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.

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

/global/software/allpathslg/41301/bin

See the main WestGrid BCFtools page.

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

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

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 .

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

Installed in /global/software/blast-2.2.18 .

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

Initialize your environment to use BMTagger on Breezy with

module load bmtagger

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

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

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 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

cc is link to gcc (gcc)

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

/global/software/wgs/bin

Set up your environment to use Circos 0.67-7 with

module load circos

Run the software with

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

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.

The GCC 4.4.7 compilers are on the default command PATH.

Initialize your environment to use the GCC 4.8.4 compilers with

module load gcc/4.8.4

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.

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

ExaML 1.0.12 has been installed on Breezy as

Initialize your environment to use FastQC on Breezy with

module load agalma

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.

Look in /global/software/fftw322.

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

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

Run the git executable with

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

/global/software/bin/gnuplot

/global/software/lib

To use, load the module

module load hmmer/3.1b2

This sets the PATH and MAN variables. 

See notes on the main IQ-TREE page.

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 .

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

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

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 .

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

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.

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.

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.

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 .

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.

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.

Prior to running MetAMOS commands, initialize your environment with:

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

Run /global/software/bin/mothur.

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.

module load python

/global/software/pdf/pdflib_lite_705

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.

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

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

/global/software/qt/qt482

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

See the WestGrid RAPSearch page.

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

See the main WestGrid Samtools page.

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

See Running SHAPEIT on Breezy.

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.

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

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

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

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

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

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

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

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

See the main WestGrid Stacks page for brief usage notes.

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

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

Start Tablet with:

/global/software/tablet/tablet130731/tablet

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.

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 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

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 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.