Difference between revisions of "HPC:Software"

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=== Other Pages ===
 
*[[HPC:Main_Page|HPC Main Page]]
 
*[[HPC:Login|Connecting to the PMACS cluster]]
 
*[[HPC:User_Guide|User Guide]]
 
  
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For information on how to use software currently installed on the cluster, please read [[HPC:Environment_Modules| <strong>Environment Modules</strong>]]
 
=== Software currently installed on the PMACS cluster ===  
 
=== Software currently installed on the PMACS cluster ===  
 
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* [[HPC:AllPaths-LG| AllPaths-LG]]
* bowtie
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* [[HPC:bamtools| bamtools]]
* bowtie2-2.1.0
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* [[HPC:bcl2fastq| bcl2fastq]]
* devtoolset-2
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* [[HPC:BLAST| BLAST+]]
* [[HPC:Java|Java]]
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* [[HPC:BLAT| BLAT]]
* [[HPC:Environment_Modules|Environment Modules]]
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* [[HPC:Boost| Boost]]
* mpich2-x86_64
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* [[HPC:bowtie| bowtie]]
* NAMD-2.9-Linux-x86_64-multicore
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* [[HPC:bwa| bwa]]
* openmpi-1.5.4-x86_64
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* [[HPC:CASAVA| CASAVA]]
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* [[HPC:CellRanger| Cell Ranger]]
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* [[HPC:cufflinks| Cufflinks]]
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* [[HPC:Developer_Tool_Set| devtoolset-2 (GCC v4.8.0)]]
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* [[HPC:eQtlBma|eQtlBma]]
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* [[HPC:FastQC| FastQC]]
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* [[HPC:FASTX-Toolkit| FASTX-Toolkit]]
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* [[HPC:Developer_Tool_Set| GCC v4.8.0]]
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* [[HPC:GCC| GCC]]
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* [[HPC:Homer| Homer]]
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* [[HPC:Java| Java]]
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* [[HPC:Jupyter| Jupyter]]
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* [[HPC:kClust| kClust]]
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* [[HPC:lftp|lftp]]
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* [[HPC:MPI| mpich2]]
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* [[HPC:MPLUS| MPLUS]]
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* [[HPC:NGSUtils| NGSUtils]]
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* [[HPC:NAMD| NAMD-2.9]]
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* [[HPC:MPI| openmpi]]
 
* [[HPC:Perl|Perl]]
 
* [[HPC:Perl|Perl]]
* picard-1.96
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* [[HPC:Picard| Picard Tools]]
 
* [[HPC:Python|Python]]
 
* [[HPC:Python|Python]]
* R
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* [[HPC:R| R]]
* ruby-1.8.7-p374
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* [[HPC:Ruby| Ruby]]
* ruby-1.9.3-p448
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* [[HPC:Rum| RUM]]
* rum-2.0.5_05
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* [[HPC:samtools| samtools]]
* samtools-0.1.19
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* [[HPC:Sailfish| Sailfish]]
* STAR-2.3.0e
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* [[HPC:SCons| SCons]]
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* [[HPC:Singularity| Singularity]]
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* [[HPC:SRAToolkit| SRA Toolkit]]
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* [[HPC:STAR| STAR]]
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* [[HPC:tophat| TopHat]]
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* [[HPC:Trimmomatic| Trimmomatic]]
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* [[HPC:zlib| zlib]]
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=== Manually installing software on the PMACS cluster ===
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If the software (or version of an already installed program) you want isn't available on the PMACS cluster, you have a couple of options:
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* [[HPC:Manual_Software_Install| <strong>Manually install the program</strong>]]
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* Send [mailto:pmacshpc@med.upenn.edu <strong>us</strong>] a note and we'll look into installing this program for you.  
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'''Note:''' Due to the high volume of requests we receive, it can take some time for us to handle software install requests. If you have an urgent need for the program, you can try to install the program yourself by following the instructions [[HPC:Manual_Software_Install| <strong>here</strong>]]
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=== Other Pages ===
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----
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<div class="mw-collapsible mw-collapsed">
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*[[HPC:Main_Page|HPC Main Page]]
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*[[HPC:User_Guide|User Guide]]
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*[[HPC:Software|Available Software]]
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</div>

Revision as of 19:47, 3 May 2021


For information on how to use software currently installed on the cluster, please read Environment Modules

Software currently installed on the PMACS cluster

Manually installing software on the PMACS cluster

If the software (or version of an already installed program) you want isn't available on the PMACS cluster, you have a couple of options:

Note: Due to the high volume of requests we receive, it can take some time for us to handle software install requests. If you have an urgent need for the program, you can try to install the program yourself by following the instructions here

Other Pages