- OS base: CentOS (x86_64) \boldsymbol{\ge} 6.6 (Rocks 6.2)
- Compiler: Intel Parallel Studio XE Cluster Edition \boldsymbol{\ge} 17.0.1
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
You will notice that it just contains a simple source file. Build it.
make
will use the compiler you have loaded in your environment.
makeNote
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
- 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 thePATH
.
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/binCronos
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
- Finally, we need to put the bowtie binaries in the
scripts
directory. Otherwise EDGE-pro will not find it, even if is load in thePATH
. 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
Apolo II
.. literalinclude:: src/1.3.1_apolo :language: tcl :caption: :download:`Module file <src/1.3.1_apolo>`
Cronos
.. literalinclude:: src/1.3.1_cronos :language: tcl :caption: :download:`Module file <src/1.3.1_cronos>`