Difference between revisions of "Apps Queue"
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|<span style="color:green">Amber16/AmberTools18</span>
|<span style="color:red">Amber16/AmberTools18</span>
|<span style="color:red">In Progress</span>
|<span style="color:red">May 2019</span>
|<span style="color:red"></span>
|<span style="color:red">Stalled due to issues with dependent packages</span>
|-
|<span style="color:green">VirMine for python 2.7.15</span>
|<span style="color:green">In Progress</span>  
|<span style="color:green">In Progress</span>  
|<span style="color:green">Apr 2019</span>
|<span style="color:green">July 2019</span>
|<span style="color:green">May 2019</span>
|<span style="color:green">Aug 2019</span>
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|-
|<span style="color:blue">Canu v1.8</span>
|<span style="color:blue">Pending</span>
|<span style="color:blue">Aug 2019</span>
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|<span style="color:green">Mathematica 12</span>
|<span style="color:blue">Clustal Omega 1.2.4</span>
|<span style="color:green">In Progress</span>  
|<span style="color:blue">Pending</span>  
|<span style="color:green">May 2019</span>
|<span style="color:blue">Aug 2019</span>
|<span style="color:green">May 2019</span>
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|<span style="color:blue">VMD 1.9.3</span>
|<span style="color:blue">Mothur 1.42.0</span>
|<span style="color:blue">Pending</span>  
|<span style="color:blue">Pending</span>  
|<span style="color:blue">May 2019</span>
|<span style="color:blue">Aug 2019</span>
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|'''Notes'''
|'''Notes'''
|'''Additional Info'''
|'''Additional Info'''
|-
|[[Mathematica|Mathematica 12]]
|07/03/2019
|USF Site License
|
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|-
|[[ANSYS_EDT_(formerly_HFSS)|Ansys Electronics Desktop Suite 2019r2]]
|07/15/2019
|Restricted - Authorized users only
|
|Electromagnetic and circuit design applications including HFSS, Maxwell, etc.
|-
|[[R_and_Rmpi|R 3.6.0]]
|07/01/2019
|Open Source
|
|GCC build for use on RHEL7 compute nodes
|-
|[[ANSYS|Ansys Multiphysics 2019r2]]
|06/28/2019
|Restricted - Authorized users only
|
|ANSYS finite-element analysis applications
|-
|[[VMD|VMD 1.9.3]]
|06/12/2019
|Academic license
|
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|-
|[[Matlab|Matlab R2019a]]
|[[Matlab|Matlab R2019a]]
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|[[Subread|Subread 1.6.3]]
|[[Subread|Subread 1.6.3]]
|01/11/2019
|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.
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|[[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
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|[[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
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|LinBox 1.5.2
|05/22/2018
|Open Source
|Required updated install of 8 additional library packages
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|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
|Open Source
|
|

Revision as of 17:29, 26 July 2019

Typical Software Installation Process

List of Current Software Projects

Application Name Installation Status Estimated Start Estimated Completion Notes
Amber16/AmberTools18 In Progress May 2019 Stalled due to issues with dependent packages
VirMine for python 2.7.15 In Progress July 2019 Aug 2019
Canu v1.8 Pending Aug 2019
Clustal Omega 1.2.4 Pending Aug 2019
Mothur 1.42.0 Pending Aug 2019

Recently Completed Software Projects

Application Name Date Completed License Type Notes Additional Info


Mathematica 12 07/03/2019 USF Site License
Ansys Electronics Desktop Suite 2019r2 07/15/2019 Restricted - Authorized users only Electromagnetic and circuit design applications including HFSS, Maxwell, etc.
R 3.6.0 07/01/2019 Open Source GCC build for use on RHEL7 compute nodes
Ansys Multiphysics 2019r2 06/28/2019 Restricted - Authorized users only ANSYS finite-element analysis applications
VMD 1.9.3 06/12/2019 Academic license
Matlab R2019a 05/16/2019 USF Site License
Maple 2019 05/09/2019 USF Site License
LAMMPS 12Dec18 (GPU Edition) 04/29/2019 Open Source
gem5 2.0 04/25/2019 Open Source
Ansys Electronics Desktop Suite 2019R1 04/19/2018 Restricted - Authorized users only Electromagnetic and circuit design applications including HFSS, Maxwell, etc.
Ansys Multiphysics 2019R1 04/18/2019 Restricted - Authorized users only ANSYS finite-element analysis applications
Stacks 2.3e 04/09/2019 Open Source
SeqTK 1.0 03/20/2019 Open Source
Deblur 1.1.0 03/18/2019 Open Source Python add-on module. Loads with apps/python/3.6.2
Anvio 5.4 03/15/2019 Open Source
Prodigal 2.6.2 03/15/2019 Open Source
Bayestraits 3.0.1 03/14/2019 Open Source
R 3.5.2 03/04/2019 Open Source
Ataqv 1.0.0 02/27/2019 Open Source
AfterQC 0.9.7 02/19/2019 Open Source
Tophat 2.1.1 02/15/2019 Open Source Revision
Intel Parallel Studio XE 2019 02/11/2019 USF Site License
HOMER 4.10 02/05/2019 Open Source
bcbio-nextgen 1.1.3 01/30/2019 Open Source
Reporter 0.7.15 01/29/2019 Open Source
DeNovoGUI 1.16.2 01/29/2019 Open Source
PeptideShaker 1.16.37 01/29/2019 Open Source
GDC-client 1.4.0 01/28/2019 Open Source Python add-on module Loads with apps/python/2.7.15
COMSOL 5.4 01/28/2019 USF Site License
SearchGUI 3.3.12 01/28/2019 Open Source
SICKLE 1.33 01/28/2019 Open Source
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.
Subread 1.6.3 01/11/2019 Open Source

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=2043"