Difference between revisions of "Apps Queue"
 
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|<span style="color:red">SURPI 1.0.18</span>
|<span style="color:red">GAP 4.11</span>
|<span style="color:red">On Hold</span>  
|<span style="color:red">In Progress</span>
|<span style="color:red">Nov 2018</span>
|<span style="color:red">June 2021</span>
|<span style="color:red">July 2021</span>
|<span style="color:red">Stalled due to issues with dependent packages</span>
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|<span style="color:green">Intel OneAPI Toolkit 2021</span>
|<span style="color:green">In Progress</span>
|<span style="color:green">June 2021</span>
|<span style="color:green">July 2021</span>
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|<span style="color:red">Application has several dependency issues that need to be resolved before build can continue.</span>
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|<span style="color:green">HOMMER 4.10</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">Jan 2019</span>
|<span style="color:green">June 2021</span>
|<span style="color:green">Jan 2019</span>
|<span style="color:green">July 2021</span>
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|<span style="color:blue">Deblur 1.1.0</span>
|<span style="color:blue">Amber20/AmberTools2020</span>
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Jan 2019</span>
|<span style="color:blue">July 2021</span>
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|<span style="color:blue">H2O.ai 3.22.1.1</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">Jan 2019</span>
|<span style="color:blue">July 2021</span>
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|<span style="color:blue">R 3.5.2</span>
|<span style="color:blue">MuTect</span>
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Jan 2019</span>
|<span style="color:blue">July 2021</span>
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|<span style="color:blue">bcbio-nextgen 1.1.2</span>
|<span style="color:blue">Mummer</span>
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Feb 2019</span>
|<span style="color:blue">July 2021</span>
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= Recently Completed Software Projects =
{| class=wikitable
|- style="background-color:#f1edbe;"
|'''Application Name'''
|'''Date Completed'''
|'''License Type'''
|'''Notes'''
|'''Additional Info'''
|-
|-
|[[COMSOL|COMSOL 5.4]]
|<span style="color:blue">Psi4 1.3.2</span>
|01/28/2019
|<span style="color:blue">Pending</span>  
|USF Site License
|<span style="color:blue">Aug 2021</span>
|
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|-
|SearchGUI 3.3.12
|01/28/2019
|Open Source
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|SICKLE 1.33
|01/28/2019
|Open Source
|
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|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.
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|[[Subread|Subread 1.6.3]]
|01/11/2019
|Open Source
|
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|[[LAMMPS|LAMMPS 12Dec18]]
|12/21/2018
|Open Source
|
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|[[ABySS|ABySS 2.1.5]]
|12/18/2018
|Open Source
|
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|Boost 1.69.0
|12/18/2018
|Open Source
|
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|SparseHash v07-26-2016
|12/18/2018
|Open Source
|
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|[[Burrows-Wheeler Alignment (BWA)|BWA 0.7.17]]
|12/14/2018
|Open Source
|
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|-
|[[ANSYS_EDT_(formerly_HFSS)|Ansys Electronics Desktop Suite v19.2]]
|11/29/2018
|Restricted - Authorized users only
|
|Electromagnetic and circuit design applications including HFSS, Maxwell, etc.
|-
|[[ANSYS|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
|
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|Trinotate 3.1.1
|11/06/2018
|Open Source
|
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|Transdecoder 5.5.0
|11/06/2018
|Open Source
|
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|PLINK 2.00a
|10/30/2018
|Open Source
|
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|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
|
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|HMMR 3.2.1
|10/29/2018
|Open Source
|
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|GffCompare v0.10.6
|10/25/2018
|Open Source
|
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|GATK 4.0.10
|10/24/2018
|Open Source
|
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|-
|Schrodinger Suite 2018
|10/23/2018
|Restricted - Authorized users only
|
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|-
|RepeatMasker 4.0.7
|10/19/2018
|Open Source
|
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|-
|MEME 5.0.2
|10/16/2018
|Open Source
|
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|-
|[[Matlab|Matlab R2018b]]
|10/12/2018
|USF Site License
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|STAR 2.6.0a
|10/11/2018
|Open Source
|
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|Cell Ranger 2.1.0
|10/08/2018
|Open Source
|
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|RUST 1.29.1
|10/05/2018
|Open Source
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|Go Programming Language 1.11.1
|10/05/2018
|Open Source
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|IBM CPLEX Optimization Studio 12.8
|10/05/2018
|Academic License
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|CellProfiler 3.1.5
|10/02/2018
|Open Source
|
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|BEDOPS 2.4.35
|10/01/2018
|Open Source
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|BEAST 1.10.1
|09/27/2018
|Open Source
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|AdapterRemoval 2.1.7
|09/27/2018
|Open Source
|
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|LiftOver 2018-0918
|09/26/2018
|Open Source
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|Kallisto 0.44.0
|09/24/2018
|Open Source
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|IGV 2.4.14
|09/21/2018
|Open Source
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|[[MAGMA|MAGMA 2.24-1]]
|09/17/2018
|Restricted - Authorized users only
|
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|FLINT 2.5.2
|09/07/2018
|Open Source
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|MPFR 4.0.1
|09/06/2018
|Open Source
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|MPIR 3.0.0
|09/05/2018
|Open Source
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|YASM 1.3.0
|09/04/2018
|Open Source
|
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|OrthoFinder 2.2.7
|08/30/2018
|Open Source
|Updated to recently released 2.2.7 and integrated with 9 additional dependencies.
|
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|[[Maple|Maple 2018]]
|08/17/2018
|USF Site License
|
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|-
|[[Mothur|Mothur 1.40.5]]
|07/31/2018
|Open Source
|
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|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.
|-
|[[Development_Tools|Perl 5.28.0]]
|07/12/2018
|Open Source
|Newer version of Perl programming language needed for some applications.
|
|-
|[[SCIP|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_EDT_(formerly_HFSS)|Ansys Electronics Desktop Suite v19.1]]
|06/29/2018
|Restricted - Authorized users only
|
|Electromagnetic and circuit design applications including HFSS, Maxwell, etc.
|-
|[[ANSYS|Ansys Multiphysics v19.1]]
|06/29/2018
|Restricted - Authorized users only
|
|ANSYS finite-element analysis applications
|-
|[[Wannier90|Wannier90 2.1.0]]
|06/29/2018
|Open Source
|
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|-
|[[Quantum_Espresso|Quantum Espresso 6.2.1]]
|06/28/2018
|Open Source
|
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|-
|[[MaxQuant|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 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
|
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|-
|[[Matlab|Matlab R2018a]]
|05/14/2018
|USF Site License
|
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|-
|[[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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|

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.
Retrieved from "https://wiki.rc.usf.edu/index.php?title=Apps_Queue&oldid=2440"