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| |<span id ="S"></span> [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.9, 1.10 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]] | | |<span id ="S"></span> [[SAMtools-Teaching|SAMtools]] || 0.1.20, 1.6, 1.14, 1.16.1 || [[:Category:Bioinformatics|Bioinformatics]] || [[:Category:Teaching|Teaching]] || [[File:Up20.png|20px|link=#top]] |
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Revision as of 13:36, 5 September 2023
,On Sapelo2 and on the Teaching cluster users have the option to install their own software or use software installed centrally by the GACRC staff. Detailed information on how to find and access software packages installed on Sapelo2 are available at the Software on Sapelo2 page and on the teaching cluster at the Software on Teaching Cluster page.
Below is a very limited list of software packages installed on Sapelo2 and on the Teaching cluster. We only intend to make an application page for software packages that requires extra documentation not covered in Software on Sapelo2 or Software on Teaching Cluster.
To view a list of all modules installed on Sapelo2/Teaching, along with a short description of each module, please run the following command on Sapelo2/Teaching:
module spider
You can also use the command above to search for a specific application. For more information, please see Lmod.
The file transfer nodes (xfer nodes) do not have environment modules installed. File transfer utilities are installed centrally on the xfer nodes and available on the users' default PATH. Such utilities include bs (basespace-cli), fpsync, rclone, rsync, etc.
Note: Although we have not made individual software pages for the applications installed on Sapelo2, there are currently over 1300 software packages installed there. For more information, please see Software on Sapelo2.
Partial List of Installed Software
Last updated 2023-09-05. This is a partial list of installed software so there may be software or versions of software available on Sapelo2 which are not included in this table.
Note: Click on the icons to the right of the column headings to sort the table.
0-9 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
| Name
|
Version
|
Category
|
Cluster
|
Top
|
| AlphaFold |
2.2.4, 2.3.1, 2.3.4 |
Bioinformatics |
Sapelo2 |
|
| AMBER |
22 |
Chemistry |
Sapelo2 |
|
| anvi'o |
4, 5.1, 5.3, 5.4, 6.1, 7, 7.1 |
Bioinformatics |
sapelo2 |
|
| basespace-cli |
1.2.1 |
Bioinformatics |
Sapelo2 |
|
| Beast |
1.10.4, 2.6.2, 2.6.3 |
Bioinformatics |
Sapelo2 |
|
| BionanoSolve |
3.6.1-11162020 |
Bioinformatics |
Sapelo2 |
|
| BioPython |
1.79 |
Bioinformatics |
Sapelo2 |
|
| Biopython |
1.79 |
Bioinformatics |
Teaching |
|
| BLAST+ |
2.12.0, 2.13.0 |
Bioinformatics |
Sapelo2 |
|
| BLAST+ |
2.12.0, 2.13.0 |
Bioinformatics |
Teaching |
|
| BLAST |
2.2.26 |
Bioinformatics |
Teaching |
|
| Bowtie2 |
2.4.1, 2.4.4, 2.4.5 |
Bioinformatics |
Teaching |
|
| BUSCO |
4.0.5, 4.0.6 |
Bioinformatics |
Sapelo2 |
|
| Canu |
2.1.1 |
Bioinformatics |
Sapelo2 |
|
| CellRanger-ATAC |
1.2.0, 2.0.0 |
Bioinformatics |
Sapelo2 |
|
| cryoSPARC |
3.3.1 |
Engineering |
Sapelo2 |
|
| CUDA |
11.3.1, 11.4.1, 11.7.0, 12.0.0 |
Programming |
Sapelo2 |
|
| Cytoscape |
3.7.2 |
Bioinformatics |
Teaching |
|
| DRAM-bio |
1.4.0 |
Bioinformatics |
Sapelo2 |
|
| EIGENSOFT |
7.2.1 |
Bioinformatics |
Teaching |
|
| GAUSSIAN |
09, 16 |
Chemistry |
Sapelo2 |
|
| GAUSSIAN |
16 |
Chemistry |
Teaching |
|
| GaussView |
5, 6.1 |
Chemistry |
Sapelo2 |
|
| GaussView |
6.1 |
Chemistry |
Teaching |
|
| GEM |
1.0, 1.1, 1.2, 1.4.1 |
Bioinformatics |
Sapelo2 |
|
| GeneMarkES |
4.57, 4.71 |
Bioinformatics |
Sapelo2 |
|
| GROMACS |
2021.5, 2023.1 |
Chemistry |
Sapelo2 |
|
| HISAT2 |
2.1.0 |
Bioinformatics |
Teaching |
|
| HPCGridRunner |
1.0.2 |
Tools |
Sapelo2 |
|
| iCommands |
4.2.8 |
Tools |
Sapelo2 |
|
| InterProScan |
5.44-90.0, 5.51-85.0 |
Bioinformatics |
Sapelo2 |
|
| IQ-Tree |
1.6.12 |
Bioinformatics |
Teaching |
|
| Java |
1.8.0_241, 11.0.16, 13.0.2, 15.0.1, 17.0.6 |
Programming |
Teaching |
|
| Jupyter |
5.0.0, 5.6.0, 6.0.3 |
Programming |
Sapelo2 |
|
| Jupyter |
6.0.2 |
Programming |
Teaching |
|
| LAMMPS |
23Jun2022 |
Chemistry |
Sapelo2 |
|
| Magma |
2.25 |
Other |
Sapelo2 |
|
| Maker |
3.01.03 |
Bioinformatics |
Sapelo2 |
|
| MATLAB |
R2022b, R2023a |
Programming |
Sapelo2 |
|
| Medusa |
1.6 |
Bioinformatics |
Sapelo2 |
|
| Meraculous |
2.2.6 |
Bioinformatics |
Sapelo2 |
|
| MetaPhlAn4 |
4.0.3.1 |
Bioinformatics |
Sapelo2 |
|
| MOTECC_qmdcp |
90 |
Chemistry |
Teaching |
|
| Mothur |
1.39.5 |
Bioinformatics |
Sapelo2 |
|
| MrBayes |
3.2.6, 3.2.7a |
Bioinformatics |
Sapelo2 |
|
| Ont-Guppy |
4.4.2 |
Bioinformatics |
Sapelo2 |
|
| ORCA |
4.2.1, 5.0.4 |
Chemistry |
Sapelo2 |
|
| ORP |
2.2.6 |
Bioinformatics |
Sapelo2 |
|
| OrthoFinder |
2.5.4 |
Bioinformatics |
Sapelo2 |
|
| OrthoMCL |
2.0.9 |
Bioinformatics |
Sapelo2 |
|
| PAML |
4.9i |
Bioinformatics |
Teaching |
|
| Perl |
5.34.1 |
Programming |
Teaching |
|
| Phenix |
1.19.2-4158 |
Bioinformatics |
Sapelo2 |
|
| Pong |
1.5 |
Bioinformatics |
Sapelo2 |
|
| Python |
2.7.18, 3.7.4, 3.8.6, 3.9.6, 3.10.4 |
Programming |
Sapelo2 |
|
| Python |
2.7.18, 3.7.4, 3.8.6, 3.9.6, 3.10.4 |
Programming |
Teaching |
|
| QIIME2 |
2019.10, 2020.2, 2020.6, 2020.11 |
Bioinformatics |
Sapelo2 |
|
| R |
4.1.2, 4.2.1, 4.3.1 |
Statistics |
Sapelo2 |
|
| R |
4.1.2, 4.2.1, 4.3.1 |
Statistics |
Teaching |
|
| Racon |
1.4.13 |
Bioinformatics |
Sapelo2 |
|
| RAxML |
8.2.11, 8.2.12 |
Bioinformatics |
Sapelo2 |
|
| RAxML |
8.2.12 |
Bioinformatics |
Teaching |
|
| RevBayes |
1.1.0 |
Bioinformatics |
Teaching |
|
| Rosetta |
2020.28.61328, 2021.16.61629 |
Chemistry |
Sapelo2 |
|
| Rstudio |
2023.06.1-524 |
Other |
Sapelo2 |
|
| SAMtools |
0.1.20, 1.6, 1.14, 1.16.1 |
Bioinformatics |
Teaching |
|
| smoke |
4.7 |
Other |
Sapelo2 |
|
| SRAToolKit |
2.9.6-1,2.10.8,2.11.1 |
Bioinformatics |
Sapelo2 |
|
| StringTie |
2.1.1 |
Bioinformatics |
Teaching |
|
| Structure |
2.3.4 |
Bioinformatics |
Sapelo2 |
|
| Structure |
2.3.4 |
Bioinformatics |
Teaching |
|
| Trinity |
2.5.1, 2.8.4, 2.8.5, 2.9.1, 2.10.0 |
Bioinformatics |
Sapelo2 |
|
| UBCG |
3.0
|
Bioinformatics |
Sapelo2 |
|
| Velvet |
1.2.10 |
Bioinformatics |
Sapelo2 |
|
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