Software:Application

The systems at the C entre for Advance Computing have a large amount of software pre-installed for use on our clusters. Here we give an overview of software installed on the Linux platform (CentOS). Note that software that was installed for the Solaris platform is not documented here, as that platform is being discontinued.

Software

Table of Software on the Linux (CentOS) Platform The following software can be accessed from the swlogin1 (login) node or through the abaqus.q queue of the Grid Engine scheduler. Most software may be accessed through usepackage entries which add software and libraries to your $PATH. As an example, "use anaconda3" replaces the default version of Python with the copy of Python provided by Anaconda. Which copy of software you are using may be verified with "which X", where X is the name of the executable. Note that some package entries are purely short cuts provided for convenience, and will add the default version of that software to your $PATH. The entries these short cuts "point to" are indicated in the "Points To" column. NOTE: Unless explicitly specified here, it is generally best to run software using the usepackage entries (i.e. "use xxxxxxx") instead of attempting to call the software directly from its absolute location in /opt. The reason for this is that "use xxxxxxx" often loads required dependencies. Software Name Version Package Name Points To Usage Notes Abaqus default abaqus abaqus-6.11 More information Abaqus 64 bit 6.10 abaqus-6.10 More information Abaqus 64 bit 6.11 abaqus-6.11 More information Abinit default Abinit Abinit6.12.3_32bit More information Abinit 6.12.3, 32 bit Abinit6.12.3_32bit More information Abinit 6.12.3, 64-bit Abinit6.12.3_64bit More information ABySS 1.9.0 abyss AllPaths-LG default allpaths-lg allpaths-lg-52488 More information AllPaths-LG 52488 allpaths-lg-52488 More information Anaconda Python 2 distribution 2.2.0 (Python 2.7.11) anaconda2 includes numpy & scipy Anaconda Python 3 distribution 3-2.3.0 (Python 3.4.4) anaconda3 includes numpy & scipy Fluent Ansys 14 ansys14 More information Fluent Ansys 16 ansys16 More information Autodock default autodock autodock425 Autodock 4.2.5, 64-bit autodock425 BEAST default beast beast-1.8.2 BEAST 1.8.2 beast-1.8.2 BioPython Python package "use anaconda2" BioScripts Python package "use anaconda2" OR "use anaconda3" Blast default blast blast-2.2.30 More information Blast 2.2.30 blast-2.2.30 More information Bowtie Version 1, default bowtie bowtie-1.1.2 Bowtie 1.1.2 bowtie-1.1.2 Bowtie2 defualt bowtie2 bowtie2-2.2.6 Bowtie2 2.2.6 bowtie2-2.2.6 BWA default bwa bwa-0.7.12 BWA 0.7.12 bwa-0.7.12 CPMD default, 32 bit CPMD CPMD3.13.2_32bit More information CPMD 3.13.2, 32-bit CPMD3.13.2_32bit More information CPMD 3.13.2, 64-bit CPMD3.13.2_64bit More information CPMD default, 64 bit CPMD_64bit More information Cufflinks default cufflinks cufflinks-2.2.1 Cufflinks 2.2.1 cufflinks-2.2.1 Cutadapt "use anaconda3" or "use anaconda2" Discovar De Novo default discovar-denovo discovar-denovo-52488 Discovar De Novo 52488 discovar-denovo-52488 ESPReSso default, 32 bit espresso espresso3.1.1_32bit ESPReSso 3.1.1, 32-bit espresso3.1.1_32bit ESPReSso 3.1.1, 64-bit espresso3.1.1_64bit ESPReSso default, 64 bit espresso_64bit FastQC default fastqc fastqc-0.11.4 FastQC 0.11.4 fastqc-0.11.4 FastX default fastx fastx-0.0.13 FastX 0.0.13, 64 bit fastx-0.0.13 FBAT 2.0.4 fbat-2.0.4 use fbat-2.0.4 Fire Dynamic Simulator (version 6) fds use fds FoamExtend (current version) foam-extend foam-extend-3.1 use foam-extend FoamExtend 3.1 foam-extend-3.1 use foam-extend-3.1 FreeFem++ current version freefem freefem-3.44 use freefem More information FreeFem++ 3.36-1 freefem-3.36 use freefem-3.36 More information FreeFem++ 3.44 freefem-3.44 use freefem-3.44 More information FreeSurfer freesurfer use freesurfer More information FSL 5.0.9 fsl use fsl More information Gamess (Dec 5 2014) gamess use gamess More Information Genome Analysis Toolkit (GATK) gatk java -jar /opt/gatk/3.5/GenomeAnalysisTK.jar <extra arguments here> GNU compiler suite v4.1.2 gcc-4.1.2 use gcc-4.1.2 GNU compiler suite v4.8.2 gcc-4.8.2 use gcc-4.8.2 GNU compiler suite v4.8.3 gcc-4.8.3 use gcc-4.8.3 GNU compiler suite v4.9.2 gcc-4.9.2 use gcc-4.9.2 Gnuplot graphics software (latest version) gnuplot gnuplot_4.6.6 use gnuplot Gnuplot graphics software (4.6.6) gnuplot_4.6.6 use gnuplot_4.6.6 Gromacs (current version) 32 bit Gromacs Gromacs4.0.7_32bit use Gromacs More information Gromacs software (version 4.0.7, 32-bit) Gromacs4.0.7_32bit use Gromacs4.0.7_32bit More information Gromacs software (version 4.0.7, 64-bit) Gromacs4.0.7_64bit use Gromacs4.0.7_64bit More information Gromacs software (version 4.6, 32-bit) Gromacs4.6_32bit use Gromacs4.6_32bit More information Gromacs software (version 4.6, 64-bit) Gromacs4.6_64bit use Gromacs4.6_64bit More information Gromacs software (version 5.0, 64-bit) Gromacs5.0.6 use Gromacs5.0.6 More information Gromacs (current version) 64 bit Gromacs_64bit use Gromacs_64bit More information Gromacs (new, test) Gromacs_test use Gromacs_test More information Gurobi (newest version, 64-bit) gurobi use gurobi More information HMMER (current version) hmmer hmmer-3.1b2 use hmmer HMMER 3.1b2 hmmer-3.1b2 use hmmer-3.1b2 HTSeq Python package HTSeq "use anaconda2" Hypre hypre located in /opt/hypre Intel Compiler Suite ics use ics Intel Compiler Suite plus Intel MPI icsmpi use icsmpi InStruct instruct use instruct Java 7 Java 7 Already on PATH, simply type "java" Java 8 java8 use java8 Jmol (current version) jmol jmol-14.2.7 use jmol Jmol 14.2.7 jmol-14.2.7 use jmol-14.2.7 LAMMPS default version lammps lammps_64bit use lammps More information LAMMPS (Dec 2013) 64 bit Intel lammps_64bit use lammps_64bit More information LAMMPS (August 2015) 64 bit gcc/openmpi 1.8 lammps_aug15 use lammps_aug15 More information matlab matlab use matlab ... Requires a user-supplied license More information matlab-2014a matlab-2014a use matlab-2014a ... Requires a user-supplied license More information migrate-n current version migrate-n migrate-n-3.6.8 use migrate-n migrate-n-3.6.8 migrate-n-3.6.8 use migrate-n-3.6.8 MPICH-1 (newest) mpich-1 use mpich-1 mrtrix3 mrtrix use mrtrix More information MUSCLE v3.8.31 muscle use muscle NAMD (current version) namd namd-2.10 use namd NAMD NAMD 2.10 namd-2.10 use namd-2.10 NAMD NWChem (current) nwchem nwchem-6.1 use nwchem More information NWChem 6.1 nwchem-6.1 use nwchem-6.1 More information octave (current version) octave octave-4.0.0 use octave More information GNU octave-4.0.0 MATLAB look-alike octave-4.0.0 use octave-4.0.0 More information OpenFOAM (current version) openfoam openfoam-2.3.0 use openfoam More information OpenFOAM 2.1.1 openfoam-2.1.1 use openfoam-2.1.1 More information OpenFOAM 2.3.0 openfoam-2.3.0 use openfoam-2.3.0 More information OpenFOAM 3.0.0 openfoam-3.0.0 use openfoam-3.0.0 More information openmpi (default version) openmpi openmpi-1.8 use openmpi openmpi (development - v1.2) openmpi-1.2 use openmpi-1.2 openmpi (development - v1.8) openmpi-1.8 use openmpi-1.8 openmpi (development - v1.8.4) openmpi-1.8.4 use openmpi-1.8.4 orca (production - r2131) orca use orca orca (production - r2360) orca-2360 use orca-2360 Paraview (current version) paraview paraview-4.3 use paraview More information Paraview (64 bit version 1.4) paraview-4.3 use paraview-4.3 More information PEAR 0.9.6 pear use pear Perl 5 (version 5.10) Perl 5 Already on PATH, simply type "perl" PETSc scientific library (current version) petsc petsc-3.5.2 use petsc More information PETSc scientific library (version 3.5.2 using OpenMPI 1.8, gcc 4.4.6 petsc-3.5.2 use petsc-3.5.2 More information PETSc scientific library (version 3.6.0 using Intel compilers and MPI petsc-3.6.0-intel use petsc-3.6.0-intel More information PETSc scientific library (current version, Intel compilers/MPI) petsc-intel use petsc-intel More information Picard Tools picardtools use java8 java -jar /opt/picardtools/2.0.1/picard.jar PLINK PLINK Already on PATH PLINK 1.9 beta 3.30 plink-1.9 use plink-1.9 PLINK/SEQ 0.10 plink-seq use plink-seq PyRx 0.9.2 Drug Screening Software PyRx use PyRx More information PyRx 0.9 Drug Screening Software PyRx-0.9 use PyRx-0.9 More information Python (version 3.4.3) python-3.4 use python-3.4 Pyzo Python distribution (includes numpy & scipy) pyzo2015a use pyzo2015a qespresso (current version) 64 bit qespresso qespresso5.2.1_64bit use qespresso More information Quantum Espresso software (version 5.0.2, 64-bit) qespresso5.0.2_64bit use qespresso5.0.2_64bit More information Quantum Espresso software (version 5.2.1, 64-bit) qespresso5.2.1_64bit use qespresso5.2.1_64bit More information R statistical software (system version) R R-3.2.3 use R More information R statistical software (older version, 32-bit) R-2.15.2 use R-2.15.2 More information R statistical software (older version, 64-bit) R-2.15.2_64bit use R-2.15.2_64bit More information R version 3.2.3 (64-bit) R-3.2.3 use R-3.2.3 More information samstat samstat use samstat SAMtools (current version) samtools samtools-1.3 use samtools SAMtools 0.1.19 samtools-0.1.19 use samtools-0.1.19 SAMtools 1.3 samtools-1.3 use samtools-1.3 samstat 1.5.1 samtstat use samtstat seqtk (current version) seqtk use seqtk Sun Grid Engine 6 sge6 use sge6 SRA Toolkit (current version) sratoolkit sratoolkit-2.5.7 use sratoolkit SRA Toolkit 2.5.7 sratoolkit-2.5.7 use sratoolkit-2.5.7 Stacks (current version) stacks stacks-1.35 use stacks Stacks 1.35 stacks-1.35 use stacks-1.35 STAR 2.5.1b star use star Tophat2 (current version) tophat2 tophat2-2.1.0 use tophat2 Tophat2 2.1.0 tophat2-2.1.0 use tophat2-2.1.0 Trinity (current version) trinity trinity-2.1.1 use trinity Trinity 2.1.1 trinity-2.1.1 use trinity-2.1.1 VisIt 2.10 visit visit use visit More information vsearch v1.9.10 vsearch use vsearch Java based data mining (version 3.6) weka use weka

Language-specific software package installation Certain programming languages require the use of multiple add-on packages to reach their full functionality. If we are missing a package you need, there are two options: either request it be installed email us at cac.help@queensu.ca or perform a local install. Both methods will give you a working copy of the software package Perl To install Perl modules to a local directory, use the following bash commands to create a localized install of whatever modules you may need. It's actually not as complicated as it looks. # install local::lib wget http://search.cpan.org/CPAN/authors/id/H/HA/HAARG/local-lib-2.000018.tar.gz tar -xzf local-lib-2.000018.tar.gz cd local-lib-2.000018 perl Makefile.PL --bootstrap make test && make install # setting up appropriate environment variables so that perl knows about our new ~/perl5/lib directory cd ~ echo 'eval "$(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib)"' >> ~/.bashrc source ~/.bashrc # check that local::lib is indeed installing to the right directory, you should see a bunch of paths beginning with ~/perl5/lib/perl5/ get printed out perl -e 'print "@INC"' Installing Perl modules from CPAN will now allow you install whatever you need. For an example of using CPAN to install BioPerl, see below. This part requires a bit of baby-sitting, just hit enter whenever a prompt comes up. cpan install CJFIELDS/BioPerl-1.6.924.tar.gz q Python We highly recommend using one of the two Anaconda installations on the SW cluster. These already have a large number of pre-installed packages and will serve you well. However, if they are missing something you need, you can make a local install using the following instructions: use anaconda3 #or "use anaconda2" for python 2.7 pip install --user packageName R When using R, make sure to use the centralized install first with "use R". The system R version on the login node has a slightly different set of installed libraries from the versions of R found on the production nodes, which can result in dependency issues. Adding "use R" to your scripts will avoid this. When installing R packages from CRAN, it's easiest to manually specify the CRAN mirror to download from with: install.packages("packageName", repos="mirrorURL") where mirrorURL is one of the repositories listed at [1]. It will tell you at some point that the directory is not writeable and ask you if you want to make a local library instead- select 'yes'. The package should install normally and be ready for use. When installing packages from Bioconductor: source("http://bioconductor.org/biocLite.R") biocLite("packageName") If you see an error about "URLs are not supported", simply change any "https" URL to "http" and it will work. Again, it will ask you to make a "personal library", select 'yes'.

Using your own software It's very easy to use software that is not pre-installed on the systems. Simply specify the absolute or relative path to your software in a script and it will run. For example, if you had a program called "test" located in ~/bin/, you could easily invoke it with "~/bin/test" in your scripts.