Tested on (Requirements)

  • OS base: CentOS (x86_64) \(\boldsymbol{\ge}\) 6.6 (Rocks 6.2)
  • Compiler: Intel Parallel Studio XE Cluster Edition \(\boldsymbol{\ge}\) 17.0.1

Build process

  1. Get the current EDGE-pro version from the official web page and enter into the source directory.

    wget http://ccb.jhu.edu/software/EDGE-pro/EDGE_pro_v1.3.1.tar.gz
tar -xvf EDGE_pro_v1.3.1.tar.gz
cd EDGE_pro_v1.3.1

  2. You will notice that it just contains a simple source file. Build it. make will use the compiler you have loaded in your environment.

make

Note

You must load the necessary modules to build (i.e. Intel Compiler).

In Apolo II:
module load intel/2017_update-1
In Cronos:
module load intel/intel-18.0.2
  1. Create the installation directories. Move the built executable and other necessary scripts. The main script of EDGE_pro is edge.pl, so is the only script we need to put in the PATH.

Apolo

mkdir -p /share/apps/edge_pro/1.3.1/intel-2017_update-1/bin
mkdir -p /share/apps/edge_pro/1.3.1/intel-2017_update-1/scripts
mv count additionalScripts /share/apps/edge_pro/1.3.1/intel-2017_update-1/scripts
mv edge.pl /share/apps/edge_pro/1.3.1/intel-2017_update-1/bin

Cronos

mkdir -p /share/apps/edge_pro/1.3.1/intel-18.0.2/bin
mkdir -p /share/apps/edge_pro/1.3.1/intel-18.0.2/scripts
mv count additionalScripts /share/apps/edge_pro/1.3.1/intel-18.0.2/scripts
mv edge.pl /share/apps/edge_pro/1.3.1/intel-18.0.2/bin
  1. Finally, we need to put the bowtie binaries in the scripts directory. Otherwise EDGE-pro will not find it, even if is load in the PATH. To do this we use symbolic links:

Apolo

cd /share/apps/edge_pro/1.3.1/intel-2017_update-1/scripts
ln -s /share/apps/bowtie2/2.3.4.1/2017_update-1/bin/bowtie2-align-l bowtie2-align
ln -s /share/apps/bowtie2/2.3.4.1/2017_update-1/bin/bowtie2-build bowtie2-build
ln -s /share/apps/bowtie2/2.3.4.1/2017_update-1/bin/bowtie2 bowtie

Cronos

cd /share/apps/edge_pro/1.3.1/intel-18.0.2/scripts
ln -s /share/apps/bowtie2/2.3.4.1/intel-18.0.2/bin/bowtie2-align-l bowtie2-align
ln -s /share/apps/bowtie2/2.3.4.1/intel-18.0.2/bin/bowtie2-build bowtie2-build
ln -s /share/apps/bowtie2/2.3.4.1/intel-18.0.2/bin/bowtie2 bowtie2

Modulefile

Apolo II

Module file
#%Module1.0####################################################################
##
## module load edge_pro/1.3.1_intel-2017_update-1
##
## /share/apps/modules/edge_pro/1.3.1_intel-2017_update-1
## Written by Juan David Arcila-Moreno
##

proc ModulesHelp {} {
     global version modroot
     puts stderr "Sets the environment for using edge_pro 1.3.1\
		  \nin the shared directory \
		  \n/share/apps/edge_pro/1.3.1/intel-2017_update-1\
		  \ncount script builded with intel-2017_update-1"
}

module-whatis "(Name________) edge_pro"
module-whatis "(Version_____) 1.3.1"
module-whatis "(Compilers___) intel-2017_update-1"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) "

# for Tcl script use only
set         topdir        /share/apps/edge_pro/1.3.1/intel-2017_update-1
set         version       1.3.1
set         sys           x86_64-redhat-linux

conflict edge_pro
module load intel/2017_update-1
module load bowtie2/2.3.0_intel-2017_update-1
 

prepend-path	PATH			$topdir/bin

Cronos

Module file
#%Module1.0####################################################################
##
## module load edge_pro/1.3.1_intel-18.0.2
##
## /share/apps/modules/edge_pro/1.3.1_intel-18.0.2
## Written by Juan David Arcila-Moreno
##

proc ModulesHelp {} {
     global version modroot
     puts stderr "Sets the environment for using edge_pro 1.3.1\
		  \nin the shared directory \
		  \n/share/apps/edge_pro/1.3.1/intel-18.0.2\
		  \ncount binary builded with intel-18.0.2"
}

module-whatis "(Name________) edge_pro"
module-whatis "(Version_____) 1.3.1"
module-whatis "(Compilers___) intel-18.0.2"
module-whatis "(System______) x86_64-redhat-linux"
module-whatis "(Libraries___) "

# for Tcl script use only
set         topdir        /share/apps/edge_pro/1.3.1/intel-18.0.2
set         version       1.3.1
set         sys           x86_64-redhat-linux

conflict edge_pro
module load intel/18.0.2
module load bowtie2/2.3.4.1_intel-18.0.2
 

prepend-path	PATH			$topdir/bin