Cheaha software: Difference between revisions

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This page shows a list of installed modules on the [[Cheaha]] research computing system.If you don't find a particular package listed on this page, please send a request to [mailto:support@vo.uabgrid.uab.edu cheaha support] to request the software.
#REDIRECT [[Cheaha_Software]]
 
This page shows a list of installed modules on the [[Cheaha]] research computing system. If you don't find a particular package listed on this page, please send a request to [mailto:support@vo.uabgrid.uab.edu cheaha support] to request the software.


This list is not exhaustive and may not reflect the accurate current versions of the different software installed on the system. This list is current as of March 15th 2012.
This list is not exhaustive and may not reflect the accurate current versions of the different software installed on the system. This list is current as of March 15th 2012.
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! Remarks
! Remarks
|-
|-
|affymetrix
|'''[[Affymetrix]]'''
|1.4.3
|1.4.3
|
|
|
|
|-
|-
|[[Amber]]
|'''[[Amber]]'''
|10
|10
|
|
|
|
|-
|-
|annovar
|'''[[ANNOVAR]]'''
|2012Feb23
|2012Feb23
|
|
|
|
|-
|-
|apbs
|'''[[APBS]]'''
|1.0
|1.0
|
|
|
|
|-
|-
|aspera
|'''[[Aspera]]'''
|2.4.7
|2.4.7
|
|
|
|
|-
|-
|atlas
|'''[[Atlas]]'''
|3.8
|3.8
|
|
|
|
|-
|-
|autodock
|'''[[AutoDock]]'''
|4.2.3
|4.2.3
|
|
|
|
|-
|-
|birdsuite
|'''[[Birdsuite]]'''
|1.5.5
|1.5.5
|1.5.3
|1.5.3
|
|
|-
|-
|bowtie
|'''[[Bowtie]]'''
|0.9
|0.9
|0.10,0.12
|0.10,0.12
|
|
|-
|-
|chase
|'''[[CHASE]]'''
|1
|1
|
|
|
|
|-
|-
|cuda
|'''[[CUDA]]'''
|4
|4
|
|
|
|
|-
|-
|[[COMSOL]]
|'''[[COMSOL]]'''
|4.2
|4.2
|
|
|
|
|-
|-
|cufflinks
|'''[[Cufflinks]]'''
|0.9
|0.9
|
|
|
|
|-
|-
|eigenstrat
|'''[[eigenstrat]]'''
|2.0
|2.0
|
|
|
|
|-
|-
|EMAN2
|'''[[EMAN2]]'''
|2.02
|2.02
|
|
|
|
|-
|-
|ent
|'''[[ENT]]'''
|1.0.2
|1.0.2
|
|
|
|
|-
|-
|fastphase
|'''[[fastPHASE]]'''
|1.4
|1.4
|
|
|
|
|-
|-
|fftw
|'''[[FFTW]]'''
|3.1.2
|3.1.2
|
|
|gnu/intel
|gnu/intel
|-
|-
|[[FreeSurfer]]
|'''[[FreeSurfer]]'''
|4.5
|4.5
|
|
|
|
|-
|-
|freegene
|'''[[FREGENE]]'''
|2008
|2008
|
|
|
|
|-
|-
|[[Fsl]]
|'''[[Fsl]]'''
|4.1.6
|4.1.6
|
|
|
|
|-
|-
|[[Galaxy]]
|'''[[Galaxy]]'''
|1.0
|1.0
|
|
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|
|
|-
|-
|[[Gromacs]]
|'''[[Gromacs]]'''
|4.5
|4.5
|4
|4
|gnu/intel
|gnu/intel
|-
|-
|gtools
|'''[[GTOOL]]'''
|0.6.7
|0.6.7
|
|
|
|
|-
|-
|hapgen
|'''[[HAPGEN]]'''
|1.3.0
|1.3.0
|
|
|
|
|-
|-
|haskell/ghc
|'''[[Haskell/GHC]]'''
|6.10.4
|6.10.4
|
|
|
|
|-
|-
|illuminus
|'''[[Illuminus]]'''
|2
|2
|
|
|
|
|-
|-
|impute
|'''[[IMPUTE2]]'''
|2.1.2
|2.1.2
|2.1.0, 2.0.3
|2.1.0, 2.0.3
|
|
|-
|-
|jags
|'''[[JAGS]]'''
|1.0
|1.0
|
|
|gnu
|gnu
|-
|-
|lammpi
|'''[[LAM-MPI]]'''
|7.1
|7.1
|
|
|gnu/intel
|gnu/intel
|-
|-
|LS-DYNA
|'''[[LS-DYNA]]'''
|9.7.1
|9.7.1
|
|
|
|
|-
|-
|MACH
|'''[[MACH]]'''
|1.0.16
|1.0.16
|
|
|
|
|-
|-
|macs
|'''[[MACS]]'''
|1.3.6
|1.3.6
|
|
|
|
|-
|-
|MAQ
|'''[[Maq]]'''
|0.7
|0.7.1
|
|
|
|
|-
|-
|marthlab
|'''[[MarthLab]]'''
|mosaik 0.9.891
|mosaik 0.9.891
|gigabayes, pyrobayes
|gigabayes, pyrobayes
|
|
|-
|-
|[[MATLAB]]
|'''[[MATLAB]]'''
|R2012a
|R2012a
|R2009(a,b),R2010(a,b),R2011(a,b)
|R2009(a,b),R2010(a,b),R2011(a,b)
|DCS-128
|DCS-128
|-
|-
|mpich
|'''[[MPICH]]'''
|2
|2
|1.2
|1.2
|gnu/intel
|gnu/intel
|-
|-
|mrbayes
|'''[[MrBayes]]'''
|3.1.2
|3.1.2
|
|
|intel
|intel
|-
|-
|mvapich
|'''[[MVAPICH]]'''
|2
|2
|
|
|gnu
|gnu
|-
|-
|[[Namd]]
|'''[[Namd]]'''
|2.8
|2.8
|2.7,2.6
|2.7,2.6
|ibverbs
|ibverbs
|-
|-
|openmp
|'''[[OpenMPI]]'''
|1.2
|1.2
|
|
|gnu/intel
|gnu/intel
|-
|-
|paraview
|'''[[ParaView]]'''
|3.8
|3.12
|3.12,3.4,3.6
|3.4,3.6,3.8
|
|
|-
|-
|PDT
|'''[[PDT]]'''
|3.17
|3.17
|3.14
|3.14
|
|
|-
|-
|penncnv
|'''[[PennCNV]]'''
|2010May01
|2010May01
|
|
|
|
|-
|-
|phase
|'''[[PHASE]]'''
|2.1.1
|2.1.1
|
|
|
|
|-
|-
|PLINK
|'''[[PLINK]]'''
|1.07
|1.07
|1.06,1.05
|1.06,1.05
|
|
|-
|-
|python
|'''[[Python]]'''
|2.7
|2.7
|2.6
|2.6
|
|
|-
|-
|[[R]]
|'''[[R]]'''
|2.12.2
|2.12.2
|2.6.2,2.7.2,2.8.1,2.9.0,2.9.2,2.11.1
|2.6.2,2.7.2,2.8.1,2.9.0,2.9.2,2.11.1
|
|
|-
|-
|RAxML
|'''[[RAxML]]'''
|7.2.6
|7.2.6
|
|
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|
|
|-
|-
|S.A.G.E.
|'''[[S.A.G.E.]]'''
|6.2
|6.2
|6.0
|6.0
|
|
|-
|-
|samtools
|'''[[SAMtools]]'''
|0.1
|0.1
|
|
|
|
|-
|-
|scalemp
|'''[[ScaleMP]]'''
|3.2.2
|3.2.2
|
|
|fftw optimized
|fftw optimized
|-
|-
|shrimp
|'''[[SHRiMP]]'''
|1.3
|1.3
|1.2
|1.2
|
|
|-
|-
|solar
|'''[[SOLAR]]'''
|4.3.1
|4.3.1
|
|
|
|
|-
|-
|spparks
|'''[[SPPARKS]]'''
|30May11
|30May11
|07Aug09
|07Aug09
|
|
|-
|-
|structure
|'''[[Structure]]'''
|2.2
|2.2
|
|
|
|
|-
|-
|tau
|'''[[TAU]]'''
|2.21.1
|2.21.1
|
|
|lam, open mpi
|lam, open mpi
|-
|-
|[[TopHat]]
|'''[[TopHat]]'''
|1.1
|1.1
|1.0.8
|1.0.8
|
|
|-
|-
|Varianttools/vtools
|'''[[varianttools]]'''
|1.0.1
|1.0.1
|1.0
|1.0
|
|
|-
|-
|VEGAS
|'''[[VEGAS]]'''
|0.8
|0.8
|
|
|
|
|-
|-
|vmd
|'''[[VMD]]'''
|1.9.0
|1.9.0
|1.8.6
|1.8.6
|
|
|}
|}

Latest revision as of 19:26, 2 April 2012

Redirect to:

This page shows a list of installed modules on the Cheaha research computing system. If you don't find a particular package listed on this page, please send a request to cheaha support to request the software.

This list is not exhaustive and may not reflect the accurate current versions of the different software installed on the system. This list is current as of March 15th 2012.

Software modules installed on Cheaha

Current as of March 15th 2012
Software Latest Version Other Versions Remarks
Affymetrix 1.4.3
Amber 10
ANNOVAR 2012Feb23
APBS 1.0
Aspera 2.4.7
Atlas 3.8
AutoDock 4.2.3
Birdsuite 1.5.5 1.5.3
Bowtie 0.9 0.10,0.12
CHASE 1
CUDA 4
COMSOL 4.2
Cufflinks 0.9
eigenstrat 2.0
EMAN2 2.02
ENT 1.0.2
fastPHASE 1.4
FFTW 3.1.2 gnu/intel
FreeSurfer 4.5
FREGENE 2008
Fsl 4.1.6
Galaxy 1.0
genn
Gromacs 4.5 4 gnu/intel
GTOOL 0.6.7
HAPGEN 1.3.0
Haskell/GHC 6.10.4
Illuminus 2
IMPUTE2 2.1.2 2.1.0, 2.0.3
JAGS 1.0 gnu
LAM-MPI 7.1 gnu/intel
LS-DYNA 9.7.1
MACH 1.0.16
MACS 1.3.6
Maq 0.7.1
MarthLab mosaik 0.9.891 gigabayes, pyrobayes
MATLAB R2012a R2009(a,b),R2010(a,b),R2011(a,b) DCS-128
MPICH 2 1.2 gnu/intel
MrBayes 3.1.2 intel
MVAPICH 2 gnu
Namd 2.8 2.7,2.6 ibverbs
OpenMPI 1.2 gnu/intel
ParaView 3.12 3.4,3.6,3.8
PDT 3.17 3.14
PennCNV 2010May01
PHASE 2.1.1
PLINK 1.07 1.06,1.05
Python 2.7 2.6
R 2.12.2 2.6.2,2.7.2,2.8.1,2.9.0,2.9.2,2.11.1
RAxML 7.2.6
RNA pipeline 0.5.0 0.31
S.A.G.E. 6.2 6.0
SAMtools 0.1
ScaleMP 3.2.2 fftw optimized
SHRiMP 1.3 1.2
SOLAR 4.3.1
SPPARKS 30May11 07Aug09
Structure 2.2
TAU 2.21.1 lam, open mpi
TopHat 1.1 1.0.8
varianttools 1.0.1 1.0
VEGAS 0.8
VMD 1.9.0 1.8.6
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