Awoonga Software

Awoonga Software

Updated 2018-09-18

This page is not automatically updated when new modules are added. 
For the latest list, always use module avail on the HPC.

Modules Listed Alphabetically

a abyss/2.0.2 anaconda/4.2.0 anaconda/4.3.1 anaconda/5.2.0 ansys/17.0 
ansys/17.1 ansys/18.0 ansys/18.1 ansys/19.1 ansys_edt/17.1 apbs/1.5  
Autoconf/2.69-GCC-4.9.2 Automake/1.15-GCC-4.9.2
b bamm/201710 bamtools/2.4.0 bbmap/201710 bcftools/1.3 beagle/2.1  
beast/1.8.0 beast/1.8.1 beast/1.8.2 bedtools/2.25.0 binutils/2.25  
binutils/2.25-GCC-4.9.2 bioconductor/3.6-rc2 biolinux/8 bioperl/1.6.924  
biopython/1.66 bio-roll bismark/0.15.0 blast/2.3.0 blat/35 boost/1.55.0  
bowtie/1.1.2 bowtie2/2.2.7 bricks/20180416 busco/1.22 bwa/0.7.13  
bx-python/0.7.3 bzip2/1.0.6-intel-2015.3.187
c canu/1.3 ccam/2016-intel celera/8.3rc2 cern/1 cgal/4.5.1-22  
checkm/1.0.11 cilk/5.4.6 CMake/3.1.3-GCC-4.9.2 CMake/3.2.3-intel-2015.3.187  
cmake/3.8.2 cnvkit/0.9.4a0 coreutils/8.22 cp2k/4.1 cp2k/5.1-sopt  
cp2k/5.1-ssmp cp2k/6.0 crystalexplorer/17.5 cst/2016 cst/2016sp1  
cufflinks/2.2.1 cURL/7.43.0-intel-2015.3.187
d dendropy/4.0.3 diamond/0.7.12 dmtcp/2.5.0 dot dssp/2.2.1
e easybuild/2.3.0 easybuild/2.3.1 easybuild/2.6.0 easybuild/3.6.1  
edena/3.131028 eigen/3.2.7 eman2/2.21 emboss/6.5.7
f falcon/201710 fastqc/0.11.4 fastx/0.0.14 ferret/7.0 fftw/2.1.5  
fftw/3.3.4 fpart/1.0.0 FPM/1.3.3-Ruby-2.1.6 frealign/v9.11 freesurfer/6.0  
freesurfer/6.1dev
g gaussian/g09 gaussian/g09_E01 GCC/4.9.2 gdal/2.0.2 gdal/2.2.3  
GenomeAnalysisTK/3.5 GenomeAnalysisTK/3.6 geos/3.5.0 git/1.7.11 glibc/2.17  
glibc/2.19 glibc/2.23 gmap_gsnap/20151231 gmp/6.0.0a gnu/7.1.0  
gnuplot/5.0.0 gnutools/2.69 graftm/0.9.4 grass/7.0.3 gromacs/2016.3  
gromacs/5.1.4-intel gromacs/5.1.4-intelMPI groopm/0.3.5 gsl/1.16 gsl/2.1  
gurobi/8.0
h Hadoop/2.5.0-cdh5.3.1-native hdf4/2.10 hdf5/1.8.14 hmmer/3.1b2  
HOWTO/IntelMPI HOWTO/Libraries HOWTO/OpenMPI HOWTO/PersonalModules  
HOWTO/R-Packages HOWTO/X11 htseq/0.6.1p1 hwrender/20180315 hyperworks/14.0  
hyperworks/20161203 hyperworks/2017.2 hyperworks/2018.1
i idba-ud/1.1.1 intel/2017.4 intel_mpi/2017.4 intel_mpi/5.0.2.044  
intel_mpi/5.0.3.048 intel_xe/2015.3.187 intel_xe/2016.2.181 ipm/2.0.3  
isolve/v3_0
j jags/4.2.0 jasper/1.900.1 Java/1.7.0_79 Java/1.8.0_45
k krona/201712
l lammps/20170331 lapack/3.6.0 libtool/2.4.2-GCC-4.9.2  
libtool/2.4.5-GCC-4.9.2 llvm/3.6.2
m macs/2-2.1.1 mafft/v7.407 masurca/3.2.4 matlab/2015a matlab/2017a  
matlab/2018a matlab/qcif-R2017a matlab/qcif-R2018a matt/1.00 Maven/3.3.3  
megahit/201710 metabat/201710 metacv/2.3.0 miRDeep2/0.0.7 miso/0.5.3  
mkl/11.2.2.164 mkl/2017.3 module-git module-info modules mpc/1.0.3  
mpfr/3.1.2 mrbayes/3.2.3 mrbayes/3.2.6 multisnv/201801 mxml/2.9  
mysql/5.6.15
n namd/2.10 namd/2.12 namd/2.9 NASM/2.11.08-intel-2015.3.187  
ncl_ncarg/6.3.0 ncview/2.1.7 netcdf/3.6.2 netcdf/4.3.2 netcdf/4.4.1-gnu  
netcdf/4.4.1-intel netlogo/6.0.3 neurodebian/0.37.2 ngsplot/2.61 null  
numactl/2.0.10-GCC-4.9.2
o octave/4.2.1 openfoam/1.2.3 openfoam/20161223 openmpi2_ib/2.0.2  
openmpi_ib/1.8.4
p pacbioeda/20140812 pacbio/smrtlink_5.0.1 pacbio/smrtlink_5.1  
papi/5.4.1 parallel/20170122 parallel/20180322 parmetis/4.0.3 pdt/3.20  
petsc/3.6.3 picard/2.18.2 picard/2.3.0 plink/1.9 pplacer/v1.1.alpha17  
prodigal/201804 proj4/4.9.3 proj/4.9.1 prokka/1.12 prokka/1.13 pylibs/1.0  
pysam/0.8.4 python/2.7.13
q qgis/2.8.6 qiime/1.9.1 qiime2/2018.6.0 qiime-modules/1.9.1  
quantumespresso/6.1
r R/3.4.0 R/3.4.3 R/3.5.0 randfold/2.0 README/AppSupport  
README/CompilerEnvironmentVariables README/Euramoo_Migration  
README/HyperWorks README/Modules README/Rolls+Modules relion/201804  
r+gcc/3.4.4 R/GenABEL/1.8.0-4 rjags/4.5.1 rseqc/2.6.4 rstudio/1.0.143  
rstudio/1.1.456-3.4.4 rstudio/1.1.456-3.5.1 Ruby/2.1.6
s samtools/1.2 samtools/1.3 samtools/1.6 scalapack/2.0.2 scipy/2.7  
singularity/2.2.1 singularity/2.3.1 singularity/2.4.0 singularity/2.4.2  
singularity/2.5.1 slepc/3.6.2 slim/20180406 snappy/1.1.2-GCC-4.9.2  
soapdenovo/240 SOAPsnp/1.03 spades/3.9.0 sprng/2.0b squid/1.9g stacks/1.37 
star/2.5.2b star/2.5.2b-static structure/2.3.4 sundials/2.6.2 superlu/4.2
t tau/2.23 tophat/2.1.1 trimmomatic/0.35 trinity/2.1.1  
tuflow/2014.01.016
u use.own
v vasp/5.3.5 vasp/5.3.5-gamma vcftools/0.1.14 velvet/1.2.10  
ViennaRNA/2.2.4 vlab/4.4.1 vlab/4.4.1-xvfb vtk/6.1.0
w wombat/20180404
x xorg-macros/1.17-GCC-4.7.2
y yacas/1.6.1
z zlib/1.2.11-gnu-7.1.0

Modules Listed by Section

Modules for software in ROCKS rolls.

abyss/2.0.2 apbs/1.5 bamtools/2.4.0 bcftools/1.3 beagle/2.1 beast/1.8.0  
beast/1.8.1 beast/1.8.2 bedtools/2.25.0 biopython/1.66 bismark/0.15.0  
blast/2.3.0 blat/35 boost/1.55.0 bowtie/1.1.2 bowtie2/2.2.7 bwa/0.7.13  
bx-python/0.7.3 celera/8.3rc2 cern/1 cp2k/4.1 cufflinks/2.2.1  
dendropy/4.0.3 diamond/0.7.12 edena/3.131028 eigen/3.2.7 emboss/6.5.7  
fastqc/0.11.4 fastx/0.0.14 fftw/2.1.5 fftw/3.3.4 gdal/2.0.2  
GenomeAnalysisTK/3.5 GenomeAnalysisTK/3.6 geos/3.5.0 gmap_gsnap/20151231  
gmp/6.0.0a gnutools/2.69 gromacs/2016.3 gsl/1.16 gsl/2.1 hdf4/2.10  
hdf5/1.8.14 hmmer/3.1b2 htseq/0.6.1p1 idba-ud/1.1.1 ipm/2.0.3 jags/4.2.0  
jasper/1.900.1 lammps/20170331 lapack/3.6.0 llvm/3.6.2 matt/1.00  
miRDeep2/0.0.7 miso/0.5.3 mkl/11.2.2.164 mkl/2017.3 mpc/1.0.3 mpfr/3.1.2  
mrbayes/3.2.3 mrbayes/3.2.6 mxml/2.9 namd/2.10 namd/2.12 namd/2.9  
ncl_ncarg/6.3.0 ncview/2.1.7 netcdf/3.6.2 netcdf/4.3.2 octave/4.2.1  
papi/5.4.1 parmetis/4.0.3 pdt/3.20 petsc/3.6.3 picard/2.3.0 plink/1.9  
proj/4.9.1 pysam/0.8.4 qiime/1.9.1 R/3.4.0 randfold/2.0 rseqc/2.6.4  
samtools/1.2 samtools/1.3 scalapack/2.0.2 scipy/2.7 slepc/3.6.2  
soapdenovo/240 SOAPsnp/1.03 spades/3.9.0 sprng/2.0b squid/1.9g stacks/1.37 
sundials/2.6.2 superlu/4.2 tau/2.23 tophat/2.1.1 trimmomatic/0.35  
trinity/2.1.1 vcftools/0.1.14 velvet/1.2.10 ViennaRNA/2.2.4 vtk/6.1.0

 

Modules for language compilers.

cilk/5.4.6 cmake/3.8.2 gnu/7.1.0 intel/2017.4 python/2.7.13

 

Modules for message passing libraries.

openmpi2_ib/2.0.2 openmpi_ib/1.8.4

 

Modules for release point software.

R/3.4.3

 

Modules for singularity container apps.

bioconductor/3.6-rc2 biolinux/8 checkm/1.0.11 cp2k/6.0  
crystalexplorer/17.5 dssp/2.2.1 glibc/2.17 glibc/2.19 glibc/2.23  
graftm/0.9.4 grass/7.0.3 neurodebian/0.37.2 openfoam/20161223 picard/2.18.2 
prokka/1.12 qgis/2.8.6 R/3.5.0 r+gcc/3.4.4 rjags/4.5.1 rstudio/1.0.143  
rstudio/1.1.456-3.4.4 rstudio/1.1.456-3.5.1 vlab/4.4.1 vlab/4.4.1-xvfb  
yacas/1.6.1

 

Modules for software that is on the way out.

gromacs/5.1.4-intel

 

Modules that inform.

HOWTO/IntelMPI HOWTO/Libraries HOWTO/OpenMPI HOWTO/PersonalModules  
HOWTO/R-Packages HOWTO/X11 README/AppSupport  
README/CompilerEnvironmentVariables README/Euramoo_Migration  
README/HyperWorks README/Modules README/Rolls+Modules

 

Modules for software that is installed centrally in /sw.

anaconda/4.2.0 anaconda/4.3.1 anaconda/5.2.0 ansys/17.0 ansys/17.1  
ansys/18.0 ansys/18.1 ansys/19.1 ansys_edt/17.1 Autoconf/2.69-GCC-4.9.2  
Automake/1.15-GCC-4.9.2 bamm/201710 bbmap/201710 binutils/2.25  
binutils/2.25-GCC-4.9.2 bricks/20180416 busco/1.22  
bzip2/1.0.6-intel-2015.3.187 canu/1.3 ccam/2016-intel cgal/4.5.1-22  
CMake/3.1.3-GCC-4.9.2 CMake/3.2.3-intel-2015.3.187 cnvkit/0.9.4a0  
coreutils/8.22 cp2k/5.1-sopt cp2k/5.1-ssmp cst/2016 cst/2016sp1  
cURL/7.43.0-intel-2015.3.187 dmtcp/2.5.0 easybuild/2.3.0 easybuild/2.3.1  
easybuild/2.6.0 easybuild/3.6.1 eman2/2.21 falcon/201710 ferret/7.0  
fpart/1.0.0 FPM/1.3.3-Ruby-2.1.6 frealign/v9.11 freesurfer/6.0  
freesurfer/6.1dev gaussian/g09 gaussian/g09_E01 GCC/4.9.2 gdal/2.2.3  
gromacs/5.1.4-intelMPI groopm/0.3.5 gurobi/8.0 Hadoop/2.5.0-cdh5.3.1-native  
hwrender/20180315 hyperworks/14.0 hyperworks/20161203 hyperworks/2017.2  
hyperworks/2018.1 intel_mpi/2017.4 intel_mpi/5.0.2.044 intel_mpi/5.0.3.048  
intel_xe/2015.3.187 intel_xe/2016.2.181 isolve/v3_0 Java/1.7.0_79  
Java/1.8.0_45 krona/201712 libtool/2.4.2-GCC-4.9.2 libtool/2.4.5-GCC-4.9.2  
macs/2-2.1.1 mafft/v7.407 masurca/3.2.4 matlab/2015a matlab/2017a  
matlab/2018a matlab/qcif-R2017a matlab/qcif-R2018a Maven/3.3.3  
megahit/201710 metabat/201710 metacv/2.3.0 multisnv/201801  
NASM/2.11.08-intel-2015.3.187 netcdf/4.4.1-gnu netcdf/4.4.1-intel  
netlogo/6.0.3 ngsplot/2.61 numactl/2.0.10-GCC-4.9.2 openfoam/1.2.3  
pacbioeda/20140812 pacbio/smrtlink_5.0.1 pacbio/smrtlink_5.1  
parallel/20170122 parallel/20180322 pplacer/v1.1.alpha17 prodigal/201804  
proj4/4.9.3 prokka/1.13 pylibs/1.0 qiime2/2018.6.0 qiime-modules/1.9.1  
quantumespresso/6.1 relion/201804 Ruby/2.1.6 samtools/1.6 singularity/2.2.1 
singularity/2.3.1 singularity/2.4.0 singularity/2.4.2 singularity/2.5.1  
slim/20180406 snappy/1.1.2-GCC-4.9.2 star/2.5.2b star/2.5.2b-static  
structure/2.3.4 tuflow/2014.01.016 vasp/5.3.5 vasp/5.3.5-gamma  
wombat/20180404 xorg-macros/1.17-GCC-4.7.2 zlib/1.2.11-gnu-7.1.0

 

Modules for other miscellany.

bioperl/1.6.924 git/1.7.11 gnuplot/5.0.0 mysql/5.6.15 R/GenABEL/1.8.0-4

 

Modules that are utilitarian in nature.

bio-roll dot module-git module-info modules null use.own

 

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