Available Software on the OBCP Cluster

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.

Datasets

NCBI - nr Database

• Path: /data/shared/seq_dbs/nr/
• Notes:

NCBI - nt Database

• Path: /data/shared/seq_dbs/nt/
• Notes:

Pfam HMMs

• Path: /data/shared/seq_dbs/Pfam/HHMs/
• Notes:

UniProt - Swiss-Prot Database

• Path: /data/shared/seq_dbs/Swiss-Prot/
• Notes:

UniProt - UniRef90 Database

• Path: /data/shared/seq_dbs/UniRef90/
• Notes:

Phylogenetic Software

Agalma

• Filename: agalma
• Version: 0.5.0
• Parallel: Yes
• Notes:

BAMM

• Filename: bamm
• Version: 2.3.1
• Parallel: Yes
• Notes:

Bayesian Serial SimCoal

• Filename: BayeSSC
• Version:
• Parallel: No
• Notes:

BEAST

• Filename: beast (BEAST v2) / beast1 (BEAST v1)
• Version: 2.2.1 / 1.8.2
• Parallel: BEAGLE threading
• Notes: BEAST v2 is installed in /opt/beast2/; BEAST v1 is installed in /opt/beast1/; see this page for a comparison between the two version

BEAUti

• Filename: beauti (BEAST v2) / beauti1 (BEAST v1)
• Version: 2.2.1 / 1.8.2
• Parallel: No
• Notes: This program is a BEAST plugin

Bioinformatics Brew

• Filename: bib
• Version: ---
• Parallel: ---
• Notes: See information on web - http://bib.bitbucket.org/

BUCKy

• Filename: bucky & mbsum
• Version: 1.4.3
• Parallel: No
• Notes:

B2G4PIPE

• Filename: see notes
• Version: 2.5.0
• Parallel: Java threading
• Notes: Must change into the B2G4PIPE directory (/etc/b2g4pipe/), then follow instructions (http://www.blast2go.com/b2glaunch/resources).

FastCodeML

• Filename: fast
• Version: 1.1.0
• Parallel: OpenMP threading
• Notes:

hBayeSSC

• Filename: hBayeSSC.py
• Version:
• Parallel: No
• Notes:

jmodeltest2

• Filename: java -jar /opt/jmodeltest/jModelTest.jar
• Version: 2.1.7
• Parallel: Java threading
• Notes: The program must be run with the full path to the executable

LASTZ

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

MrBayes

• Filename: mb
• Version: 3.2.5
• Parallel: MPI-enabled
• Notes: This version of MrBayes now works on Linux kernels using MPI

MUSCLE

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

PAML

• Filename: multiple executables
• Version: 4.8a
• Parallel: No
• Notes: copy configuration files from /opt/paml/

PHASE

• Filename: multiple executables
• Version: 2.0
• Parallel: No
• Notes:

ProtTest

• Filename: java -jar /opt/prottest/prottest.jar
• Version: 3.4
• Parallel: Java threading
• Notes: The program must be run with the full path to the executable

pyRAD

• Filename: pyRAD
• Version: 3.0
• Parallel: threading
• Notes:

RaxML

• Filename: raxml
• Version: 8.1.16
• Parallel: Pthreads threading
• Notes:

RaxML Light

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

SINA

• Filename: /etc/sina/sina
• Version: 1.2.11
• Parallel: No
• Notes: The program must be run with the full path to the executable

SNAPP

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

TNT

• Filename: tnt
• Version: 1.1
• Parallel: No
• Notes: Use the command cp /etc/tnt/.passwordfile.tnt ~/ prior to the first run of TNT

USEARCH

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

VSEARCH

• Filename: vsearch
• Version: 1.0.7
• Parallel: threading
• Notes:

Genomic/Transcriptomic Software

ABySS

• Filename: abyss-pe
• Version: 1.3.4
• Parallel: MPI-enabled
• Notes: see documentation on how to run in parallel: http://www.bcgsc.ca/downloads/abyss/doc/#parallelprocessing

AlignGraph

• Filename: AlignGraph & Eval-AlignGraph
• Version: n/a
• Parallel: No
• Notes:

ALLPATHS-LG

• Filename: multiple executables
• Version: 52188
• Parallel: threaded
• Notes:

AUGUSTUS

• Filename: augustus
• Version: 3.0.3
• Parallel: No* Notes:

Burrows-Wheeler Aligner (BWA)

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

Barrnap

• Filename: barrnap
• Version: 0.6
• Parallel: threading
• Notes:

CASAVA

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

CEGMA

• Filename: cegma
• Version: 2.5
• Parallel: Pthreads threading
• Notes:

Circos

• Filename: circos
• Version: 0.67-7
• Parallel: No
• Notes:

Cufflinks

• Filename: cufflinks
• Version: 2.2.1
• Parallel: PThreads threading
• Notes:

DISCOVAR de novo

• Filename: DiscovarDeNovo
• Version: 52325
• 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:

Glimmer

• Filename: glimmer3
• Version: 3.02
• 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:

Infernal

• Filename: multiple executables
• Version: 1.1.1
• Parallel: Threading
• Notes:

KmerGenie

• Filename: kmergenie
• Version: 1.6741
• Parallel: Threading
• Notes:

MAKER

• Filename: maker
• Version: 2.31.8
• Parallel: MPI-enabled
• Notes:

MinCED

• Filename: minced
• Version: 0.1.6
• Parallel: Java threading
• 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.

PEAR

• Filename: pear
• Version: 0.9.5
• Parallel: threading
• Notes:

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

Prodigal

• Filename: prodigal
• Version: 2.6.2
• Parallel: No
• Notes:

Prokka

• Filename: prokka
• Version: 1.11
• Parallel: Yes
• Notes:

PyMsBayes

• Filename: multiple executables
• Version: 0.2.4
• Parallel: Yes
• Notes:

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.

RNAmmer

• Filename: rnammer
• Version: 1.2
• Parallel: unknown
• Notes:

RSEM

• Filename: multiple executables
• Version: 1.2.19
• Parallel: unknown
• Notes:

SAMtools

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

Seqtk

• Filename: seqtk
• Version: 1.0-r75-dirty
• Parallel: No
• Notes:

SignalP

• Filename: signalp
• Version: 4.1c
• Parallel: unknown
• Notes:

SISRS

• Filename: sisrs
• Version: 1.6
• Parallel: yes
• Notes:

SOAPaligner

• Filename: soap and 2bwt-builder
• Version: 2.21
• Parallel: Pthreads threading
• Notes:

SOAPdenovo

• Filename: SOAPdenovo-127mer and SOAPdenovo-63mer
• Version: 2.04
• Parallel: Pthreads threading
• Notes:

SPAdes

• Filename: spades.py
• Version: 3.5.0
• Parallel: threading
• Notes:

Structure

• Filename: structure
• Version: 2.3.4
• Parallel: No
• Notes: uses this command 'structure -m /usr/local/bin/mainparams -e /usr/local/bin/extraparams' to run with default parameter files

tbl2asn

• Filename: tbl2asn
• Version: 11-12-2014
• Parallel: unknown
• Notes:

TMHMM

• Filename: tmhmm
• Version: 2.0c
• Parallel: unknown
• Notes:

TopHat

• Filename: tophat
• Version: 2.0.13
• Parallel: Threading
• Notes:

Trimmomatic

• Filename: java -jar /usr/local/bin/trimmomatic.jar
• Version: 0.32
• Parallel: Java threading
• Notes:

Trinotate

• Filename: Trinotate
• Version: r20131110
• Parallel: unknown
• Notes: Trinotate directory is located at '/etc/trinotate' if needed. The NCBI sequence databases are located in '/data/shared/seq_dbs/'

Trinity

• Filename: /etc/trinity/Trinity
• Version: 2.0.6
• Parallel: Threading
• Notes: Use the argument "--bypass_java_version_check" to ignore checking for a specific, earlier Java version

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:

vtBuilder

• Filename: vt-builder.jar
• Version: unknown (preview)
• Parallel: Threading
• Notes: run from command line as java -jar -Xmx97152M /usr/local/lib/vt-builder.jar -a n -d ./output.txt -e ./log.txt -f 32 -g 150 -h 250 -j 96

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: 3.6.11
• Parallel: MPI-enabled
• Notes:

Migrate-N (beta)

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

ms

• Filename: ms
• Version: 3.13.2014
• Parallel: No
• Notes:

RTD

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

Stacks

• Filename: multiple executables
• Version: 1.24
• Parallel: OpenMP threading
• Notes:

Ecological Modelling Software

Maxent

• Filename: java -jar /usr/local/lib/maxent.jar
• Version: 3.3.3k
• Parallel: Java threading
• Notes:

Mothur

• Filename: mothur
• Version: 1.33
• Parallel: MPI-enabled
• Notes:

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

Python Packages

ACOR

• Version: 1.1.1

BCBio

• Version: 0.6.1

BioPython

• Version: 1.6.3

Geneland

• Version: 4.0.5

NumPy

• Version: 1.8.2

PypeR

• Version: 1.1.2

OJ_Break

• Version: 0.1

QIIME

• Version: 1.8.0

scatR

• Version: 0.1