Cheaha Software

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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.
 
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. Please see the output of the '''module avail''' command for the official list of software modules installed on Cheaha.
  
 
==Software modules installed on Cheaha==
 
==Software modules installed on Cheaha==
 
{| border="1" align="center" cellpadding="10" style="text-align:center;"
 
{| border="1" align="center" cellpadding="10" style="text-align:center;"
|+ Current as of March 15th 2012
+
|+
 
! Software
 
! Software
 
! Latest Version
 
! Latest Version
Line 12: Line 12:
 
|-
 
|-
 
|'''[[AFNI]]'''
 
|'''[[AFNI]]'''
 +
|AFNI_Jun_25_2013
 
|AFNI_2011_12_21_1014
 
|AFNI_2011_12_21_1014
|
+
|linux openmp 64, linux Xorg7 64
|linux openmp 64
+
 
|-
 
|-
 
|'''[[Affymetrix]]'''
 
|'''[[Affymetrix]]'''
|1.4.3
+
|1.14.3
 
|
 
|
 
|
 
|
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|2012Feb23
 
|2012Feb23
 
|
 
|
 +
|ngs-ccts 2013.09.11/2013.04.03
 +
|-
 +
|'''[[ANSYS]]'''
 +
|14.5
 +
|14.0
 
|
 
|
 
|-
 
|-
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|0.9
 
|0.9
 
|0.10,0.12
 
|0.10,0.12
|
+
|ngs-ccts 2.1.0
 +
|-
 +
|'''[[bwa]]'''
 +
|0.6.2
 +
|0.5.10,0.5.9
 +
|ngs-ccts
 +
|-
 +
|'''[[cgatools]]'''
 +
|1.8.0
 +
|1.7.1,1.5.0
 +
|ngs-ccts
 
|-
 
|-
 
|'''[[CHASE]]'''
 
|'''[[CHASE]]'''
 
|1
 
|1
 +
|
 +
|
 +
|-
 +
|'''[[cmake]]'''
 +
|2.8.10.2
 
|
 
|
 
|
 
|
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|'''[[Cufflinks]]'''
 
|'''[[Cufflinks]]'''
 
|0.9
 
|0.9
 +
|
 +
|ngs-ccts 2.1.1
 +
|-
 +
|'''[[DSSP]]'''
 +
|2.0.4
 +
|
 +
|
 +
|-
 +
|'''[[Eclipse]]'''
 +
|4.3.1
 
|
 
|
 
|
 
|
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|2.02
 
|2.02
 
|
 
|
|
+
|??
 
|-
 
|-
 
|'''[[ENT]]'''
 
|'''[[ENT]]'''
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|-
 
|-
 
|'''[[FreeSurfer]]'''
 
|'''[[FreeSurfer]]'''
|4.5
+
|5.3.0
|
+
|4.5,5.2.0
 
|
 
|
 
|-
 
|-
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|-
 
|-
 
|'''[[Fsl]]'''
 
|'''[[Fsl]]'''
 +
|5.0.6
 
|4.1.6
 
|4.1.6
|
 
 
|
 
|
 
|-
 
|-
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|
 
|
 
|-
 
|-
|genn
+
|'''[[gcc]]'''
 +
|4.8.1
 +
|
 +
|
 +
|-
 +
|'''[[genn]]'''
 
|
 
|
 
|
 
|
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|-
 
|-
 
|'''[[Gromacs]]'''
 
|'''[[Gromacs]]'''
|4.5
+
|4.6.1
|4
+
|4,4.5
 
|gnu/intel
 
|gnu/intel
 
|-
 
|-
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|'''[[Haskell/GHC]]'''
 
|'''[[Haskell/GHC]]'''
 
|6.10.4
 
|6.10.4
 +
|
 +
|
 +
|-
 +
|'''[[HYPERWORKS]]'''
 +
|12.0
 
|
 
|
 
|
 
|
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|-
 
|-
 
|'''[[IMPUTE2]]'''
 
|'''[[IMPUTE2]]'''
|2.1.2
+
|2.3.0
|2.1.0, 2.0.3
+
|2.1.2,2.1.0, 2.0.3
 
|
 
|
 
|-
 
|-
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|'''[[MACS]]'''
 
|'''[[MACS]]'''
 
|1.3.6
 
|1.3.6
 +
|
 +
|
 +
|-
 +
|'''[[Magma]]'''
 +
|5.2
 
|
 
|
 
|
 
|
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|-
 
|-
 
|'''[[MATLAB]]'''
 
|'''[[MATLAB]]'''
|R2012a
+
|R2013a
|R2009(a,b),R2010(a,b),R2011(a,b)
+
|R2009(a,b),R2010(a,b),R2011(a,b),R2012a
 
|DCS-128
 
|DCS-128
 
|-
 
|-
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|1.2
 
|1.2
 
|gnu/intel
 
|gnu/intel
 +
|-
 +
|'''[[mplayer]]'''
 +
|1.1.1
 +
|
 +
|
 
|-
 
|-
 
|'''[[MrBayes]]'''
 
|'''[[MrBayes]]'''
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|-
 
|-
 
|'''[[Namd]]'''
 
|'''[[Namd]]'''
|2.8
+
|2.9
|2.7,2.6
+
|2.8,2.7,2.6
 
|ibverbs
 
|ibverbs
 
|-
 
|-
 
|'''[[OpenMPI]]'''
 
|'''[[OpenMPI]]'''
 +
|1.6.4
 
|1.2
 
|1.2
|
 
 
|gnu/intel
 
|gnu/intel
 
|-
 
|-
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|-
 
|-
 
|'''[[PDT]]'''
 
|'''[[PDT]]'''
|3.17
+
|3.19
|3.14
+
|3.14,3.17
 
|
 
|
 
|-
 
|-
 
|'''[[PennCNV]]'''
 
|'''[[PennCNV]]'''
 
|2010May01
 
|2010May01
 +
|
 +
|
 +
|-
 +
|'''[[petsc]]'''
 +
|3.4.3
 
|
 
|
 
|
 
|
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|-
 
|-
 
|'''[[R]]'''
 
|'''[[R]]'''
|2.12.2
+
|3.0.1
|2.6.2,2.7.2,2.8.1,2.9.0,2.9.2,2.11.1,2.12.2,2.14.2,2.15.0,2.15.3
+
|2.6.2,2.7.2,2.8.1,2.9.0,2.9.2,2.11.1,2.12.2,2.14.2,2.15.0,2.15.3,3.0.0
 
|
 
|
 
|-
 
|-
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|
 
|
 
|-
 
|-
|RNA pipeline
+
|'''[[RNA pipeline]]'''
 
|0.5.0
 
|0.5.0
 
|0.31
 
|0.31
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|0.1
 
|0.1
 
|
 
|
|
+
|ngs-ccts 0.1.19
 
|-
 
|-
 
|'''[[ScaleMP]]'''
 
|'''[[ScaleMP]]'''
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|
 
|
 
|
 
|
 +
|-
 +
|'''[[tabix]]'''
 +
|0.2.6
 +
|
 +
|ngs-ccts
 
|-
 
|-
 
|'''[[TAU]]'''
 
|'''[[TAU]]'''
 +
|2.22.2
 
|2.21.1
 
|2.21.1
|
 
 
|lam, open mpi
 
|lam, open mpi
 
|-
 
|-
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|1.1
 
|1.1
 
|1.0.8
 
|1.0.8
|
+
|ngs-ccts 2.0.10
 
|-
 
|-
 
|'''[[varianttools]]'''
 
|'''[[varianttools]]'''
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|1.0
 
|1.0
 
|
 
|
 +
|-
 +
|'''[[vcftools]]'''
 +
|0.1.11
 +
|
 +
|ngs-ccts
 
|-
 
|-
 
|'''[[VEGAS]]'''
 
|'''[[VEGAS]]'''
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|
 
|
 
|
 
|
 +
|-
 +
|'''[[velvet]]'''
 +
|1.2.10
 +
|
 +
|ngs-ccts
 
|-
 
|-
 
|'''[[VMD]]'''
 
|'''[[VMD]]'''

Latest revision as of 10:06, 6 October 2017

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. Please see the output of the module avail command for the official list of software modules installed on Cheaha.

[edit] Software modules installed on Cheaha

Software Latest Version Other Versions Remarks
AFNI AFNI_Jun_25_2013 AFNI_2011_12_21_1014 linux openmp 64, linux Xorg7 64
Affymetrix 1.14.3
Amber 10
ANNOVAR 2012Feb23 ngs-ccts 2013.09.11/2013.04.03
ANSYS 14.5 14.0
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 ngs-ccts 2.1.0
bwa 0.6.2 0.5.10,0.5.9 ngs-ccts
cgatools 1.8.0 1.7.1,1.5.0 ngs-ccts
CHASE 1
cmake 2.8.10.2
CUDA 4
COMSOL 4.2
Cufflinks 0.9 ngs-ccts 2.1.1
DSSP 2.0.4
Eclipse 4.3.1
eigenstrat 2.0
EMAN2 2.02 ??
ENT 1.0.2
fastPHASE 1.4
FFTW 3.1.2 gnu/intel
FreeSurfer 5.3.0 4.5,5.2.0
FREGENE 2008
Fsl 5.0.6 4.1.6
Galaxy 1.0
gcc 4.8.1
genn
Gromacs 4.6.1 4,4.5 gnu/intel
GTOOL 0.6.7
HAPGEN 1.3.0
Haskell/GHC 6.10.4
HYPERWORKS 12.0
Illuminus 2
IMPUTE2 2.3.0 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
Magma 5.2
Maq 0.7.1
MarthLab mosaik 0.9.891 gigabayes, pyrobayes
MATLAB R2013a R2009(a,b),R2010(a,b),R2011(a,b),R2012a DCS-128
MPICH 2 1.2 gnu/intel
mplayer 1.1.1
MrBayes 3.1.2 intel
MVAPICH 2 gnu
Namd 2.9 2.8,2.7,2.6 ibverbs
OpenMPI 1.6.4 1.2 gnu/intel
ParaView 3.12 3.4,3.6,3.8
PDT 3.19 3.14,3.17
PennCNV 2010May01
petsc 3.4.3
PHASE 2.1.1
PLINK 1.07 1.06,1.05
Python 2.7 2.6
R 3.0.1 2.6.2,2.7.2,2.8.1,2.9.0,2.9.2,2.11.1,2.12.2,2.14.2,2.15.0,2.15.3,3.0.0
RAxML 7.2.6
RNA pipeline 0.5.0 0.31
S.A.G.E. 6.2 6.0
SAMtools 0.1 ngs-ccts 0.1.19
ScaleMP 3.2.2 fftw optimized
SHRiMP 1.3 1.2
SOLAR 4.3.1
SPPARKS 30May11 07Aug09
Structure 2.2
tabix 0.2.6 ngs-ccts
TAU 2.22.2 2.21.1 lam, open mpi
TopHat 1.1 1.0.8 ngs-ccts 2.0.10
varianttools 1.0.1 1.0
vcftools 0.1.11 ngs-ccts
VEGAS 0.8
velvet 1.2.10 ngs-ccts
VMD 1.9.0 1.8.6
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