Difference between revisions of "Apps Queue"
 
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|<span style="color:red">SCIP 5.0.1</span>
|<span style="color:red">GAP 4.11</span>
|<span style="color:red">Stalled</span>
|<span style="color:red">In Progress</span>  
|<span style="color:red">Apr 2018</span>
|<span style="color:red">June 2021</span>
|
|<span style="color:red">July 2021</span>
|Stalled due to issues with some dependencies
|<span style="color:red">Stalled due to issues with dependent packages</span>
|-
|-
|<span style="color:green">OrthoFinder 2.2.1</span>
|<span style="color:green">Intel OneAPI Toolkit 2021</span>
|<span style="color:green">In Progress</span>  
|<span style="color:green">In Progress</span>  
|<span style="color:green">May 2018</span>
|<span style="color:green">June 2021</span>
|<span style="color:green">July 2018</span>
|<span style="color:green">July 2021</span>
|Requires 9 additional dependencies
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|<span style="color:green">Quantum ESPRESSO v6.2.1</span>
|<span style="color:green">Haddock 2.4</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">June 2021</span>
|<span style="color:green">Jun 2018</span>
|<span style="color:green">July 2021</span>
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|-
|<span style="color:blue">Wannier90 v2.1.0</span>
|<span style="color:blue">Pending</span>
|<span style="color:blue">Jun 2018</span>
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|-
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|<span style="color:blue">Maple 2018</span>
|<span style="color:blue">Amber20/AmberTools2020</span>
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Jun 2018</span>
|<span style="color:blue">July 2021</span>
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|<span style="color:blue">Antelope 5.8</span>
|<span style="color:blue">GNUplot 5.4</span>
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Pending</span>  
|<span style="color:blue">July 2018</span>
|<span style="color:blue">July 2021</span>
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|<span style="color:blue">GISMO 1.1.0</span>
|<span style="color:blue">MuTect</span>
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Pending</span>  
|<span style="color:blue">July 2018</span>
|<span style="color:blue">July 2021</span>
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|<span style="color:blue">MPIR</span>
|<span style="color:blue">Mummer</span>
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Pending</span>  
|<span style="color:blue">July 2018</span>
|<span style="color:blue">July 2021</span>
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|-
|<span style="color:blue">Yasm</span>
|<span style="color:blue">Psi4 1.3.2</span>
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Pending</span>  
|<span style="color:blue">July 2018</span>
|<span style="color:blue">Aug 2021</span>
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|<span style="color:blue">MPFR</span>
|<span style="color:blue">Pending</span>
|<span style="color:blue">July 2018</span>
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|<span style="color:blue">FLINT</span>
|<span style="color:blue">Pending</span>
|<span style="color:blue">July 2018</span>
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|}
 
= Recently Completed Software Projects =
 
{| class=wikitable
|- style="background-color:#f1edbe;"
|'''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
|
|-
|[[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
|05/22/2018
|Open Source
|Required updated install of 8 additional library packages
|
|-
|[[Matlab|Matlab R2018a]]
|05/14/2018
|USF Site License
|
|
|-
|[[Mathematica|Mathematica 11.3]]
|05/11/2018
|USF Site License
|
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|-
|[[Julia|Julia 0.6.2]]
|05/03/2018
|Open Source
|
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|-
|[[R_and_Rmpi|R 3.5.0]]
|04/30/2017
|Open Source
|
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|-
|RSEM 1.3.0
|04/27/2018
|Open Source
|
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|-
|Tophat 2.1.1
|04/26/2018
|Open Source
|
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|-
|Pear 0.9.11
|04/20/2018
|Open Source
|
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|-
|[[Bowtie2|Bowtie 2.3.4.1]]
|04/19/2018
|Open Source
|
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|-
|Intel Parallel Studio XE 2018
|04/18/2018
|USF Site License
|
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|-
|Trimmomatic 0.36
|04/12/2018
|Open Source
|
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|-
|[[SIESTA|SIESTA 4.0.1]]
|04/05/2018
|Open Source
|
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|-
|[[SPAdes|SPAdes 3.11.1]]
|03/30/2018
|Open Source
|
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|-
|Psi4 1.1
|03/15/2018
|Open Source
|
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|-
|[[Development_Tools|GCC 7.3.0]]
|02/28/2018
|GNU License
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|-
|[[Development_Tools|OpenMPI 2.0.4]]
|03/14/2018
|GNU License
|
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|-
|[[COMSOL|COMSOL 5.3a]]
|02/28/2018
|USF Site License
|
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|-
|[[Trinity|Trinity 2.6.5]]
|02/26/2018
|Open Source
|
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|-
|[[SageMath|SageMath 7.5.1]]
|02/12/2018
|Open Source
|
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|-
|[[Cufflinks|Cufflinks 2.2.1]]
|02/07/2018
|Open Source
|
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|-
|[[ORCA|ORCA 4.0.1]]
|02/05/2018
|Open Source
|
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|-
|[[SPECFEM3D|SPECFEM3D 3.0]]
|01/30/2018
|Open Source
|
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|-
|[[MEGA|MEGA-CC 7.0.26-1]]
|01/08/2018
|Open Source
|
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|-
|[[MUSCLE|MUSCLE 3.8.31]]
|01/08/2018
|Open Source
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|-
|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-client|GDC Data Transfer Tool 1.3.0]]
|11/22/2017
|Open Source
|
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|-
|epiGBS
|11/01/2017
|Open Source
|
|Python tools and scripts for analysis of epiGBS data.
|-
|[[xHLA|xHLA 10.04.2017]]
|10/26/2017
|Open Source
|
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|-
|[[R_and_Rmpi|R 3.4.2]]
|10/23/2017
|Open Source
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|-
|[[Matlab|Matlab R2017b]]
|10/18/2017
|USF Site License
|
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|-
|[[Gurobi|Gurobi 7.5.1]]
|10/17/2017
|Academic Use License
|
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|-
|[[FastQC|FastQC 0.11.5]]
|10/16/2017
|Open Source
|
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|-
|[[Bcbio-nextgen|bcbio-nextgen 1.0.5]]
|10/09/2017
|Open Source
|
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|-
|[[QIIME|QIIME2 2017.8]]
|10/04/2017
|Open Source
|
|-
|[[Development_Tools|Anaconda 5.0.0]]
|09/27/2017
|Open Source
|
|Tools for use with python
|-
|[[TrimGalore|Trim Galore 0.4.4]]
|09/15/2017
|Open Source
|
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|-
|[[Apache_Maven|Apache Maven 3.5.0]]
|08/14/2017
|Open Source
|
|Tools for Java-based projects
|-
|[[Rosetta|Rosetta 3.5]]
|08/11/2017
|Academic Use License
|
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|-
|[[Agilent ADS|Agilent ADS 2016_01]]
|08/10/2017
|USF Site License
|
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|-
|[[Maple|Maple 2017]]
|08/04/2017
|USF Site License
|
|
|-
|[[MaSuRCA|MaSuRCA 3.2.2]]
|07/28/2017
|Academic Use License
|
|
|-
|[[Jellyfish|Jellyfish 2.2.6]]
|07/14/2017
|Open Source
|
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|-
|[[TraCeR|TraCeR 0.15.2]]
|07/12/2017
|Open Source
|
|
|-
|[[SAS|SAS 9.4 Rev TS1M4]]
|07/11/2017
|USF Site License
|
|
|
|

Latest revision as of 17:53, 30 June 2021

Typical Software Installation Process

List of Current Software Projects

Application Name Installation Status Estimated Start Estimated Completion Notes
GAP 4.11 In Progress June 2021 July 2021 Stalled due to issues with dependent packages
Intel OneAPI Toolkit 2021 In Progress June 2021 July 2021
Haddock 2.4 In Progress June 2021 July 2021
Amber20/AmberTools2020 Pending July 2021
GNUplot 5.4 Pending July 2021
MuTect Pending July 2021
Mummer Pending July 2021
Psi4 1.3.2 Pending Aug 2021

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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