Difference between revisions of "Apps Queue"
Line 6: Line 6:
|'''Application Name'''  
|'''Application Name'''  
|'''Installation Status'''  
|'''Installation Status'''  
|'''Estimated Start'''
|'''Estimated Completion'''
|'''Estimated Completion'''
|'''Notes'''
|'''Notes'''
|-
|-
|-
|-
|<span style="color:green">SCIP 5.0.1</span>
|<span style="color:red">SCIP 5.0.1</span>
|<span style="color:green">In Progress</span>
|<span style="color:red">Stalled</span>
|<span style="color:green">Jun 2018</span>
|<span style="color:red">Apr 2018</span>
|
|
|Stalled due to issues with some dependencies
|-
|<span style="color:green">OrthoFinder 2.2.1</span>
|<span style="color:green">In Progress</span>
|<span style="color:green">May 2018</span>
|<span style="color:green">July 2018</span>
|Requires 9 additional dependencies
|-
|-
|<span style="color:green">Quantum ESPRESSO v6.2.1</span>
|<span style="color:green">Quantum ESPRESSO v6.2.1</span>
|<span style="color:green">In Progress</span>  
|<span style="color:green">In Progress</span>  
|<span style="color:green">Jun 2018</span>
|<span style="color:green">Jun 2018</span>
|<span style="color:green">Jun 2018</span>
|
|
Line 23: Line 32:
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Jun 2018</span>
|<span style="color:blue">Jun 2018</span>
|
|
|
|-
|-
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|<span style="color:blue">Pending</span>  
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Jun 2018</span>
|<span style="color:blue">Jun 2018</span>
|
|
|-
|<span style="color:blue">Antelope 5.8</span>
|<span style="color:blue">Pending</span>
|<span style="color:blue">July 2018</span>
|
|
|-
|<span style="color:blue">GISMO 1.1.0</span>
|<span style="color:blue">Pending</span>
|<span style="color:blue">July 2018</span>
|
|
|-
|<span style="color:blue">MPIR</span>
|<span style="color:blue">Pending</span>
|<span style="color:blue">July 2018</span>
|
|
|-
|<span style="color:blue">Yasm</span>
|<span style="color:blue">Pending</span>
|<span style="color:blue">July 2018</span>
|
|
|-
|<span style="color:blue">MPFR</span>
|<span style="color:blue">Pending</span>
|<span style="color:blue">July 2018</span>
|
|
|-
|<span style="color:blue">FLINT</span>
|<span style="color:blue">Pending</span>
|<span style="color:blue">July 2018</span>
|
|
|
|}
|}
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|'''Date Completed'''
|'''Date Completed'''
|'''License Type'''
|'''License Type'''
|'''Notes'''
|'''Additional Info'''
|'''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
|
|-
|[[Blast|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 and an update to Perl 5.27
|
|-
|-
|LinBox 1.5.2
|LinBox 1.5.2
|05/22/2018
|05/22/2018
|Open Source
|Open Source
|Required updated install of 8 additional library packages
|
|
|-
|-
|Matlab R2018a
|[[Matlab|Matlab R2018a]]
|05/14/2018
|05/14/2018
|USF Site License
|USF Site License
|
|
|
|-
|-
|Mathematica 11.3
|[[Mathematica|Mathematica 11.3]]
|05/11/2018
|05/11/2018
|USF Site License
|USF Site License
|
|
|
|-
|-
|Julia 0.6.2
|[[Julia|Julia 0.6.2]]
|05/03/2018
|05/03/2018
|Open Source
|Open Source
|
|
|
|-
|-
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|04/30/2017
|04/30/2017
|Open Source
|Open Source
|
|
|
|-
|-
|rsem 1.3.0
|RSEM 1.3.0
|04/27/2018
|04/27/2018
|Open Source
|Open Source
|
|
|
|-
|-
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|04/26/2018
|04/26/2018
|Open Source
|Open Source
|
|
|
|-
|-
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|04/20/2018
|04/20/2018
|Open Source
|Open Source
|
|
|
|-
|-
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|04/19/2018
|04/19/2018
|Open Source
|Open Source
|
|
|
|-
|-
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|04/18/2018
|04/18/2018
|USF Site License
|USF Site License
|
|
|
|-
|-
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|04/12/2018
|04/12/2018
|Open Source
|Open Source
|
|
|
|-
|-
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|04/05/2018
|04/05/2018
|Open Source
|Open Source
|
|
|
|-
|-
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|03/30/2018
|03/30/2018
|Open Source
|Open Source
|
|
|
|-
|-
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|03/15/2018
|03/15/2018
|Open Source
|Open Source
|
|
|
|-
|-
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|02/28/2018
|02/28/2018
|GNU License
|GNU License
|
|
|
|-
|-
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|03/14/2018
|03/14/2018
|GNU License
|GNU License
|
|
|
|-
|-
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|02/28/2018
|02/28/2018
|USF Site License
|USF Site License
|
|
|
|-
|-
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|02/26/2018
|02/26/2018
|Open Source
|Open Source
|
|
|
|-
|-
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|02/12/2018
|02/12/2018
|Open Source
|Open Source
|
|
|
|-
|-
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|02/07/2018
|02/07/2018
|Open Source
|Open Source
|
|
|
|-
|-
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|02/05/2018
|02/05/2018
|Open Source
|Open Source
|
|
|
|-
|-
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|01/30/2018
|01/30/2018
|Open Source
|Open Source
|
|
|-
|-
|[[MEGA|MEGA-CC 7.0.26-1]]
|[[MEGA|MEGA-CC 7.0.26-1]]
|01/08/2018
|01/08/2018
|Open Source
|Open Source
|
|
|
|-
|-
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|01/08/2018
|01/08/2018
|Open Source
|Open Source
|
|
|
|-
|-
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|12/14/2017
|12/14/2017
|Restricted - Authorized users only
|Restricted - Authorized users only
|
|Electrical Engineering
|Electrical Engineering
|-
|-
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|12/14/2017
|12/14/2017
|Restricted - Authorized users only
|Restricted - Authorized users only
|
|Electrical Engineering
|Electrical Engineering
|-
|-
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|11/22/2017
|11/22/2017
|Open Source
|Open Source
|
|
|
|-
|-
Line 177: Line 271:
|11/01/2017
|11/01/2017
|Open Source
|Open Source
|
|Python tools and scripts for analysis of epiGBS data.
|Python tools and scripts for analysis of epiGBS data.
|-
|-
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|10/26/2017
|10/26/2017
|Open Source
|Open Source
|
|
|
|-
|-
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|10/23/2017
|10/23/2017
|Open Source
|Open Source
|
|
|
|-
|-
Line 192: Line 289:
|10/18/2017
|10/18/2017
|USF Site License
|USF Site License
|
|
|
|-
|-
Line 197: Line 295:
|10/17/2017
|10/17/2017
|Academic Use License
|Academic Use License
|
|
|
|-
|-
Line 202: Line 301:
|10/16/2017
|10/16/2017
|Open Source
|Open Source
|
|
|
|-
|-
Line 207: Line 307:
|10/09/2017
|10/09/2017
|Open Source
|Open Source
|
|
|
|-
|-
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|09/27/2017
|09/27/2017
|Open Source
|Open Source
|
|Tools for use with python
|Tools for use with python
|-
|-
Line 222: Line 324:
|09/15/2017
|09/15/2017
|Open Source
|Open Source
|
|
|
|-
|-
Line 227: Line 330:
|08/14/2017
|08/14/2017
|Open Source
|Open Source
|
|Tools for Java-based projects
|Tools for Java-based projects
|-
|-
Line 232: Line 336:
|08/11/2017
|08/11/2017
|Academic Use License
|Academic Use License
|
|
|
|-
|-
Line 237: Line 342:
|08/10/2017
|08/10/2017
|USF Site License
|USF Site License
|
|
|
|-
|-
Line 242: Line 348:
|08/04/2017
|08/04/2017
|USF Site License
|USF Site License
|
|
|
|-
|-
Line 247: Line 354:
|07/28/2017
|07/28/2017
|Academic Use License
|Academic Use License
|
|
|
|-
|-
Line 252: Line 360:
|07/14/2017
|07/14/2017
|Open Source
|Open Source
|
|
|
|-
|-
Line 257: Line 366:
|07/12/2017
|07/12/2017
|Open Source
|Open Source
|
|
|
|-
|-
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|USF Site License
|USF Site License
|
|
|-
|[[NAMD|NAMD 2.12]]
|06/30/2016
|Academic Use License
|Includes CUDA support
|-
|[[MHC|MHC epitope predictors 2.17]]
|06/16/2017
|Academic Use License
|
|-
|[[R_and_Rmpi|R 3.4.0]]
|06/12/2017
|Open Source
|
|-
|[[ANSYS|ANSYS Suite 18.1]]
|06/07/2016
|Restricted - Authorized users only
|ANSYS finite-element analysis applications
|-
|[[ANSYS_EDT_(formerly_HFSS)|Ansys Electronics Desktop 18.1]]
|06/07/2016
|Restricted - Authorized users only
|ANSYS electromagnetic and circuit design applications
|-
|[[Genome_Analysis_ToolKit_(GATK)|GATK 3.7]]
|06/02/2016
|Academic Use License
|
|-
|[[STATA|STATA 14]]
|05/26/2016
|Restricted - Authorized users only
|
|-
|[[COMSOL|COMSOL 5.3]]
|05/22/2016
|USF Site License
|
|-
|[[Julia|Julia 0.5.2]]
|05/15/2017
|Open Source
|
|-
|[[GMT|GMT 5.4.0]]
|05/11/2017
|Open Source
|
|-
|[[Mathematica|Mathematica 11.1]]
|05/08/2017
|USF Site License
|
|-
|[[VASP|VASP 5.4.4]]
|05/04/2017
|Restricted - Authorized users only
|Includes CUDA support
|-
|[[CUDA_Toolkit_and_Compilers|CUDA 8.0 toolkit]]
|05/01/2017
|Free-to-use
|Nvidia drivers updated to 375.26
|-
|[[SAS|SAS 9.4 Rev TS1M2]]
|04/28/2017
|USF Site License
|
|-
|[[Matlab|Matlab R2017a]]
|04/13/2017
|USF Site License
|
|-
|[[Development_Tools|Java JDK 1.8.1_121]]
|03/22/2017
|Open Source
|
|-
|[[CircuitScape|CircuitScape 4.0.5]]
|03/14/2017
|Open Source
|Python module built with Python 2.7.5
|-
|DeepMask v0.1
|03/03/2017
|Open Source
|
|-
|SMRT Analysis v2.3.0
|02/17/2017
|Open Source
|
|
|}
|}

Revision as of 19:19, 19 June 2018

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
Wannier90 v2.1.0 Pending Jun 2018
Maple 2018 Pending Jun 2018
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 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

  1. New request is submitted via email to: rc-help@usf.edu
    • Please include name of software, license type, and URL to software's website.
  2. Application is reviewed by RC staff for compatibility with Linux and cluster resources.
    • Also, is it open source or is a license required?
  3. Source code or installer is downloaded to cluster filesystem.
  4. 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.
  5. Once a working executable has been built, it must then be integrated with the filesystem, modules, scheduler, and other services.
  6. Testing and verification of compatibility with scheduler and cluster resources.
  7. Documentation and release.
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