bowtie2 2.3.0

Basic information

Tested on (Requirements)

  • OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 6.6 (Rocks 6.2)
  • Dependencies:
    • Intel Parallel Studio XE Cluster Edition 2017 Update 1

Installation

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

    cd /home/mgomezzul/apps/bowtie2/
wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.0/bowtie2-2.3.0-source.zip/download
unzip bowtie2-2.3.0-source.zip

  2. Do the following changes in the Makefile

    cd bowtie2-2.3.0
module load intel/2017_update-1
emacs Makefile
...
prefix = /share/apps/bowtie2/2.3.0/intel/2017_update-1
bindir = $(prefix)/bin

INC =
GCC_PREFIX = $(shell dirname `which icc`)
GCC_SUFFIX =
CC ?= $(GCC_PREFIX)/icc$(GCC_SUFFIX)
CPP ?= $(GCC_PREFIX)/icpc$(GCC_SUFFIX)
CXX ?= $(CPP)
HEADERS = $(wildcard *.h)
BOWTIE_MM = 1
BOWTIE_SHARED_MEM = 0
...
make 2>&1 | tee bowtie2-make.log

  3. After compiling bowtie2, continue with the following steps:

    sudo mkdir -p /share/apps/bowtie2/2.3.0/intel/2017_update-1
sudo chown -R mgomezzul.apolo /share/apps/bowtie2/2.3.0/intel/2017_update-1
make install 2>&1 | tee bowtie2-make-install.log
sudo chown -R root.root /share/apps/bowtie2/2.3.0/intel/2017_update-1

Module

#%Module1.0#####################################################################
##
## module bowtie2/2.3.0_intel-2017_update-1
##
## /share/apps/modules/bowtie2/2.3.0_intel-2017_update-1     Written by Mateo Gomez-Zuluaga
##

proc ModulesHelp { } {
    puts stderr "\tbowtie2/2.3.0_intel-2017_update-1 - sets the Environment for Bowtie2 in \
    \n\tthe share directory /share/apps/bowtie2/2.3.0/intel/2017_update-1\n"
}

module-whatis "\n\n\tSets the environment for using Bowtie2 2.3.0 \
            \n\tbuilded with Intel Parallel Studio XE 2017\n"

# for Tcl script use only
set       topdir     /share/apps/bowtie2/2.3.0/intel/2017_update-1
set       version    2.3.0
set       sys        x86_64-redhat-linux

module load intel/2017_update-1

prepend-path PATH    $topdir/bin

Usage mode

module load bowtie2/2.3.0_intel-2017_update-1

Author

  • Mateo Gómez Zuluaga