Software

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Software Policies

RC team maintains a core collection of software/library packages to aid in advanced scientific computing in multiple core disciplines. Software products are chosen based on need, performance, system compatibility, and benefit to the scientific community. Software installs on the clusters falls into two categories, software that is centrally maintained or software that is self-maintained by a respective user or group. In order for the software to be maintained centrally, typically one of the following criteria must be met:

  • Will be a benefit to numerous users
  • Requires root/privileged access
  • Requires access to license manager
  • Upgrade to already installed software that provides an significant enhancement

Central software install requests can be made at the RC Help Desk by selecting the "Software Central Install/Upgrade" Help Topic when opening a new ticket.

For software that does not meet the criteria for being managed centrally, users are encouraged to install software in one of their own user space locations (i.e. home directory or group directory). If a user has issues with the install, the RC team would be happy to assist. Please visit RC Help Desk and select "Software Local Install Request" Help Topic when opening a new ticket.

Centrally Managed Software

Name Category System
abyss Genomics Spruce Knob
ALLPATHS-LG Genomics Spruce Knob
BEAGLE Genomics Spruce Knob
BEDTools Genomics Spruce Knob
BLAST+ Genomics Spruce Knob
Bowtie2 Genomics Spruce Knob
CLUMPP Genomics Spruce Knob
Cufflinks Genomics Spruce Knob
Distruct Genomics Spruce Knob
Eigensoft Genomics Spruce Knob
Emboss Genomics Spruce Knob
Fasta36 Genomics Spruce Knob
FastQC Genomics Spruce Knob
Fastx Genomics Spruce Knob
GATK Genomics Spruce Knob
Hmmer Genomics Spruce Knob
IGV Genomics Spruce Knob
Muscle Genomics Spruce Knob
Phase Genomics Spruce Knob
Phrap Genomics Spruce Knob
Picard-tools Genomics Spruce Knob
PLINK Genomics Spruce Knob
RepeatExplorer Genomics Spruce Knob
RSEM Genomics Spruce Knob
Samtools Genomics Spruce Knob
Shapeit Genomics Spruce Knob
SoapDenovo Genomics Spruce Knob
Structure Genomics Spruce Knob
Tabix Genomics Spruce Knob
Tablet Genomics Spruce Knob
Tophat2 Genomics Spruce Knob
Tandem Repeat Finder Genomics Spruce Knob
Trinity Genomics Spruce Knob
Vcftools Genomics Spruce Knob
GNU Parallel GNU Spruce Knob
Matlab Mathematics Spruce Knob
Paraview Visualization Mountaineer
Gaussian Chemistry Spruce Knob/Mountaineer
Lastz Genomics Spruce Knob
Qiime Genomics Spruce Knob
gcc GNU Spruce Knob/Mountaineer
boost Library Spruce Knob
mkl Library Spruce Knob/Mountaineer
openmpi Library Spruce Knob/Mountaineer
mvapich Library Spruce Knob/Mountianeer
intel mpi Library Spruce Knob/Montaineer
R Mathematics Spruce Knob/Mountaineer
Java Compiler Spruce Knob/Mountaineer
Python Compiler Spruce Knob/Mountaineer
Matplotlib Library Spruce Knob/Mountaineer
Numpy Library Spruce Knob
Intel Parallel Studio Compiler Spruce Knob/Mountaineer