You are here
Breezy
Software Available on Breezy
Title | Version | Usage Notes | |
---|---|---|---|
64-bit Linux CentOS | 5.7 2.6.18...el5 #1 SMP | ||
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. |
|
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:$PATH
|
|
ALLPATHS-LG | Revision 52488 |
Initialize your environment to use ALLPATHS-LG revision 52488 on Breezy with (bash shell example): module load gcc/gcc-4.9-20140406-beta |
|
ALLPATHS-LG | Revision 41301 |
/global/software/allpathslg/41301/bin |
|
bash (default) | 3.2.25 or later | ||
BCFtools (VCF/BCF file manipulation) | 1.3 |
See the main WestGrid BCFtools page. |
|
BCFtools (VCF/BCF file manipulation) | 1.2 |
See the main WestGrid BCFtools page. |
|
bcl2fastq - Illumina BCL to FASTQ conversion utility | 2.16 |
See the main WestGrid page for bcl2fastq for instructions on running the software on Breezy. |
|
BEAGLE (beagle-lib) | 2.1.2 |
Include files and libraries compiled by Intel 12.0 compilers with OpenMP support have been installed under /global/software/beagle/beagle212. A similar installation compiled with GCC compilers is in /global/software/beagle/beagle212_gcc. To use the latter, initialize your environment with module load gcc/gcc-4.9-20140406-beta |
|
BEAST | 2.4.1 |
To set up your environment to run BEAST 2.4.1 with a version of the BEAGLE 2.1.2 libraries compiled with GNU GCC compilers, use module load beast/2.4.1 |
|
BEAST | 1.8.2 |
To set up your environment to run BEAST 1.8.2 with a version of the BEAGLE 2.1.2 libraries compiled with Intel compilers, use module load beast/1.8.2 |
|
BEDTools | 2.17.0 |
Initialize your environment to use BEDTools 2.17.0 on Breezy with export PATH=/global/software/bedtools/bedtools2170/bin:$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 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+ 2.2.30+ |
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. |
|
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 |
|
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 | 1.48.0 |
(gcc) /global/software/boost/gcc |
|
Boost | 1.58.0 |
Compiled with GCC. The library is in /global/software/boost/boost-1.58.0-gnu/ .
|
|
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 | 0.7.5a |
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 | 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 |
|
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 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. |
|
ExaML/RAxML - Phylogenetic tree analysis | RAxML 7.28a | ||
FastQC | 0.11.5 |
You can run FastQC version 0.11.5 on Breezy with: module load java 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 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 | 3.3.4 |
/global/software/fftw/fftw-3.3.4-gcc447 /global/software/fftw/fftw-3.3.4-intel12 |
|
FFTW | 3.2.2 |
Look in /global/software/fftw322. |
|
FFTW | 2.15 |
/global/software/fftw215_gcc |
|
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 | ||
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 | 1.1.6 |
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 | 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 | 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 The MaSuRCA binaries have been installed in /global/software/masurca/masurca210/bin . |
|
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 | Release 2011b (7.13.0) |
(U of C only) /global/software/bin/matlab |
|
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) | 7.16 |
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) | 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) | 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) | 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. |
|
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) | 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) | 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) | 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) | 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. |
|
Matplotlib | 1.1.0 rc1 |
Use module load under python 2.7.2 |
|
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> Please pay close attention to the -m and -t flags for memory and threads, respectively. |
|
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. |
|
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 |
|
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 | 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 |
|
R | 2.15.1 |
/global/software/r/R-2.15.1/bin/R |
|
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 | 0.1.19 |
Look in /global/software/samtools/samtools0119/bin . |
|
SAMtools and HTSlib utilities | 1.2 |
See the main WestGrid Samtools page. |
|
SAMtools and HTSlib utilities | 1.3 |
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 | ||
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 | 3.6.2 |
See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage. |
|
SPAdes Genome Assembler | 3.6.1 |
See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage. |
|
SPAdes Genome Assembler | 3.5.0 |
See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage. |
|
SPAdes Genome Assembler | 3.7.1 |
See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage. |
|
SPAdes Genome Assembler | 3.1.0 |
See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage. |
|
SPAdes Genome Assembler | 3.9.1 |
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 | 3.1.1 |
See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage. |
|
SPAdes Genome Assembler | 3.0.0 |
See the Breezy SPAdes running instructions for the installation location and hints about controlling the number of threads and memory usage. |
|
Stacks | 1.42 |
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:$PATH |
|
Stacks | 1.41 |
See the main WestGrid Stacks page for brief usage notes. |
|
Stacks | 1.35 |
For a bash shell user, add the following to your batch job script before running Stacks: export PATH=/global/software/stacks/stacks135/bin:$PATH |
|
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:$PATH |
|
Stacks | 1.31 |
For a bash shell user, add the following to your batch job script before running Stacks: export PATH=/global/software/stacks/stacks131/bin:$PATH |
|
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:$PATH |
|
Stacks | 1.44 |
See the main WestGrid Stacks page for brief usage notes. |
|
Stacks | 1.09 |
Initialize your environment with export PATH=/global/software/stacks/stacks109/bin:$PATH |
|
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:$PATH |
|
Stacks | 1.46 |
See the main WestGrid Stacks page for brief usage notes. |
|
Stacks | 1.34 |
For a bash shell user, add the following to your batch job script before running Stacks: export PATH=/global/software/stacks/stacks134/bin:$PATH |
|
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:$PATH |
|
Subversion | 1.6.11 | ||
Szip | 2.1 |
/global/software/lib |
|
Tablet - Next Generation Sequence Assembly Visualization | 1.13.07.31 |
Start Tablet with: /global/software/tablet/tablet130731/tablet |
|
tcsh | NA | ||
TopHat | 2.0.10 |
TopHat has been installed in /global/software/tophat/tophat_2.0.10/bin. However, TopHat calls associated software, including Bowtie 2, SAM tools and Python. See the main WestGrid TopHat page for a sample script that was used in preliminary testing. |
|
Trimmomatic | 0.36 |
See instructions on the WestGrid Trimmomatic page. |
|
Trinity | 2.0.2 |
Trinity has been installed on Breezy in /global/software/trinity/trinityrnaseq-2.0.2, but, not tested. Initialize your environment before calling Trinity commands with (bash shell example): module load gcc/gcc-4.9-20140406-beta It is expected that additional PATH modifications will be necessary depending on what components of Trinity are used, such as: module load java/1.7.0_67 An alternative approach would be to use a pipeline called Agalma. It includes Trinity. However, as of this writing (2015-11-12), Agalma has not been documented on the WestGrid web site. To initialize your environment to use Trinity with Agalma, use module load agalma |
|
Trinity | 2.2.0 |
Set up your enivronment to use Trinity 2.2.0 with module load trinity/2.2.0 |
|
Trinity | 2.4.0 |
Trinity 2.4.0 has been installed on Breezy as part of the Bioconda suite. Set up your enivronment to use this version of Trinity with module load trinity/bioconda_2.4.0 |
|
tvmet | 1.7.2 |
/global/software/tvmet/tvmet172 |
|
VCFtools | 0.1.12b |
Initialize your environment (example shown for bash shell users) with: export PERL5LIB=/global/software/vcftools/vcftools_0.1.12b/perl:$PERL5LIB |
|
Velvet | 1.1.06 |
See /global/software/velvet/velvet1106/bin. |
|
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. |
|
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. |