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 1.5.1 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.

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

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 1.8.2 with a version of the BEAGLE 2.1.2 libraries compiled with Intel compilers, use

module load beast/1.8.2

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.

linked from /global/software/ncbi-blast

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

Initialize your environment to use BMTagger on Breezy with

module load bmtagger

(gcc) /global/software/boost/gcc

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

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 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

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

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.

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.

/global/software/fftw215_gcc

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 1.1.6 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 .

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 .

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.

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 .

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.

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.

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.

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.

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.

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

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

See the WestGrid RAPSearch page.

See the main WestGrid Samtools page.

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/stacks129/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/stacks135/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/stacks124/bin:$PATH
module load perl_modules
module load gcc/gcc-4.9-20140406-beta

Initialize your environment with

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

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.

Set up your enivronment to use Trinity 2.2.0 with

module load trinity/2.2.0

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

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

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