Apps Queue
Revision as of 14:03, 29 January 2019 by Desantis (talk | contribs) (→Recently Completed Software Projects)
Typical Software Installation Process
List of Current Software Projects
Application Name | Installation Status | Estimated Start | Estimated Completion | Notes |
SURPI 1.0.18 | On Hold | Nov 2018 | Application has several dependency issues that need to be resolved before build can continue. | |
HOMMER 4.10 | In Progress | Jan 2019 | Jan 2019 | |
Deblur 1.1.0 | Pending | Jan 2019 | ||
H2O.ai 3.22.1.1 | Pending | Jan 2019 | ||
R 3.5.2 | Pending | Jan 2019 | ||
bcbio-nextgen 1.1.2 | Pending | Feb 2019 |
Recently Completed Software Projects
Application Name | Date Completed | License Type | Notes | Additional Info |
GDC-client 1.4.0 | 01/28/2019 | Open Source | Python add-on module | Uses 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.