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Software Available on Breezy

Title Version Usage Notes
64-bit Linux CentOS 5.7 2.6.18...el5 #1 SMP
ABySS 1.9.0

ABySS 1.9.0 was built on Breezy with the GNU 4.4.7 compiler, using Boost 1.56 and sparsehash 2.0.2 libraries, with MPI enabled and the default maximum k-mer length of 64.  The scripts and binaries were installed to /global/software/abyss/abyss190/bin, so, add that directory to your command PATH.  For a bash shell user:

export PATH=/global/software/abyss/abyss190/bin:$PATH

A second version was built with a maximum k-mer length of 192, installed to /global/software/abyss/abyss190_kmer192/bin. For this version, set up your environment with:

export PATH=/global/software/abyss/abyss190_kmer192/bin:$PATH

Use the default version with the maximum k-mer length of 64 whenever possible, as it is expected to use less memory than one with the maximum k-mer length of 192.

ABySS 1.3.6

ABySS 1.3.6 was built on Breezy with the Intel 12.0 compiler, using Boost 1.50 and sparsehash 2.0.2 libraries, with MPI enabled and the default maximum k-mer length of 64.  The scripts and binaries were installed to /global/software/abyss/abyss136/bin, so, add that directory to your command PATH.  For a bash shell user:

export PATH=/global/software/abyss/abyss136/bin:$PATH

 

ABySS 1.5.1

ABySS 1.5.1 was built on Breezy with the Intel 12.0 compiler, using Boost 1.55 and sparsehash 2.0.2 libraries, with MPI enabled and the default maximum k-mer length of 64.  The scripts and binaries were installed to /global/software/abyss/abyss151/bin, so, add that directory to your command PATH.  For a bash shell user:

export PATH=/global/software/abyss/abyss151/bin:$PATH

A second version was built with a maximum k-mer length of 128, installed to /global/software/abyss/abyss151_kmer128/bin. For this version, set up your environment with:

export PATH=/global/software/abyss/abyss151_kmer128/bin:$PATH

Use the default version with the maximum k-mer length of 64 whenever possible, as it is expected to use less memory than one with the maximum k-mer length of 128.

ALLPATHS-LG Revision 41301

/global/software/allpathslg/41301/bin

ALLPATHS-LG Revision 52488

Initialize your environment to use ALLPATHS-LG revision 52488 on Breezy with (bash shell example):

module load gcc/gcc-4.9-20140406-beta
export PATH=/global/software/allpathslg/52488/bin:$PATH

bash (default) 3.2.25 or later
BCFtools (VCF/BCF file manipulation) 1.3

See the main WestGrid BCFtools page.

BCFtools (VCF/BCF file manipulation) 1.2

See the main WestGrid BCFtools page.

bcl2fastq - Illumina BCL to FASTQ conversion utility 2.16

See the main WestGrid page for bcl2fastq for instructions on running the software on Breezy.

BEAGLE (beagle-lib) 2.1.2

Include files and libraries compiled by Intel 12.0 compilers with OpenMP support have been installed under /global/software/beagle/beagle212.

A similar installation compiled with GCC compilers is in /global/software/beagle/beagle212_gcc. To use the latter, initialize your environment with

module load gcc/gcc-4.9-20140406-beta

BEAST 1.8.2

To set up your environment to run BEAST 1.8.2 with a version of the BEAGLE 2.1.2 libraries compiled with Intel compilers, use

module load beast/1.8.2

BEAST 2.4.1

To set up your environment to run BEAST 2.4.1 with a version of the BEAGLE 2.1.2 libraries compiled with GNU GCC compilers, use

module load beast/2.4.1

BEDTools 2.17.0

Initialize your environment to use BEDTools 2.17.0 on Breezy with

export PATH=/global/software/bedtools/bedtools2170/bin:$PATH

A user manual is available at /global/software/bedtools/docs/BEDTools-User-Manual.v4.pdf .

BEDTools 2.26.0

Initialize your environment to use BEDTools 2.26.0 on Breezy with

module load samtools
export PATH=/global/software/bamtools/bamtools223/bin:$PATH
export PATH=/global/software/bedtools/bedtools2260/bin:$PATH

Note, not all of the tests distributed with the software passed.

A user manual is available at /global/software/bedtools/docs/BEDTools-User-Manual.v4.pdf .

biobambam 0.0.92

The software has been installed on Breezy in /global/software/biobambam/biobambam_0_0_92/bin. See the WestGrid biobambam page for details.

Biopython 1.59

module load python

BLAS In MKL
BLAST NCBI BLAST 2.2.18 (Legacy BLAST)

Installed in /global/software/blast-2.2.18 .

BLAST NCBI BLAST+ 2.2.23+

linked from /global/software/ncbi-blast

BLAST NCBI BLAST+ 2.2.30+

A precompiled version of NCBI BLAST+ (ncbi-blast-2.2.30+) has been installed on Breezy, for potential use with Trinity.  The BLAST+ executables are in /global/software/blast/ncbi-blast-2.2.30+/bin.

BLAT 3.5

/global/software/blat/blat34 (linked from /global/software/bin)

Blitz++ 0.9

/global/software/blitz/blitz09

BMTagger 1.1.0

Initialize your environment to use BMTagger on Breezy with

module load bmtagger

Boost 1.58.0

Compiled with GCC. The library is in /global/software/boost/boost-1.58.0-gnu/ .

 

Boost 1.48.0

(gcc) /global/software/boost/gcc

Bowtie 1.0.0

/global/software/bowtie/bowtie-1.0.0/bin

Bowtie2 2.1.0

The executables for the software have been installed in /global/software/bowtie/bowtie2-2.1.0/bin .

BUCKy (phylogenetic analysis) 1.4.3

See the main WestGrid BUCKy page for instructions on running BUCKy on Breezy.

BWA 0.7.12

BWA version 0.7.12, compiled as distributed with GCC compilers with default settings, can be run as /global/software/bwa/bwa0712/bin/bwa or as

module load bwa/0.7.12
bwa

BWA 0.7.5a

BWA 0.7.5a has been installed on Breezy as /global/software/bwa/bwa075a/bin/bwa.  Building the software with the Intel icc compiler failed, so, this version was built with gcc.

BWA 0.7.15

BWA version 0.7.15, compiled as distributed with GCC compilers with default settings can be run as /global/software/bwa/bwa0715/bin/bwa or as

module load bwa/0.7.15
bwa

C - GNU GCC, Intel, Portland Group (PGI) compilers Intel 12.0.4

(icc)

C - GNU GCC, Intel, Portland Group (PGI) compilers GNU 4.1.2

cc is link to gcc (gcc)

C++ - GNU GCC, Intel, Portland Group (PGI) compilers GNU 4.4.4

(g++44)

C++ - GNU GCC, Intel, Portland Group (PGI) compilers GNU 4.1.2

c++ is same as g++ (g++)

Celera Whole-Genome Shotgun Assembler 7.0

/global/software/wgs/wgs-7.0/Linux-amd64/bin

Celera Whole-Genome Shotgun Assembler 6.1

/global/software/wgs/bin

Celera Whole-Genome Shotgun Assembler 8.3rc2

Binaries for version 8.3rc2 of the Celera Whole-Genome Shotgun (wgs) assembler have been installed in /global/software/wgs/wgs-8.3rc2/Linux-amd64/bin .  Use module load python before using the software.

Circos 0.67-7

Set up your environment to use Circos 0.67-7 with

module load circos

Climate Data Operators (CDO) 1.5.8

module load cdo

Clustal Omega 1.2.0

Run the software with

/global/software/clustal/clustalomega120/bin/clustalo

CMake 2.8.11.2

CMake was installed to /global/software/cmake/cmake_2.8.11.2, with the cmake executable as /global/software/cmake/cmake_2.8.11.2/bin/cmake.

CMake 3.3.2

Pre-compiled binaries (cmake, ccmake, cmake-gui, cpack and ctest) for CMake 3.3.2 have been installed in /global/software/cmake/cmake_3.3.2/bin.

Compilers - C, C++ and Fortran Intel 12.0.4

The Intel 12.0.4 compilers are on the default command PATH, but, you can also explicitly initialize your environment to use them with

module load intel/12

Compilers - C, C++ and Fortran GCC 4.4.7

The GCC 4.4.7 compilers are on the default command PATH.

Compilers - C, C++ and Fortran GCC 4.9.0 20140406 (experimental)

Initialize your environment to use the GCC 4.9.0 20140406 (experimental) compilers with

module load gcc/gcc-4.9-20140406-beta

Compilers - C, C++ and Fortran GCC 4.8.4

Initialize your environment to use the GCC 4.8.4 compilers with

module load gcc/4.8.4

Compilers - C, C++ and Fortran GCC 5.1.0

Initialize your environment to use the GCC 5.1.0 compilers with

module load gcc/5.1.0

Coral 1.4
csh Link to tcsh
Cufflinks 2.1.1

Cufflinks 2.1.1 binaries (cufflinks and related utilities including cuffcompare, cuffdiff, cuffmerge, gffread and gtf_to_sam) have been installed in /global/software/cufflinks/cufflinks211.

DIAMOND - sequence aligner 0.7.9

See the Breezy instructions on the main DIAMOND page.

DISCOVAR and DISCOVAR de novo - genome assembly 52488 (2015-04-17)

See the main WestGrid DISCOVAR de novo page for instructions on running the software on Breezy.

Emacs 23.1.1
ExaML/RAxML - Phylogenetic tree analysis ExaML 1.0.12

ExaML 1.0.12 has been installed on Breezy as

/global/software/examl/bin/examl_1.0.12_gcc

ExaML/RAxML - Phylogenetic tree analysis RAxML 7.28a
ExaML/RAxML - Phylogenetic tree analysis RAxML 8.0.19

Various versions (serial, threaded parallel, MPI parallel, with both GCC and Intel compilers) have been installed in /global/software/raxml/raxml809/bin . Test with more than one version to see which gives better performance for your case. For most software, Intel compilers produce faster code, but, we have not tested this for RAxML.

FastQC 0.11.5

You can run FastQC version 0.11.5 on Breezy with:

module load java
/global/software/fastqc/fastqc0115/fastqc --threads $PBS_NUM_PPN <other arguments>

 Note the use of the environment variable PBS_NUM_PPN, to limit the number of threads used to the number of cores assigned to the job.

FastQC 0.10.1

Initialize your environment to use FastQC on Breezy with

module load agalma

fastStructure (population genetics) 2015-03-19

Initialize your environment (bash shell assumed) with:

module load python
export LD_LIBRARY_PATH=/global/software/gsl/gsl115/lib:$LD_LIBRARY_PATH

before running the software with

python /global/software/faststructure/faststructure_20150319/structure.py command_line_arguments

FASTX-Toolkit (sequence pre-processing) 0.0.13

Set up the command PATH and Perl environment with:

module load fastx

Note the version of gnuplot on Breezy (4.0) is older than required for the fastq_quality_boxplot_graph.sh script.

FFTW 3.2.2

Look in /global/software/fftw322.

FFTW 2.15

/global/software/fftw215_gcc

FFTW 3.3.4
/global/software/fftw/fftw-3.3.4-gcc447
/global/software/fftw/fftw-3.3.4-intel12

Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers f95 is link to gfortran
Fortran - GNU GCC, Intel, Portland Group (PGI) and Absoft compilers Intel 12.0.4 (ifort)
GATK 3.2.2

Run GATK through the script gatk.sh, optionally specifying Java memory-related arguments (-Xmx and -Xms) followed by GATK arguments. For example:

/global/software/gatk/gatk322/bin/gatk.sh -Xmx1g -Xms1g --help

GDAL 1.9.2

/global/software/gdal/gdal192

Git 1.8.3

Installed under /global/software/git/git183 (without documentation).

Run the git executable with

/global/software/git/git183/bin/git

GMAP (with GSNAP) - Genomic mapping and alignment 2014-10-22

The executables for the software are in /global/software/gmap/gmap_20141022/bin.  See the file /global/software/gmap/gmap_20141022/README for instructions.

Gnuplot 4.4p0

/global/software/bin/gnuplot

GSL 1.15 -lgsl

/global/software/gsl/gsl115
HDF 4 4.2.8

/global/software/lib

HDF 5 1.8.10

/global/software/lib

HMMER 3.1b2

To use, load the module

module load hmmer/3.1b2

This sets the PATH and MAN variables. 

IDBA-UD 1.1.1

The binary files are in /global/software/idba-ud/idba-ud-1.1.1-gnu/bin/.

To get the bin directory in the path use:

module load idba-ud/1.1.1

 

ImageMagick 6.2.8
IMPUTE (genotype imputation) 2.3.2

See Running IMPUTE2 on Breezy.

IQ-TREE (phylogenetics) 1.3.3

See notes on the main IQ-TREE page.

JAGS 3.3.0 module load jags

/global/software/jags/jags330
Jam N
Java Sun Java SE JRE 1.7.0_67

Set up your environment to use the Java 1.7.0_67 run-time software with

module load java/1.7.0_67

Java Sun Java 1.6.0_16-b01
JELLYFISH 1.1.11

JELLYFISH 1.1.11 is available on Breezy as /global/software/masurca/masurca210/bin/jellyfish but you may prefer to use version 2.1.4, available as /global/software/trinity/trinityrnaseq-2.2.0/trinity-plugins/jellyfish-2.1.4/bin/jellyfish .

JELLYFISH 1.1.6

JELLYFISH 1.1.6 is available on Breezy as /global/software/jellyfish/jellyfish-1.1.6/bin/jellyfish but, more recent versions are available as part of other bioinformatics packages.  For example, /global/software/masurca/masurca210/bin/jellyfish is version 1.1.11 and /global/software/trinity/trinityrnaseq-2.2.0/trinity-plugins/jellyfish-2.1.4/bin/jellyfish is version 2.1.4 .

JELLYFISH 2.1.4

JELLYFISH 2.1.4, installed as part of the Trinity package, is available as /global/software/trinity/trinityrnaseq-2.2.0/trinity-plugins/jellyfish-2.1.4/bin/jellyfish .

Kraken 0.10.4-beta

See /global/software/kraken/kraken_0104b for executables and /global/software/kraken/kraken_std_db_20150109 for a database.

ksh Y (ksh93)
kSNP3 - find SNPs in DNA sequences and estimate phylogenetic trees 3.021

See the main WestGrid kSNP page for running instructions on Breezy.

LAPACK In MKL
MaSuRCA - whole genome assembler 2.1.0

To set up your environment (bash shell example) prior to running MaSuRCA, use:

export PATH=/global/software/perl/perl-5.17.4/bin:$PATH
module load python/2.7.2

The MaSuRCA binaries have been installed in /global/software/masurca/masurca210/bin .

MATLAB Release 2011b (7.13.0)

(U of C only) /global/software/bin/matlab

MATLAB R2013a

Licensed for U of C researchers only, primarily for using the MATLAB compiler, mcc for creating standalone applications.  See full instructions.

Compiler is /global/software/matlab/r2013a/bin/mcc.

MATLAB Compiler Runtime (MCR) 8.1

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2013a of MATLAB.

Installed to /global/software/matlab/mcr/v81

See full instructions for creating standalone applications.

MATLAB Compiler Runtime (MCR) 8.5

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2015a of MATLAB.

Installed in /global/software/matlab/mcr/v85 .

MATLAB Compiler Runtime (MCR) 8.0

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2012b of MATLAB.

Installed to /global/software/matlab/mcr/v80.

See full instructions for creating standalone applications.

MATLAB Compiler Runtime (MCR) 7.17

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2012a of MATLAB.

Installed to /global/software/matlab/mcr/v717.

See full instructions for creating standalone applications.

 

MATLAB Compiler Runtime (MCR) 7.16

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2011b of MATLAB.

Installed to /global/software/matlab/mcr/v716.

See full instructions for creating standalone applications.

MATLAB Compiler Runtime (MCR) 9.0

The MATLAB Compiler Runtime files were installed to /global/software/matlab/mcr/v90 for use with standalone applications compiled with the version of the MATLAB compiler distributed with R2015b of MATLAB.  See the main MATLAB page for details.

MATLAB Compiler Runtime (MCR) 8.4

Version 8.4 of the MATLAB Compiler Runtime files for use with standalone applications compiled with version 5.2 of the MATLAB compiler (distributed with MATLAB R2014b) has been installed to /global/software/matlab/mcr/v84.

MATLAB Compiler Runtime (MCR) 9.1

The MATLAB Compiler Runtime files were installed to /global/software/matlab/mcr/v91 for use with standalone applications compiled with the version of the MATLAB compiler distributed with R2016b of MATLAB.  See the main MATLAB page for details.

MATLAB Compiler Runtime (MCR) 7.14

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2010b of MATLAB.

Installed to /global/software/matlab/mcr/v714.

See full instructions for creating standalone applications.

MATLAB Compiler Runtime (MCR) 7.15

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2011a of MATLAB.

Installed to /global/software/matlab/mcr/v715.

See full instructions for creating standalone applications.

MATLAB Compiler Runtime (MCR) 7.11

For use with standalone applications compiled with the version of the MATLAB compiler distributed with R2009b of MATLAB.

Installed to /global/software/matlab/mcr/v711.

See full instructions for creating standalone applications.

Matplotlib 1.1.0 rc1 Use module load

under python 2.7.2
MEGAHIT 1.1.1

A pre-compiled version of MEGAHIT 1.1.1 has been installed on Breezy in /global/software/megahit/megahit111/bin.  For a list of command-line options, type:

/global/software/megahit/megahit111/bin/megahit -h

Please pay close attention to the -m and -t flags for memory and threads, respectively.

MEGAHIT 0.2.1

MEGAHIT was installed in /global/software/megahit/megahit021/bin at the request of one researcher but never fully tested.  If you want to try it, set up your environment with

module load gcc/gcc-4.9-20140406-beta>
module load python

Please pay close attention to the -m and -t flags for memory and threads, respectively.

Mercurial 2.9

You can run Mercurial as /global/software/mercurial/mercurial29/bin/hg.

MetAMOS 1.1

Prior to running MetAMOS commands, initialize your environment with:

module load python
export PATH=/global/software/metamos/metAMOS_1.1:$PATH

MKL 10.3.x

In default Intel 12 environment

Mothur 1.21.1

Run /global/software/bin/mothur.

nano 1.3.12

pico is just a link to nano

NCAR Graphics and NCL 6.3.0

Initialize your enivronment (NCARG_ROOT and PATH) to use NCAR Command Language 6.3.0 on Breezy with

module load ncl/6.3.0

Please note that this installation provides NCL only. NCAR Graphics does not work due to the Cairo library on Breezy being too old.

NetCDF C 4.2.1.1 Fortran 4.2

/global/software/lib

NetworkX 1.6

module load python

Open Babel 2.3.2

Initialize your environment (bash shell example) to use Open Babel 2.3.2 on Breezy with

export PATH=/global/software/openbabel/openbabel232/bin:$PATH

OpenBUGS 3.2.2 module load openbugs

/global/software/openbugs/openbugs322
PARI/GP - computer algebra system 2.5.5

Start the interactive shell with /global/software/pari/pari255/bin/gp.  See the main PARI page for hints on using the PARI C library.

pdflib 7.05

/global/software/pdf/pdflib_lite_705

Perl 5.10.1

Perl 5.10.1 is the default on Breezy, but, does not have many add-on modules.  See version 5.22.0 for a more full-features version.

Perl 5.22.0

To initialize your environment to use Perl 5.22.0 on Breezy, use:

module load perl/5.22.0

Many modules from BioPerl and other packages have been added to this version of Perl. You can look in /global/software/perl/perl-5.22.0/lib/site_perl/5.22.0 to get an idea of what has been installed.

PHAST (Phylogenic Analysis with Space/Time Models) 1.3

Initialize your environment (PATH and MANPATH) to use PHAST 1.3 on Breezy with

module load phast/1.3

Picard tools 1.106

Look for the .jar files for this Java-based software in /global/software/picard/picard1106.

Picard tools 1.57

/global/software/picard/picard157/picard-tools-1.57

PLINK 1.07

PLINK has been installed for convenience for researchers doing other bioinformatics work on Breezy even though it may not be a good match for the Breezy hardware.  If you are using it extensively and it does not require more than a few GB of memory to run, please consider running it on Hermes instead of Breezy.  To run it on Breezy, use

/global/software/plink/plink107/plink --noweb other_command_line_arguments

Python 2.7.2

Initialize your environment to use Python 2.7.2 on Breezy with

module load python/2.7.2

Among the add-on modules installed for this version of Python are NumPy 1.6.1, SciPy 0.10.0b2, matplotlib 1.1.0, and mpi4py 1.3.1. Use pip freeze to see a longer list.

Qt 4.8.2

/global/software/qt/qt482

R 3.1.0

Initialize your environment before running R with:

module load R/3.1.0_intel

R 2.15.1

/global/software/r/R-2.15.1/bin/R

R 3.2.2

R 3.2.2 and some add-on packages have been built on Breezy using the Intel 16 compiler. Initialize your environment before using R with

module load R/3.2.2_intel

RAPSearch (protein similarity search) 2.23

See the WestGrid RAPSearch page.

Ray 2.3.1

The Ray binary compiled for the default maximum k-mer length of 32 is /global/software/ray/ray231/Ray .  A second version with a maximum k-mer length of 201 is /global/software/ray/ray231_maxkmer201/Ray.  Use the latter version only if necessary as it will use more memory than the one with the more restricted maximum k-mer length.

SAMtools and HTSlib utilities 1.3

See the main WestGrid Samtools page.

SAMtools and HTSlib utilities 0.1.19

Look in /global/software/samtools/samtools0119/bin .

SAMtools and HTSlib utilities 1.2

See the main WestGrid Samtools page.

ScaLAPACK MKL

ScaLAPACK is available through the Math Kernel Library (MKL).

SGA 632929a

The sga binary and some associated Python scripts were installed to /global/software/sga/sga632929a/bin.  Some additional example Python scripts are in /global/software/src/sga/jts-sga-632929a/src/bin, but, would require some editing before use.  Set up the Python environment before running sga with

module load python/2.7.2

sh Link to bash
SHAPEIT (estimation of haplotypes) 2.r790

See Running SHAPEIT on Breezy.

SNPTEST 2.5.2

You can run SNPTEST on Breezy using the absolute path to the binary executable file:

/global/software/snptest/snptest252/snptest_v2.5.2 <program options>

SOAPdenovo SOAPdenovo 2.04

GNU and Intel compiler versions, each for maximum k-mer lengths of 63 and 127  have been installed in /global/software/soapdenovo/204_r240/bin.  See that directory for naming conventions. An older version is in /global/software/soapdenovo/r223/bin.  This includes pregraph_sparse 1.0.3.

SOAPdenovo-Trans 1.02
SPAdes Genome Assembler 3.5.0

See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage.

SPAdes Genome Assembler 3.0.0

See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage.

SPAdes Genome Assembler 3.6.2

See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage.

SPAdes Genome Assembler 3.1.1

See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage.

SPAdes Genome Assembler 3.7.1

See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage.

SPAdes Genome Assembler 3.6.1

See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage.

SPAdes Genome Assembler 3.9.1

See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage.

SPAdes Genome Assembler 3.10.1

See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage.

SPAdes Genome Assembler 3.1.0

See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage.

Stacks 1.46

See the main WestGrid Stacks page for brief usage notes.

Stacks 1.29

For a bash shell user, add the following to your batch job script before running Stacks:

export PATH=/global/software/stacks/stacks129/bin:$PATH
module load perl_modules
module load gcc/gcc-4.9-20140406-beta

Stacks 1.41

See the main WestGrid Stacks page for brief usage notes.

Stacks 1.42

See the main WestGrid Stacks page for brief usage notes.

Stacks 1.34

For a bash shell user, add the following to your batch job script before running Stacks:

export PATH=/global/software/stacks/stacks134/bin:$PATH
module load perl_modules
module load gcc/gcc-4.9-20140406-beta

Stacks 1.35

For a bash shell user, add the following to your batch job script before running Stacks:

export PATH=/global/software/stacks/stacks135/bin:$PATH
module load perl_modules
module load gcc/gcc-4.9-20140406-beta

Stacks 1.21

For a bash shell user, add the following to your batch job script before running Stacks:

export PATH=/global/software/stacks/stacks121/bin:$PATH
module load perl_modules
module load gcc/gcc-4.9-20140406-beta

Stacks 1.44

See the main WestGrid Stacks page for brief usage notes.

Stacks 1.19

For a bash shell user, add the following to your batch job script before running Stacks:

export PATH=/global/software/stacks/stacks119/bin:$PATH
module load perl_modules
module load gcc/gcc-4.9-20140406-beta

Stacks 1.24

For a bash shell user, add the following to your batch job script before running Stacks:

export PATH=/global/software/stacks/stacks124/bin:$PATH
module load perl_modules
module load gcc/gcc-4.9-20140406-beta

Stacks 1.31

For a bash shell user, add the following to your batch job script before running Stacks:

export PATH=/global/software/stacks/stacks131/bin:$PATH
module load perl_modules
module load gcc/gcc-4.9-20140406-beta

Stacks 1.09

Initialize your environment with

export PATH=/global/software/stacks/stacks109/bin:$PATH
module load perl_modules

Stacks 1.27

For a bash shell user, add the following to your batch job script before running Stacks:

export PATH=/global/software/stacks/stacks127/bin:$PATH
module load perl_modules
module load gcc/gcc-4.9-20140406-beta

Subversion 1.6.11
Szip 2.1

/global/software/lib

Tablet - Next Generation Sequence Assembly Visualization 1.13.07.31

Start Tablet with:

/global/software/tablet/tablet130731/tablet

tcsh NA
TopHat 2.0.10

TopHat has been installed in /global/software/tophat/tophat_2.0.10/bin.  However, TopHat calls associated software, including Bowtie 2, SAM tools and Python. See the main WestGrid TopHat page for a sample script that was used in preliminary testing.

Trimmomatic 0.36

See instructions on the WestGrid Trimmomatic page.

Trinity 2.2.0

Set up your enivronment to use Trinity 2.2.0 with

module load trinity/2.2.0

Trinity 2.0.2

Trinity has been installed on Breezy in /global/software/trinity/trinityrnaseq-2.0.2, but, not tested.  Initialize your environment before calling Trinity commands with (bash shell example):

module load gcc/gcc-4.9-20140406-beta
module load perl/5.22.0
export PATH=/global/software/trinity/trinityrnaseq-2.0.2:$PATH

It is expected that additional PATH modifications will be necessary depending on what components of Trinity are used, such as:

module load java/1.7.0_67
module load samtools/1.2
export PATH=/global/software/bowtie/bowtie-1.0.0:$PATH

An alternative approach would be to use a pipeline called Agalma. It includes Trinity. However, as of this writing (2015-11-12), Agalma has not been documented on the WestGrid web site. To initialize your environment to use Trinity with Agalma, use

module load agalma

Trinity 2.4.0

Trinity 2.4.0 has been installed on Breezy as part of the Bioconda suite. Set up your enivronment to use this version of Trinity with

module load trinity/bioconda_2.4.0

tvmet 1.7.2

/global/software/tvmet/tvmet172

VCFtools 0.1.12b

Initialize your environment (example shown for bash shell users) with:

export PERL5LIB=/global/software/vcftools/vcftools_0.1.12b/perl:$PERL5LIB
export PATH=/global/software/htslib/htslib121/bin:$PATH
export PATH=/global/software/vcftools/vcftools_0.1.12b/bin:$PATH

Velvet 1.2.10

Velvet binaries (both serial and OpenMP parallel versions) have been installed to /global/software/velvet/velvet1210/bin.  Additional binaries, velvetg_maxkmer100_openmp and velveth_maxkmer100_openmp, were built with the make arguments 'MAXKMERLENGTH=100' 'BIGASSEMBLY=1' 'LONGSEQUENCES=1' 'OPENMP=1' to allow handling of larger cases. Similarly velvetg_maxkmer127_openmp and velveth_maxkmer127_openmp, were built with the make arguments 'MAXKMERLENGTH=127' 'BIGASSEMBLY=1' 'LONGSEQUENCES=1' 'OPENMP=1'.

A sample OpenMP job is shown on the Running Jobs page.

Velvet 1.1.06

See /global/software/velvet/velvet1106/bin.

Vim 7.0.237
WHAM/WHAMG - WHole-genome Alignment Metrics 1.7.0

To run version 1.7.0 on Breezy, see the main WestGrid WHAM/WHAMG page.