Available Software on the OBCP Cluster

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Available Software on the OBCP Cluster

This section of the wiki is designed to help a user locate particular software that is present on the OBCP cluster. Send any software requests to Joe Cora.


Introduction

Standard software packages that are present on most Linux operating systems like Python, Perl, R, etc. are already installed on the OBCP cluster. Some software are designed to be run in parallel by using the message passing interface (MPI) and/or through thread support built into the software. For more information on running programs in parallel, visit the Multiple Processor Runs on the OBCP Cluster page.


Phylogenetic Software

BEAST

  • Filename: beast
  • Version: 2.1.0
  • Parallel: BEAGLE threading
  • Notes:

BEAUti

  • Filename: beauti
  • Version: 2.0.1
  • Parallel: No
  • Notes: This program is a BEAST plugin

B2G4PIPE

LASTZ

  • Filename: lastz & lastz_D
  • Version: 1.03.54
  • Parallel: No
  • Notes:

MrBayes

  • Filename: mb
  • Version: 3.2.1
  • Parallel: MPI-enabled
  • Notes: This version of MrBayes as well as 3.1.x do not operate properly on operating systems using the newer Linux kernels. An attempt to address this problem with the authors was fruitless.

MUSCLE

  • Filename: muscle
  • Version: 3.8.31
  • Parallel: No
  • Notes:

pyRAD

  • Filename: pyRAD
  • Version: 2.11
  • Parallel: No
  • Notes:

RaxML

  • Filename: raxml
  • Version: 7.3.1
  • Parallel: Pthreads threading
  • Notes:

RaxML Light

  • Filename: raxmlLight
  • Version: 1.0.8
  • Parallel: Pthreads threading
  • Notes:

SNAPP

  • Filename: snapp
  • Version: 1.1.1
  • Parallel: BEAGLE threading
  • Notes: This program is a BEAST plugin

USEARCH

  • Filename: usearch
  • Version: 6.0.307
  • Parallel: threading
  • Notes:

Genomic/Transcriptomic Software

ABySS

Burrows-Wheeler Aligner (BWA)

  • Filename: bwa
  • Version: 0.7.8-r455
  • Parallel: No
  • Notes:

CASAVA

  • Filename: multiple executables
  • Version: 1.8.2
  • Parallel: Pthreads threading
  • Notes:

FASTX Toolkit

  • Filename: multiple executables
  • Version: 0.0.12
  • Parallel: Unknown
  • Notes:

GATK

  • Filename: java -jar /usr/local/bin/GenomeAnalysisTK.jar
  • Version: 3.1-1
  • Parallel: Unknown
  • Notes:

GENSCAN

  • Filename: genscan
  • Version: ??
  • Parallel: No
  • Notes:

GMAP

  • Filename: gmap & other executables
  • Version: 2014-02-20
  • Parallel: No
  • Notes:

GSNAP

  • Filename: gsnap
  • Version: 2014-02-20
  • Parallel: No
  • Notes:

MIRA

  • Filename: mira
  • Version: 4.0
  • Parallel: No
  • Notes:

msBayes

  • Filename: msbayes.pl
  • Version: 20140305
  • Parallel: No
  • Notes:

Oases

  • Filename: oases
  • Version: 0.2
  • Parallel: OpenMP threading
  • Notes: Default parameters were used. Oases (as with Velvet) should be compiled within your home directory with the specific compilation parameters (max k-mer length, # of read categories, etc.) tailored to your reads at hand.

Picard

  • Filename: java -jar /etc/picard-tools/[command].jar
  • Version: 1.111
  • Parallel: Java threading
  • Notes: [command] is replaced with the specific picard command you would like to run

QDD

  • Filename: multiple executables
  • Version: 3.0 (beta)
  • Parallel: threading
  • Notes: Must change into the QDD directory (/usr/local/qdd), then follow instructions (http://net.imbe.fr/~emeglecz/qdd_run.html) for running the program from there.

SAMtools

  • Filename: samtools
  • Version: 0.1.19+
  • Parallel: No
  • Notes:

Trimmomatic

  • Filename: java -jar /usr/local/bin/trimmomatic.jar
  • Version: 0.30
  • Parallel: Java threading
  • Notes:

Trinity

  • Filename: /etc/trinity/Trinity.pl
  • Version: 2013-11-10
  • Parallel: Threading
  • Notes:

Velvet

  • Filename: velveth & velvetg
  • Version: 1.2.09
  • Parallel: OpenMP threading
  • Notes: Default parameters were used with the exception of enabling OpenMP. Velvet should be compiled within your home directory with the specific compilation parameters (max k-mer length, # of read categories, etc.) tailored to your reads at hand.

VCFtools

  • Filename: multiple executables
  • Version: 0.1.12a
  • Parallel: No
  • Notes:

VelvetOptimiser

  • Filename: VelvetOptimiser.pl
  • Version: 2.2.5
  • Parallel: Threading
  • Notes:


Population Genetic/Genomic Software

BP&P

  • Filename: bpp
  • Version: 2.1b
  • Parallel: No
  • Notes:

∂a∂i

  • Filename: python package
  • Version: 1.6.3
  • Parallel: No
  • Notes:

IMa2

  • Filename: IMa2
  • Version: 8.27.12
  • Parallel: No
  • Notes: version is the date of release (August 27, 2012)

Migrate-N

  • Filename: migrate-n
  • Version: 3.3.1
  • Parallel: MPI-enabled
  • Notes:

Migrate-N (beta)

  • Filename: migrate-n-beta
  • Version: 3.4.4
  • Parallel: MPI-enabled
  • Notes: This is a beta version

RTD

  • Filename: multiple executables
  • Version: 06-10-2013
  • Parallel: GNU parallel
  • Notes:

Stacks

  • Filename: multiple executables
  • Version: 0.99998
  • Parallel: OpenMP threading
  • Notes:


Ecological Modelling Software

R Packages

akima

  • Version: 0.5-11

ape

  • Version: 3.1-1

bGMYC

  • Version: 1.0.2

genalg

  • Version: 0.1.1

rlecuyer

  • Version: 0.3-3

VGAM

  • Version: 0.9-3
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