Typical Software Installation Process
List of Current Software Projects
Application Name
|
Installation Status
|
Estimated Start
|
Estimated Completion
|
Notes
|
HOMMER 4.10
|
In Progress
|
Jan 2019
|
Jan 2019
|
|
SURPI 1.0.18
|
Pending
|
Jan 2019
|
|
|
MultiQC Version 1.7
|
Pending
|
Jan 2019
|
|
|
H2O.ai 3.22.1.1
|
Pending
|
Jan 2019
|
|
|
R 3.5.2
|
Pending
|
Jan 2019
|
|
|
SICKLE 1.33
|
Pending
|
Feb 2019
|
|
|
Recently Completed Software Projects
Application Name
|
Date Completed
|
License Type
|
Notes
|
Additional Info
|
ImageMagick++ 7.0.8-23
|
01/11/2018
|
Open Source
|
|
Built with Intel compiler suite 2017
|
Subread 1.6.3
|
01/11/2018
|
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.