View source for 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.

==Software modules installed on Cheaha==
{| border="1" align="center" cellpadding="10" style="text-align:center;"
|+ 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
|
|
|-
|freegene
|2008
|
|
|-
|'''[[Fsl]]'''
|4.1.6
|
|
|-
|'''[[Galaxy]]'''
|1.0
|
|
|-
|genn
|
|
|
|-
|'''[[Gromacs]]'''
|4.5
|4
|gnu/intel
|-
|gtools
|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
|
|
|-
|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
|3.8
|3.12,3.4,3.6
|
|-
|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
|
|}