Typical Software Installation Process
List of Current Software Projects
Application Name
|
Installation Status
|
Estimated Start
|
Estimated Completion
|
Notes
|
SCIP 5.0.1
|
Stalled
|
Apr 2018
|
|
Stalled due to issues with some dependencies
|
OrthoFinder 2.2.1
|
In Progress
|
May 2018
|
July 2018
|
Requires 9 additional dependencies
|
Quantum ESPRESSO v6.2.1
|
In Progress
|
Jun 2018
|
Jun 2018
|
Main install completed on Jun 28. Minor cleanup remaining.
|
Wannier90 v2.1.0
|
In Progress
|
Jun 2018
|
July 2018
|
|
Maple 2018
|
In Progress
|
July 2018
|
July 2018
|
|
FastTree v2.1
|
In Progress
|
Jun 2018
|
July 2018
|
Required dependency for Orthofinder
|
Antelope 5.8
|
Pending
|
July 2018
|
|
|
GISMO 1.1.0
|
Pending
|
July 2018
|
|
|
MPIR
|
Pending
|
July 2018
|
|
|
Yasm
|
Pending
|
July 2018
|
|
|
MPFR
|
Pending
|
July 2018
|
|
|
FLINT
|
Pending
|
July 2018
|
|
|
Recently Completed Software Projects
Application Name
|
Date Completed
|
License Type
|
Notes
|
Additional Info
|
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
|
|
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
|
|
|
Xilinx ISE 14.7
|
12/14/2017
|
Restricted - Authorized users only
|
|
Electrical Engineering
|
Xilinx Vivado 2017.3
|
12/14/2017
|
Restricted - Authorized users only
|
|
Electrical Engineering
|
GDC Data Transfer Tool 1.3.0
|
11/22/2017
|
Open Source
|
|
|
epiGBS
|
11/01/2017
|
Open Source
|
|
Python tools and scripts for analysis of epiGBS data.
|
xHLA 10.04.2017
|
10/26/2017
|
Open Source
|
|
|
R 3.4.2
|
10/23/2017
|
Open Source
|
|
|
Matlab R2017b
|
10/18/2017
|
USF Site License
|
|
|
Gurobi 7.5.1
|
10/17/2017
|
Academic Use License
|
|
|
FastQC 0.11.5
|
10/16/2017
|
Open Source
|
|
|
bcbio-nextgen 1.0.5
|
10/09/2017
|
Open Source
|
|
|
QIIME2 2017.8
|
10/04/2017
|
Open Source
|
|
Anaconda 5.0.0
|
09/27/2017
|
Open Source
|
|
Tools for use with python
|
Trim Galore 0.4.4
|
09/15/2017
|
Open Source
|
|
|
Apache Maven 3.5.0
|
08/14/2017
|
Open Source
|
|
Tools for Java-based projects
|
Rosetta 3.5
|
08/11/2017
|
Academic Use License
|
|
|
Agilent ADS 2016_01
|
08/10/2017
|
USF Site License
|
|
|
Maple 2017
|
08/04/2017
|
USF Site License
|
|
|
MaSuRCA 3.2.2
|
07/28/2017
|
Academic Use License
|
|
|
Jellyfish 2.2.6
|
07/14/2017
|
Open Source
|
|
|
TraCeR 0.15.2
|
07/12/2017
|
Open Source
|
|
|
SAS 9.4 Rev TS1M4
|
07/11/2017
|
USF Site License
|
|
|
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.