Difference between revisions of "HPC:Software"

From HPC wiki
 
(18 intermediate revisions by 2 users not shown)
Line 1: Line 1:
=== Other Pages ===
 
*[[HPC:Main_Page|HPC Main Page]]
 
*[[HPC:Login|Connecting to the PMACS cluster]]
 
*[[HPC:User_Guide|User Guide]]
 
*[[HPC:Archive System|PMACS Archive System]]
 
  
 +
 +
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 ===  
 
* [[HPC:AllPaths-LG| AllPaths-LG]]
 
* [[HPC:AllPaths-LG| AllPaths-LG]]
 
* [[HPC:bamtools| bamtools]]
 
* [[HPC:bamtools| bamtools]]
 
* [[HPC:bcl2fastq| bcl2fastq]]
 
* [[HPC:bcl2fastq| bcl2fastq]]
 +
* [[HPC:bclconvert| BCL Convert]]
 
* [[HPC:BLAST| BLAST+]]
 
* [[HPC:BLAST| BLAST+]]
 
* [[HPC:BLAT| BLAT]]
 
* [[HPC:BLAT| BLAT]]
Line 15: Line 13:
 
* [[HPC:bwa| bwa]]
 
* [[HPC:bwa| bwa]]
 
* [[HPC:CASAVA| CASAVA]]
 
* [[HPC:CASAVA| CASAVA]]
 +
* [[HPC:CellRanger| Cell Ranger]]
 +
* [[HPC:CMake| CMake]]
 +
* [[HPC:GPU| CUDA]]
 
* [[HPC:cufflinks| Cufflinks]]
 
* [[HPC:cufflinks| Cufflinks]]
* [[HPC:Developer_Tool_Set| devtoolset-2 (GCC)]]
+
* [[HPC:Developer_Tool_Set| devtoolset-2 (GCC v4.8.0)]]
* [[HPC:Environment_Modules| Environment Modules]]
 
 
* [[HPC:eQtlBma|eQtlBma]]
 
* [[HPC:eQtlBma|eQtlBma]]
 
* [[HPC:FastQC| FastQC]]
 
* [[HPC:FastQC| FastQC]]
 
* [[HPC:FASTX-Toolkit| FASTX-Toolkit]]
 
* [[HPC:FASTX-Toolkit| FASTX-Toolkit]]
 +
* [[HPC:Developer_Tool_Set| GCC v4.8.0]]
 +
* [[HPC:GCC| GCC]]
 
* [[HPC:Homer| Homer]]
 
* [[HPC:Homer| Homer]]
 
* [[HPC:Java| Java]]
 
* [[HPC:Java| Java]]
 +
* [[HPC:Jupyter| Jupyter]]
 
* [[HPC:kClust| kClust]]
 
* [[HPC:kClust| kClust]]
 +
* [[HPC:lftp|lftp]]
 
* [[HPC:MPI| mpich2]]
 
* [[HPC:MPI| mpich2]]
 +
* [[HPC:MPLUS| MPLUS]]
 
* [[HPC:NGSUtils| NGSUtils]]  
 
* [[HPC:NGSUtils| NGSUtils]]  
 
* [[HPC:NAMD| NAMD-2.9]]
 
* [[HPC:NAMD| NAMD-2.9]]
Line 37: Line 42:
 
* [[HPC:Sailfish| Sailfish]]
 
* [[HPC:Sailfish| Sailfish]]
 
* [[HPC:SCons| SCons]]
 
* [[HPC:SCons| SCons]]
 +
* [[HPC:Singularity| Singularity]]
 
* [[HPC:SRAToolkit| SRA Toolkit]]
 
* [[HPC:SRAToolkit| SRA Toolkit]]
 
* [[HPC:STAR| STAR]]
 
* [[HPC:STAR| STAR]]
Line 47: Line 53:
 
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:
 
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:
  
* [[HPC:Manual_Software_Install| Manually install the program]]
+
* [[HPC:Manual_Software_Install| <strong>Manually install the program</strong>]]
* Send [mailto:pmacshpc@med.upenn.edu us] a note and we'll look into installing this program for you.  
+
* Send [mailto:pmacshpc@med.upenn.edu <strong>us</strong>] a note and we'll look into installing this program for you.  
 +
 
 +
'''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>]]
  
'''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| here]]
+
=== Other Pages ===
 +
----
 +
<div class="mw-collapsible mw-collapsed">
 +
*[[HPC:Main_Page|HPC Main Page]]
 +
*[[HPC:User_Guide|User Guide]]
 +
*[[HPC:Software|Available Software]]
 +
</div>

Latest revision as of 19:00, 24 August 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