Difference between revisions of "Apps Queue"
Line 11: | Line 11: | ||
|- | |- | ||
|- | |- | ||
|<span style="color:green"> | |<span style="color:green">Amber16/AmberTools18</span> | ||
|<span style="color:green">In Progress</span> | |<span style="color:green">In Progress</span> | ||
|<span style="color:green">Apr 2019</span> | |<span style="color:green">Apr 2019</span> | ||
Line 17: | Line 17: | ||
| | | | ||
|- | |- | ||
|<span style="color:green"> | |<span style="color:green">Mathematica 12</span> | ||
|<span style="color:green"> | |<span style="color:green">In Progress</span> | ||
|<span style="color:green"> | |<span style="color:green">May 2019</span> | ||
|<span style="color:green">May 2019</span> | |<span style="color:green">May 2019</span> | ||
| | | | ||
|- | |- | ||
Line 51: | Line 39: | ||
|'''Notes''' | |'''Notes''' | ||
|'''Additional Info''' | |'''Additional Info''' | ||
|- | |||
|[[Matlab|Matlab R2019a]] | |||
|05/16/2019 | |||
|USF Site License | |||
| | |||
| | |||
|- | |||
|[[Maple|Maple 2019]] | |||
|05/09/2019 | |||
|USF Site License | |||
| | |||
| | |||
|- | |- | ||
|[[LAMMPS|LAMMPS 12Dec18]] (GPU Edition) | |[[LAMMPS|LAMMPS 12Dec18]] (GPU Edition) |
Revision as of 21:10, 22 May 2019
Typical Software Installation Process
List of Current Software Projects
Application Name | Installation Status | Estimated Start | Estimated Completion | Notes |
Amber16/AmberTools18 | In Progress | Apr 2019 | May 2019 | |
Mathematica 12 | In Progress | May 2019 | May 2019 | |
VMD 1.9.3 | Pending | May 2019 |
Recently Completed Software Projects
Application Name | Date Completed | License Type | Notes | Additional Info |
Matlab R2019a | 05/16/2019 | USF Site License | ||
Maple 2019 | 05/09/2019 | USF Site License | ||
LAMMPS 12Dec18 (GPU Edition) | 04/29/2019 | Open Source | ||
gem5 2.0 | 04/25/2019 | Open Source | ||
Ansys Electronics Desktop Suite 2019R1 | 04/19/2018 | Restricted - Authorized users only | Electromagnetic and circuit design applications including HFSS, Maxwell, etc. | |
Ansys Multiphysics 2019R1 | 04/18/2019 | Restricted - Authorized users only | ANSYS finite-element analysis applications | |
Stacks 2.3e | 04/09/2019 | Open Source | ||
SeqTK 1.0 | 03/20/2019 | Open Source | ||
Deblur 1.1.0 | 03/18/2019 | Open Source | Python add-on module. | Loads with apps/python/3.6.2 |
Anvio 5.4 | 03/15/2019 | Open Source | ||
Prodigal 2.6.2 | 03/15/2019 | Open Source | ||
Bayestraits 3.0.1 | 03/14/2019 | Open Source | ||
R 3.5.2 | 03/04/2019 | Open Source | ||
Ataqv 1.0.0 | 02/27/2019 | Open Source | ||
AfterQC 0.9.7 | 02/19/2019 | Open Source | ||
Tophat 2.1.1 | 02/15/2019 | Open Source | Revision | |
Intel Parallel Studio XE 2019 | 02/11/2019 | USF Site License | ||
HOMER 4.10 | 02/05/2019 | Open Source | ||
bcbio-nextgen 1.1.3 | 01/30/2019 | Open Source | ||
Reporter 0.7.15 | 01/29/2019 | Open Source | ||
DeNovoGUI 1.16.2 | 01/29/2019 | Open Source | ||
PeptideShaker 1.16.37 | 01/29/2019 | Open Source | ||
GDC-client 1.4.0 | 01/28/2019 | Open Source | Python add-on module | Loads with apps/python/2.7.15 |
COMSOL 5.4 | 01/28/2019 | USF Site License | ||
SearchGUI 3.3.12 | 01/28/2019 | Open Source | ||
SICKLE 1.33 | 01/28/2019 | Open Source | ||
MultiQC Version 1.7 | 01/22/2019 | Open Source | Python add-on module. | Loads with apps/python/2.7.15 |
ImageMagick++ 7.0.8-23 | 01/11/2019 | Open Source | Built with Intel compiler suite 2017. | |
Subread 1.6.3 | 01/11/2019 | Open Source | ||
LAMMPS 12Dec18 | 12/21/2018 | Open Source | ||
ABySS 2.1.5 | 12/18/2018 | Open Source | ||
Boost 1.69.0 | 12/18/2018 | Open Source | ||
SparseHash v07-26-2016 | 12/18/2018 | Open Source | ||
BWA 0.7.17 | 12/14/2018 | Open Source | ||
Ansys Electronics Desktop Suite v19.2 | 11/29/2018 | Restricted - Authorized users only | Electromagnetic and circuit design applications including HFSS, Maxwell, etc. | |
Ansys Multiphysics v19.2 | 11/29/2018 | Restricted - Authorized users only | ANSYS finite-element analysis applications | |
Artemis 17.0.2 | 11/08/2018 | Open Source | ||
Trinotate 3.1.1 | 11/06/2018 | Open Source | ||
Transdecoder 5.5.0 | 11/06/2018 | Open Source | ||
PLINK 2.00a | 10/30/2018 | Open Source | ||
HTSeq 0.11.0 | 10/29/2018 | Open Source | Python add-on module. | Loads with apps/python/2.7.15 |
METAL r2018-08-28 | 10/29/2018 | Open Source | ||
HMMR 3.2.1 | 10/29/2018 | Open Source | ||
GffCompare v0.10.6 | 10/25/2018 | Open Source | ||
GATK 4.0.10 | 10/24/2018 | Open Source | ||
Schrodinger Suite 2018 | 10/23/2018 | Restricted - Authorized users only | ||
RepeatMasker 4.0.7 | 10/19/2018 | Open Source | ||
MEME 5.0.2 | 10/16/2018 | Open Source | ||
Matlab R2018b | 10/12/2018 | USF Site License | ||
STAR 2.6.0a | 10/11/2018 | Open Source | ||
Cell Ranger 2.1.0 | 10/08/2018 | Open Source | ||
RUST 1.29.1 | 10/05/2018 | Open Source | ||
Go Programming Language 1.11.1 | 10/05/2018 | Open Source | ||
IBM CPLEX Optimization Studio 12.8 | 10/05/2018 | Academic License | ||
CellProfiler 3.1.5 | 10/02/2018 | Open Source | ||
BEDOPS 2.4.35 | 10/01/2018 | Open Source | ||
BEAST 1.10.1 | 09/27/2018 | Open Source | ||
AdapterRemoval 2.1.7 | 09/27/2018 | Open Source | ||
LiftOver 2018-0918 | 09/26/2018 | Open Source | ||
Kallisto 0.44.0 | 09/24/2018 | Open Source | ||
IGV 2.4.14 | 09/21/2018 | Open Source | ||
MAGMA 2.24-1 | 09/17/2018 | Restricted - Authorized users only | ||
FLINT 2.5.2 | 09/07/2018 | Open Source | ||
MPFR 4.0.1 | 09/06/2018 | Open Source | ||
MPIR 3.0.0 | 09/05/2018 | Open Source | ||
YASM 1.3.0 | 09/04/2018 | Open Source | ||
OrthoFinder 2.2.7 | 08/30/2018 | Open Source | Updated to recently released 2.2.7 and integrated with 9 additional dependencies. | |
Maple 2018 | 08/17/2018 | USF Site License | ||
Mothur 1.40.5 | 07/31/2018 | Open Source | ||
GISMO 1.1.0 | 07/26/2018 | Open Source | Matlab add-on package for seismic data analysis | Installed and available in /apps/matlab/share/GISMO on the CIRCE cluster. |
Perl 5.28.0 | 07/12/2018 | Open Source | Newer version of Perl programming language needed for some applications. | |
SCIP 6.0.0 | 07/02/2018 | Open Source | Dependency issues prevented 5.X versions from installing properly. A work-around was developed and found to be valid with the 6.0.0 version. | Contact rc-help@usf.edu for details regarding work-around if SCIP > 3.1.1 is needed. |
Ansys Electronics Desktop Suite v19.1 | 06/29/2018 | Restricted - Authorized users only | Electromagnetic and circuit design applications including HFSS, Maxwell, etc. | |
Ansys Multiphysics v19.1 | 06/29/2018 | Restricted - Authorized users only | ANSYS finite-element analysis applications | |
Wannier90 2.1.0 | 06/29/2018 | Open Source | ||
Quantum Espresso 6.2.1 | 06/28/2018 | Open Source | ||
MaxQuant 1.6.2.3 | 06/15/2018 | Academic License | Required an update of system tool "mono" to the specific version 5.4.1.7 | |
NCBI Blast 2.7.1+ | 06/07/2018 | Open Source | Issues encountered and resolved when compiling on RHEL6 using Intel compilers | Standalone and dependency for OrthoFinder |
Circos 0.69-6 | 06/06/2018 | Open Source | Requires additional Perl modules for full functionality and an update to Perl 5.27 | |
LinBox 1.5.2 | 05/22/2018 | Open Source | Required updated install of 8 additional library packages | |
MPlus 8 | 05/15/2018 | Restricted - Authorized users only | ||
Matlab R2018a | 05/14/2018 | USF Site License | ||
Mathematica 11.3 | 05/11/2018 | USF Site License | ||
Julia 0.6.2 | 05/03/2018 | Open Source | ||
R 3.5.0 | 04/30/2017 | Open Source | ||
RSEM 1.3.0 | 04/27/2018 | Open Source | ||
Tophat 2.1.1 | 04/26/2018 | Open Source | ||
Pear 0.9.11 | 04/20/2018 | Open Source | ||
Bowtie 2.3.4.1 | 04/19/2018 | Open Source | ||
Intel Parallel Studio XE 2018 | 04/18/2018 | USF Site License | ||
Trimmomatic 0.36 | 04/12/2018 | Open Source | ||
SIESTA 4.0.1 | 04/05/2018 | Open Source | ||
SPAdes 3.11.1 | 03/30/2018 | Open Source | ||
Psi4 1.1 | 03/15/2018 | Open Source | ||
GCC 7.3.0 | 02/28/2018 | GNU License | ||
OpenMPI 2.0.4 | 03/14/2018 | GNU License | ||
COMSOL 5.3a | 02/28/2018 | USF Site License | ||
Trinity 2.6.5 | 02/26/2018 | Open Source | ||
SageMath 7.5.1 | 02/12/2018 | Open Source | ||
Cufflinks 2.2.1 | 02/07/2018 | Open Source | ||
ORCA 4.0.1 | 02/05/2018 | Open Source | ||
SPECFEM3D 3.0 | 01/30/2018 | Open Source | ||
MEGA-CC 7.0.26-1 | 01/08/2018 | Open Source | ||
MUSCLE 3.8.31 | 01/08/2018 | Open Source |
Typical Software Installation Process
- New request is submitted via email to: rc-help@usf.edu
- Please include name of software, license type, and URL to software's website.
- Application is reviewed by RC staff for compatibility with Linux and cluster resources.
- Also, is it open source or is a license required?
- Source code or installer is downloaded to cluster filesystem.
- Application is built using latest Intel Cluster Studio release, if possible.
- Compilation for cluster systems and troubleshooting can take several hours to a few days depending on the complexity of the application.
- Once a working executable has been built, it must then be integrated with the filesystem, modules, scheduler, and other services.
- Testing and verification of compatibility with scheduler and cluster resources.
- Documentation and release.