAST 2.6.0\n"

# for Tcl script use only
set     topdir     /share/apps/ncbi-blast+/2.6.0
set     version    2.6.0
set     sys        x86_64-redhat-linux

conflict ncbi-blast+
module load intel/2017_update-1
module load mkl/2017_update-1
module load python/2.7.12_intel-2017_update-1

prepend-path PATH $topdir/bin

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 ncbi-blast/2.6.0_x86_64

xxx

Author

  • Mateo Gómez Zuluaga