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.
Contents
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 64 bit current version | abaqus | abaqus-6.11 | use abaqus More information |
| Abaqus 6.10 64-bit version | abaqus-6.10 | use abaqus-6.10 More information | |
| Abaqus 6.11 64-bit version | abaqus-6.11 | use abaqus-6.11 More information | |
| Abinit (current version) 64 bit | Abinit | Abinit6.12.3_32bit | use Abinit More information |
| Abinit software (version 6.12.3, 32-bit) | Abinit6.12.3_32bit | use Abinit6.12.3_32bit More information | |
| Abinit software (version 6.12.3, 64-bit) | Abinit6.12.3_64bit | use Abinit6.12.3_64bit More information | |
| ABySS 1.9.0 | abyss | use abyss | |
| AllPaths-LG (current version) | allpaths-lg | allpaths-lg-52488 | use allpaths-lg More information |
| AllPaths-LG (version 52488) | allpaths-lg-52488 | use allpaths-lg-52488 More information | |
| Anaconda Python 2 distribution (includes numpy & scipy) | anaconda2 | anaconda20 | use anaconda2 |
| Anaconda Python 2 distribution (includes numpy & scipy) | anaconda20 | use anaconda20 | |
| Anaconda Python 3 distribution (includes numpy & scipy) | anaconda3 | use anaconda3 | |
| Fluent (Ansys 14 on Linux) | ansys14 | use ansys14 More information | |
| Fluent (Ansys 16 on Linux) | ansys16 | use ansys16 More information | |
| Autodock current version | autodock | autodock425 | use autodock |
| Autodock 4.2.5 64-bit version | autodock425 | use autodock425 | |
| Initial Settings | basic | use basic | |
| BEAST (current version) | beast | beast-1.8.2 | use beast |
| BEAST 1.8.2 | beast-1.8.2 | use beast-1.8.2 | |
| BioPython Python package | BioPython | "use anaconda2" | |
| BioScripts Python package | BioScripts | "use anaconda2" OR "use anaconda3" | |
| Blast current version | blast | blast-2.2.30 | use blast More information |
| Blast 2.2.30+ | blast-2.2.30 | use blast-2.2.30 More information | |
| Bowtie (VERSION 1!!!) | bowtie | bowtie-1.1.2 | use bowtie |
| Bowtie 1.1.2 | bowtie-1.1.2 | use bowtie-1.1.2 | |
| Bowtie2 (current version) | bowtie2 | bowtie2-2.2.6 | use bowtie2 |
| Bowtie2 2.2.6 | bowtie2-2.2.6 | use bowtie2-2.2.6 | |
| BWA (current version) | bwa | bwa-0.7.12 | use bwa |
| BWA 0.7.12 | bwa-0.7.12 | use bwa-0.7.12 | |
| CPMD (current version) 32 bit | CPMD | CPMD3.13.2_32bit | use CPMD More information |
| CPMD software (version 3.13.2, 32-bit) | CPMD3.13.2_32bit | use CPMD3.13.2_32bit More information | |
| CPMD software (version 3.13.2, 64-bit) | CPMD3.13.2_64bit | use CPMD3.13.2_64bit More information | |
| CPMD (current version) 64 bit | CPMD_64bit | use CPMD_64bit More information | |
| Cufflinks (current version) | cufflinks | cufflinks-2.2.1 | use cufflinks |
| Cufflinks 2.2.1 | cufflinks-2.2.1 | use cufflinks-2.2.1 | |
| Cutadapt | Cutadapt | "use anaconda3" or "use anaconda2" | |
| Discovar De Novo (current version) | discovar-denovo | discovar-denovo-52488 | use discovar-denovo |
| Discovar De Novo (version 52488) | discovar-denovo-52488 | use discovar-denovo-52488 | |
| ESPReSso (current version) 32 bit | espresso | espresso3.1.1_32bit | use espresso |
| ESPReSso software (version 3.1.1, 32-bit) | espresso3.1.1_32bit | use espresso3.1.1_32bit | |
| ESPReSso software (version 3.1.1, 64-bit) | espresso3.1.1_64bit | use espresso3.1.1_64bit | |
| ESPReSso (current version) 64 bit | espresso_64bit | use espresso_64bit | |
| FastQC (current version) | fastqc | fastqc-0.11.4 | use fastqc |
| FastQC 0.11.4 | fastqc-0.11.4 | use fastqc-0.11.4 | |
| FastX current version | fastx | fastx-0.0.13 | use fastx |
| FastX 0.0.13 (64 bit) | fastx-0.0.13 | use 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.
