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Software Available on Hungabee
Title | Version | Usage Notes | |
---|---|---|---|
64-bit SLES 11 | SP1 2.6.32.54-0.3-default | ||
ABySS | 1.5.2 |
module load application/ABySS/1.5.2 |
|
ABySS | 1.5.1 |
module load application/ABySS/1.5.1 |
|
ABySS | 1.3.2 |
module load application/ABySS/1.3.2 |
|
ABySS | 1.3.5 |
module load application/ABySS/1.3.5 |
|
ALLPATHS-LG | Also available: 40691 | ||
ALLPATHS-LG | 49962 |
application/allpathslg/49962 |
|
ALLPATHS-LG | Revision 43500 |
module load application/allpathslg/43500 |
|
ALLPATHS-LG | Also available: 42069 | ||
Augustus | 2.5.5 |
module load application/augustus/2.5.5 |
|
bamUtil | 1.0.13 |
module load application/bamutil/1.0.13 |
|
BCFtools (VCF/BCF file manipulation) | 1.3 |
module load application/bcftools/1.3 |
|
BEDTools | 2.26.0 |
module load application/bedtools/2.26.0 |
|
BLAS | In MKL | ||
BLAST | 2.2.31+ |
module load application/blast/2.2.31 |
|
BLAST | ncbi-blast-2.2.29+ |
module load application/blast/2.2.29 |
|
BLAST | ncbi-blast-2.6.0+ |
module load application/blast/2.6.0 |
|
BLAST | ncbi-blast-2.2.28+ |
module load application/blast/2.2.28 |
|
BLAT | 3.5 |
module load application/blat/3.5 |
|
Boost | 1.60.0 (gcc52) |
module load library/boost/1_60_0 |
|
Boost | 1.54.0 |
Initialize your environment to use Boost 1.54.0 with module load library/boost/1_54_0 |
|
Boost | 1.49.0 |
module load library/boost/1_49_0 |
|
Bowtie | 0.12.8 |
module load application/bowti /0.12.8 |
|
Bowtie | 1.0.0 |
module load application/bowtie/1.0.0 |
|
Bowtie2 | 2.2.2 |
module load application/bowtie2/2.2.2 |
|
Bowtie2 | 2.0.0 |
module load application/bowtie2/2.1.0 |
|
BWA | 0.6.2 |
module load application/bwa/0.6.2 |
|
BWA | 0.7.12 |
module load application/bwa/0.7.12 |
|
C - GNU GCC, Intel, Portland Group (PGI) compilers | GNU 4.8.3 |
module load compiler/gcc/4.8.3 |
|
C - GNU GCC, Intel, Portland Group (PGI) compilers | Portland Group 13.9 |
(pgcc - module load compiler/pgi/13.9) |
|
C - GNU GCC, Intel, Portland Group (PGI) compilers | Intel 12.1.5 |
(icc, module load compiler/ intel/12.1, loaded by default) |
|
C - GNU GCC, Intel, Portland Group (PGI) compilers | Portland Group 12.10 |
(pgcc - module load compiler/pgi/12.10) |
|
C - GNU GCC, Intel, Portland Group (PGI) compilers | GNU 4.5.0 |
(gcc - module load compiler/gcc/4.5.0) |
|
C - GNU GCC, Intel, Portland Group (PGI) compilers | GNU 4.3.4 |
(gcc) |
|
C++ - GNU GCC, Intel, Portland Group (PGI) compilers | Portland Group 12.10 |
pgCC |
|
C++ - GNU GCC, Intel, Portland Group (PGI) compilers | GNU 4.5.0 |
(g++ - module load compiler/gcc/4.5.0) |
|
C++ - GNU GCC, Intel, Portland Group (PGI) compilers | GNU 4.3.4 |
(g++) |
|
C++ - GNU GCC, Intel, Portland Group (PGI) compilers | GNU 4.8.3 |
module load compiler/gcc/4.8.3 |
|
C++ - GNU GCC, Intel, Portland Group (PGI) compilers | Portland Group 13.9 |
(pgCC - module load compiler/pgi/13.9) |
|
C++ - GNU GCC, Intel, Portland Group (PGI) compilers | Intel 12.1.5 |
(icpc, module load compiler/ intel/12.1, loaded by default) |
|
CAP3 | 02-10-15 |
module load application/CAP3/02-10-15 |
|
Cd-hit | v4.6.4-2015-0603 |
module load application/cd-hit/v4.6.4-2015-0603 |
|
Cd-hit | v4.6.1-2012-08-27 |
module load application/cd-hit/v4.6.1-2012-08-27 |
|
Celera Whole-Genome Shotgun Assembler | 7.0 |
module load application/wgs/7.0 |
|
Chaste | 3.1 |
module load application /chaste /release_3.1 |
|
Chaste | 3.4 |
module load application/chaste/release_3.4 |
|
CMake | 2.8.10.2 |
module load utility/cmake/2.8.10.2 |
|
Compilers - C, C++ and Fortran | PGI 12.10-0 |
Initialize your environment to use the Portland Group 12.10-0 compilers with module load compiler/pgi/12.10 |
|
Compilers - C, C++ and Fortran | PGI 13.9-0 |
Initialize your environment to use the Portland Group 13.9-0 compilers with module load compiler/pgi/13.9 |
|
Compilers - C, C++ and Fortran | GCC 4.3.4 |
The GCC 4.3.4 compilers are on the default command PATH. |
|
Compilers - C, C++ and Fortran | GCC 4.5.0 |
Initialize your environment to use the GCC 4.5.0 compilers with module load compiler/gcc/4.5.0 |
|
Compilers - C, C++ and Fortran | GCC 4.8.3 |
Initialize your environment to use the GCC 4.8.3 compilers with module load compiler/gcc/4.8.3 |
|
Compilers - C, C++ and Fortran | GCC 4.9.2 |
Initialize your environment to use the GCC 4.9.2 compilers with module load compiler/gcc/4.9.2 |
|
Compilers - C, C++ and Fortran | Intel 12.1.5 |
The Intel 12.1.5 compilers are on the default command PATH, but, you can also explicitly initialize your environment to use them with module load compiler/intel/12.1 |
|
CP2K | 3.0 |
module load application/cp2k/3.0 |
|
CPMD | 3_15_3 |
module load application/cpmd/v3_15_3 |
|
csh | Link to tcsh | ||
Cufflinks | 2.2.1 |
Set up your environment to use Cufflinks 2.2.1 with: module load application/cufflinks/2.2.1 |
|
Emacs | 22.3.1 | ||
ESTScan | 2.1 |
module load application/estscan/2.1 |
|
Exonerate | 2.2.0 |
module load application/exonerate/2.2.0 |
|
Eye of GNOME | 2.28.2 | ||
FastQC | 0.11.3 |
module load application/fastqc/0.11.3 |
|
FEniCS | DOLFIN 1.1.0 |
module load application /dolfin/1.1.0 |
|
FFTW | 3.3.1 |
module load library/fftw/3.3.1 |
|
Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers | 12.1.5 |
ifort, module load compiler/ intel/12.1, loaded by default |
|
Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers | GNU 4.8.3 |
module load compiler/gcc/4.8.3 |
|
Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers | Portland Group 12.10 |
(pgf77, pgf90, pgf95 - module load compiler/pgi/12.10) |
|
Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers | GNU 4.5.0 |
(gfortran - module load compiler/gcc/4.5.0) |
|
Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers | GNU 4.3.4 |
(gfortran) |
|
Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers | Portland Group 13.9 |
(pgf77, pgf90, pgf95 - module load compiler/pgi/13.9) |
|
freebayes | 1.0.2 |
module load application/freebayes/1.0.2 |
|
GATK | 3.7 |
module load application/gatk/3.7 |
|
GATK | 3.5 |
module load application/gatk/3.5 gatk.sh -Xmx1g -Xms1g --help |
|
Gaussian | G09 B.01 |
For U of A researchers only. Initialize your environment with: module load uofa/gaussian/g09-b1 |
|
Gaussian | G09 D.01 |
For U of A researchers only. Initialize your environment with: module load uofa/gaussian/g09-d1 |
|
gdb | 7.3-0.6.1 | ||
gedit - graphical text editor | 2.28.3 |
See general gedit usage notes. |
|
Git | 1.6.0.2 | ||
GMAP (with GSNAP) - Genomic mapping and alignment | 2014-12-02 |
module load application/gmap/2014-12-02 |
|
GMAP (with GSNAP) - Genomic mapping and alignment | 2017-04-13 |
module load application/gmap/2017-04-13 |
|
Gnuplot | 4.2 | ||
GROMACS | 4.5.5 |
Initialize the environment with module load application/gromacs/4.5.5 . |
|
GSL | 1.16 |
module load library/gsl/1.16 |
|
HDF 5 | 1.8.8 |
module load library/hdf5/1.8.8 |
|
hisat2 | 2.0.4 |
module load application/hisat2/2.0.4 |
|
HMMER | 3.1b1 |
module load application/hmmer/3.1b1 |
|
Homer | 4.8.3 |
module load application/homer/4.8.3 |
|
idb | 12.1 |
module load compiler/intel/12.1 |
|
ImageMagick | 6.4.3 | ||
IQ-TREE (phylogenetics) | 1.3.2 |
Initialize your environment to use IQ-TREE 1.3.2 on Hungabee with: module load application/iq_tree/1.3.2 |
|
IQ-TREE (phylogenetics) | 1.3.1 |
Initialize your environment to use IQ-TREE 1.3.1 on Hungabee with: module load application/iq_tree/1.3.1 |
|
JAGS | 4.2.0 |
module load application/jags/4.2.0 |
|
Jam | 3.1.16 | ||
Java | Java 1.6.0_25 | ||
Java | Oracle JDK 1.8.0 update 92 |
module load application/jdk/1.8.0_92 |
|
JELLYFISH | 1.1.11 |
module load application/jellyfish/1.1.11 |
|
Julia | 0.3 |
module load application/julia/0.3 |
|
Julia | 0.5.0 |
module load application/julia/0.5.0 |
|
Kraken | 0.10.6-beta |
module load application/kraken/0.10.6-beta minikraken database in /global/software/kraken/db/minikraken_20141208 |
|
ksh | Y | ||
LAPACK | In MKL | ||
LibYAML | 0.14 |
module load library/yaml/0.1.4 |
|
Mathematica | 8.0 |
U of A only module load uofa/Mathematica/8.0 |
|
MATLAB | R2013a |
module load uofa/matlab/R2013a (UofA only) |
|
MEGAHIT | 1.1.1 |
module load application/megahit/1.1.1 |
|
Minia | 2.0.7 |
module load application/minia/v2.0.7 |
|
MKL | In Intel 12 environment | ||
Mothur | 1.39.5 |
module load application/mothur/1.39.5 |
|
Mothur | 1.32.1 |
module load application/mothur/1.32.1 |
|
nano | 2.2.6 | ||
Nektar++ | 3.2.0 |
module load application /nektar++/3.2.0 |
|
NetCDF | 4.1.3 |
module load library/netcdf/4.1.3 $NETCDFHOME |
|
NetworkX | 1.7 |
module load application/python/2.7.3 |
|
NWChem | 6.1.1 |
module load application/nwchem/6.1.1 |
|
Parallel | 20150922 |
module load application/parallel/20150922 |
|
Perl | 5.10.0 | ||
PETSc | 3.4.5 |
module load application/petsc/3.4.5 |
|
PETSc | 3.5.3 |
application/petsc/3.5.3 |
|
Picard tools | 1.60 |
/global/software/picard-tools/picard-tools-1.60 |
|
Picard tools | 1.98 |
Set up your environment with: module load application/picard-tools/1.98 This sets various aliases. To see them, type module show application/picard-tools/1.98 |
|
Picard tools | 2.1.1 |
module load application/picard-tools/2.1.1 picard -h |
|
Picard tools | 2.9.0 |
module load application/picard-tools/2.9.0 |
|
Python | Anaconda 2.3.0 |
module load application/anaconda/2.3.0 |
|
Python | 2.7.3 |
Initialize your environment with: module load application/python/2.7.3 This installation includes NumPy 1.6.2 and SciPy 0.11.0. |
|
Python | 2.6 |
(default) |
|
Python | 3.4.2 |
module load application/python/3.4.2 |
|
R | 3.2.5 |
Set up your environment to use R 3.2.5 on Hungabee with module load application/R/3.2.5 |
|
R | 3.3.2 |
module load application/R/3.3.2 |
|
R | 2.15.0 |
module load application/R/2.15.0 |
|
R | 3.1.2 |
module load application/R/3.1.2 |
|
R | 3.0.1 |
module load application/R/3.0.1 |
|
Ray | 2.3.1 |
module load application/Ray/2.3.1 (MAXKMERLENGTH=399) |
|
Relion | 1.3 |
module load application/relion/1.3 |
|
RepeatMasker | open-4-0-3 |
module load application/repeatmasker/open-4-0-3 |
|
RMBlast | 2.2.28 |
module load application/rmblastn/2.2.28 |
|
RNAmmer | 1.2 |
module load application/rnammer/1.2 |
|
RSEM | 1.2.21 |
module load application/rsem/1.2.21 |
|
RSEM | 1.2.7 |
module load application/rsem/1.2.7 |
|
Ruby | 1.8.7 | ||
SAMtools and HTSlib utilities | 1.3 |
module load application/samtools/1.3 |
|
SAMtools and HTSlib utilities | 0.1.18 |
Initialize the environment with module load application/samtools/0.1.18. |
|
SAMtools and HTSlib utilities | 0.1.19 |
Initialize the environment with module load application/samtools/0.1.19. |
|
SAMtools and HTSlib utilities | 1.4 |
module load application/samtools/1.4 |
|
ScaLAPACK | MKL |
ScaLAPACK is available through the Math Kernel Library (MKL). |
|
sh | Link to bash | ||
SignalP | 4.1c |
module load application/signalp/4.1c |
|
SNAP | 2013-02-16 |
module load application/snap/2013-02-16 |
|
SOAPdenovo-Trans | 1.02 |
module load application/SOAPdenovo-Trans/1.02 |
|
SPAdes Genome Assembler | 3.6.1 |
module load application/SPAdes/3.6.1 |
|
SPAdes Genome Assembler | 3.10.1 |
To use SPAdes 3.10.1 on Hungabee, initialize your environment with module load application/SPAdes/3.10.1 |
|
SPAdes Genome Assembler | 3.10.0 |
module load application/SPAdes/3.10.0 |
|
Stacks | 1.25 |
module load application/stacks/1.25 |
|
Structure | 2.3.4 |
Either one of module load application/structure/2.3.4 or application/structure-frontend/2.3.4 |
|
Subversion | 1.5.7 | ||
Swig | 2.0.9 |
module load application/swig/2.0.9 |
|
Tandem Repeats Finder | 407b |
module load application/trf/407b |
|
tcsh | NA | ||
TMHMM | 2.0c |
module load application/tmhmm/2.0c |
|
TopHat | 2.0.14 |
module load application/tophat/2.0.14 |
|
Trans-ABySS | 1.5.2 |
module load application/Trans-ABySS/1.5.2 |
|
Trans-ABySS | 1.5.1 |
module load application/Trans-ABySS/1.5.1 |
|
Trans-ABySS | 1.5.5 |
module load application/Trans-ABySS/1.5.5 |
|
TransDecoder | 3.0.1 |
module load application/transdecoder/3.0.1 |
|
TransDecoder | 2.0.1 |
module load application/transdecoder/2.0.1 |
|
Trimmomatic | 0.33 |
See instructions on the WestGrid Trimmomatic page. |
|
Trinity | 2.0.6 |
module load application/trinity/2.0.6 |
|
Trinity | 2012-06-08 |
module load application/trinity/r2012-06-08 |
|
Trinity | 2012-10-05 |
module load application/trinity/r2012-10-05 |
|
Trinity | r2013-02-25 |
application/trinity/r2013-02-25 |
|
Trinity | r20140413p1 |
module load application/trinity/r20140413p1 |
|
Trinity | 2.2.0 |
Set up your enivronment to use Trinity 2.2.0 with module load application/trinity/2.2.0 |
|
Trinity | 2.1.1 |
module load application/trinity/2.1.1 |
|
Trinity | 2.3.2 |
module load application/trinity/2.3.2 |
|
Trinity | 2.4.0 |
module load application/trinity/2.4.0 |
|
Trinotate | r20131110 |
module load application/trinotate/r20131110 |
|
Trinotate | 3.0.1 |
module load application/trinotate/3.0.1 |
|
Trinotate | 2.0.2 |
module load application/trinotate/2.0.2 |
|
VarSim | 0.5.1 |
module load application/varsim/0.5.1 |
|
VCFtools | 0.1.10 |
Initialize your environment with module load application/vcftools/0.1.10 Note, the VCFtools Perl utilities were not installed. |
|
Velvet | 1.2.03 |
module load application/velvet/1.2.03 |
|
Vim | 7.2 | ||
VMD | 1.9.2 |
module load application/vmd/1.9.2 |
|
VTK - Visualization Toolkit | 5.10.1 |
module load application/vtk/5.10.1 |
|
WebLogo | 2.8.2 |
module load application/weblogo/2.8.2 |