Software

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The following software packages are available on the eureka and yucca clusters. If you want additional packages, installed please contact the NSCEE staff and we will try and accommodate your request. Most of the packages below need to be "activated" by including a modulefile in either your shell startup script or manually entered during your shell session.

Modules are activated by using the module load <name> or module initadd <name> command:

module load gnu/gcc-4.7.1
module initadd R/3.0.3

For a current list of the available modules: module avail.
For a list of your currently active modules: module list.
For more information on using module files, see: man module.

Cluster Package Module File Description
eureka
yucca
R R/3.0.3 The R statistical analysis package. Includes Rmpi, snow, and multicore modules.
eureka cuda cuda NVIDA supplied cuda gpu toolkit *** WILL BE INSTALLED SHORTLY ***
eureka
yucca
Bowtie bio/bowtie Bowtie short read aligner
eureka
yucca
boost Boost provides free peer-reviewed portable C++ source libraries. No modulefile is provided. Use -I/share/apps/boost_1_55_0/include and -L/share/apps/boots_1_55_0 when you compile
eureka
yucca
htslib htslib - C library for high-throughput sequencing data formats. No modulefile is provided. Use -I/share/apps/bio/htslib/include and -L/share/apps/bio/lib when you compile
eureka
yucca
samtools bio/samtools SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments.
eureka
yucca
sparsehash sparsehash - An extremely memory-efficient hash_map implementation.No modulefile is provided. Use -I/share/apps/bio/sparsehash/include and -L/share/apps/bio/sparsehash/lib when you compile
eureka
yucca
stacks bio/stacks-1.15 Stacks - software pipeline for building loci from short-read sequences
eureka
yucca
intel-12 intel/intel-12 Vendor (Intel) supplied version of the Intel cluster suite, including C/C++/Fortran and associated high-performance libraries.
eureka
yucca
intel-12-impi intel/intel-12-impi Vendor (Intel) supplied version of the Intel cluster suite, including C/C++/Fortran and associated high-performance libraries. Configured to use the infiniband high-speed interconnect.
eureka
yucca
python python/python-2.7 python 2.7 with additional packages pre-installed.
eureka
yucca
python python/3.4.0 python 3.4.0 with additional packages pre-installed.
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