Cheaha software
https://docs.rc.uab.edu/
Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.
As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.
Thank you,
The Research Computing Team
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
| 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 | 3.12 | 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 |