Difference between revisions of "HPC:Software"
From HPC wiki
| (16 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| + | |||
| + | 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 v4.8.0)]] | * [[HPC:Developer_Tool_Set| devtoolset-2 (GCC v4.8.0)]] | ||
| − | |||
* [[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:Developer_Tool_Set| GCC v4.8.0]] | ||
| − | * [[HPC: | + | * [[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 40: | 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 50: | 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>]] | ||
| − | + | === 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
- AllPaths-LG
- bamtools
- bcl2fastq
- BCL Convert
- BLAST+
- BLAT
- Boost
- bowtie
- bwa
- CASAVA
- Cell Ranger
- CMake
- CUDA
- Cufflinks
- devtoolset-2 (GCC v4.8.0)
- eQtlBma
- FastQC
- FASTX-Toolkit
- GCC v4.8.0
- GCC
- Homer
- Java
- Jupyter
- kClust
- lftp
- mpich2
- MPLUS
- NGSUtils
- NAMD-2.9
- openmpi
- Perl
- Picard Tools
- Python
- R
- Ruby
- RUM
- samtools
- Sailfish
- SCons
- Singularity
- SRA Toolkit
- STAR
- TopHat
- Trimmomatic
- zlib
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:
- Manually install the program
- Send us 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 here
