bioinformatics software on gowonda

Owned by Indy Siva
Last updated: Jul 24, 2018
3 min read

These are some of the bioinformatcs software installed on gowonda.

plinkseq

module load bioinformatics/plinkseq/0.10

 

plink

module load bioinformatics/plink/1.90b

 

 

 

 

picard:

module load bioinformatics/picard/1.68 
 module display bioinformatics/picard/1.68
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/picard/1.68:

module-whatis    adds picard directories to PATH etc.
prepend-path     CLASSPATH /sw/bioinformatics/picard-tools/1.68/jar
-------------------------------------------------------------------

ABySS:

module load bioinformatics/abyss/1.3.3-openmpi
module display bioinformatics/abyss/1.3.3-openmpi
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/abyss/1.3.3-openmpi:

module-whatis    adds abyss directories to PATH etc.
Remember to add the following to your ~/.bashrc or ABYSS will not work between nodes

export ABYSS_LOADED_IN_SHELL=1
export OPENMPI_LOADED_IN_SHELL=1
module load bioinformatics/abyss/1.3.3-openmpi
setenv           OPENMPI_LOADED_IN_SHELL 1
prepend-path     PATH /sw/bioinformatics/abyss/1.3.3/openmpi/bin
prepend-path     MANPATH /sw/bioinformatics/abyss/1.3.3/openmpi/share/man
module           load boost/mpi/1.4.8-openmpi
module           load mpi/openMPI/1.4.3-gnu
module           load bioinformatics/sparsehash/2.0.2
-------------------------------------------------------------------

sparsehash

module load bioinformatics/sparsehash/2.0.2 
 module display bioinformatics/sparsehash/2.0.2
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/sparsehash/2.0.2:

module-whatis    Name: sparseharsh
module-whatis    Version: 2.0.2
module-whatis    Category: Library,AbySS
module-whatis    url: http://code.google.com/p/sparsehash/
module-whatis    Description: An extremely memory-efficient hash_map implementation
prepend-path     LD_LIBRARY_PATH /sw/bioinformatics/sparsehash/2.0.2/lib/pkgconfig
prepend-path     INCLUDE /sw/bioinformatics/sparsehash/2.0.2/include
prepend-path     INCLUDE /sw/bioinformatics/sparsehash/2.0.2/include/sparsehash
prepend-path     INCLUDE /sw/bioinformatics/sparsehash/2.0.2/include/sparsehash/internal
prepend-path     INCLUDE /sw/bioinformatics/sparsehash/2.0.2/include/google
prepend-path     INCLUDE /sw/bioinformatics/sparsehash/2.0.2/include/google/sparsehash
prepend-path     LDFLAGS -L/sw/bioinformatics/sparsehash/2.0.2/lib/pkgconfig
prepend-path     CPPFLAGS -I/sw/bioinformatics/sparsehash/2.0.2/include/sparsehash
prepend-path     CPPFLAGS -I/sw/bioinformatics/sparsehash/2.0.2/include/sparsehash/internal
prepend-path     CPPFLAGS -I/sw/bioinformatics/sparsehash/2.0.2/include/google
prepend-path     CPPFLAGS -I/sw/bioinformatics/sparsehash/2.0.2/include/sparsehash/internal
-------------------------------------------------------------------

Velvet

module load bioinformatics/velvet/1.2.03
module load bioinformatics/velvet/1.2.03-omp
module load bioinformatics/velvet/1.2.03-max101
module load bioinformatics/velvet/1.2.03-color
module load bioinformatics/velvet/1.2.03-category57
 module display bioinformatics/velvet/1.2.03-max101
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/velvet/1.2.03-max101:

module-whatis    adds velvet 1.2.03 directories to PATH etc.
prepend-path     PATH /sw/bioinformatics/velvet/1.2.03-MAXKMERLENGTH101/bin
Velvet compiled with MAXKMERLENGTH=101
module           load bioperl
module           load library/zlib/1.2.5
-------------------------------------------------------------------

fastqc

module load bioinformatics/fastqc/0.10.1
  module display bioinformatics/fastqc/0.10.1
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/fastqc/0.10.1:

prepend-path     PATH /sw/bioinformatics/FastQC/0.10.1/
-------------------------------------------------------------------

cutadapt

http://confluence.rcs.griffith.edu.au:8080/display/GHPC/cutadapt

module load python/2.7.1-shared

FASTX-Toolkit

 module load bioinformatics/FASTX-Toolkit 
 module display bioinformatics/FASTX-Toolkit
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/FASTX-Toolkit/0.0.13:

module-whatis    adds FASTX-Toolkit directories to PATH etc.
prepend-path     PATH /sw/bioinformatics/FASTX-Toolkit/0.0.13/bin
prepend-path     PATH /sw/bioinformatics/FASTX-Toolkit/0.0.13/share/aclocal
-------------------------------------------------------------------

VarScan

module load bioinformatics/VarScan/2.2.11
 module display bioinformatics/VarScan/2.2.11
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/VarScan/2.2.11:

module-whatis    adds VarScan bits
prepend-path     PATH /sw/bioinformatics/VarScan/2.2.11
prepend-path     CLASSPATH /sw/bioinformatics/VarScan/2.2.11
-------------------------------------------------------------------

raxml:

module load bioinformatics/raxml/7.2.8a-mpi
 module display bioinformatics/raxml/7.2.8a-mpi
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/raxml/7.2.8a-mpi:

module-whatis    Sets the environment for RAxML mpi
module           load mpi/openMPI/1.4.3-gnu
conflict         bioinformatics/raxml/7.2.8a-ompi
conflict         bioinformatics/raxml/7.2.8a-serial
prepend-path     PATH /sw/bioinformatics/raxml/7.2.8a/mpi/ompi
prepend-path     PATH /sw/bioinformatics/raxml/7.2.8a/mpi/ompi/bin
set-alias        raxml raxmlHPC-MPI
-------------------------------------------------------------------

Sample pbs script to run an mpi job

#! /bin/bash

#PBS -N nimr_raxml
#PBS -m e
#PBS -M <YourEmail>@griffith.edu.au
#PBS -q mpi
#PBS -l select=1:ncpus=2:mem=2g:mpiprocs=2
#PBS -l walltime=00:10:00

source $HOME/.bashrc

module load bioinformatics/raxml/7.2.8a-mpi

NODES=1
NPROCS=2

/sw/openMPI/1.4.3-gnu/bin/mpirun -np $NPROCS raxmlHPC-MPI -f a -x 12345 -p 12345 -# 1000 -m GTRGAMMA -s /scratch/s111111/RAxML/120524_NIMR_RAxML/110302_GenBank_UK_NIMR_seqs_indexed.phy -w /scratch/s111111//RAxML/120524_NIMR_RAxML/ -n 120524

mrbayes:

module load bioinformatics/mrbayes/3.2.1-openmpi-cuda-gnu
OR
 module load bioinformatics/mrbayes/3.2.1-openmpi-gnu
OR
 module load bioinformatics/mrbayes/3.2.1-serial-gnu
OR
 module load bioinformatics/mrbayes/3.2.1-serial-intel
module display bioinformatics/mrbayes/3.2.1-openmpi-gnu
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/mrbayes/3.2.1-openmpi-gnu:

module-whatis    adds MrBayes bits
prepend-path     PATH /sw/mrbayes/3.2.1/openmpi-gnu
module           load mpi/openMPI/1.4.3-gnu
module           load library/beagle/beagle-lib-nocuda
conflict         library/beagle/beagle-lib-cuda
conflict         library/beagle/3.2.1-openmpi-cuda-gnu
conflict         library/beagle/3.2.1-openmpi-gnu~
conflict         bioinformatics/mrbayes/3.2.1-serial-gnu
conflict         bioinformatics/mrbayes/3.2.1-serial-intel
-------------------------------------------------------------------

VEGAS

  module load bioinformatics/vegas/0.7.30
 module display bioinformatics/vegas/0.7.30
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/vegas/0.7.30:

module           load bioinformatics/plink/1.07
module           load R/2.13.0
prepend-path     PATH /sw/bioinformatics/VEGAS
-------------------------------------------------------------------

magenta

  module load bioinformatics/magenta/2  
module display bioinformatics/magenta/2
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/magenta/2:

prepend-path     PATH /sw/bioinformatics/magenta/vs2
-------------------------------------------------------------------

bwa

module load bioinformatics/bwa/0.5.9rc1
 module display bioinformatics/bwa/0.5.9rc1
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/bwa/0.5.9rc1:

module-whatis    adds bin directory to PATH etc.
prepend-path     PATH /sw/BWA/0.5.9rc1/bin
-------------------------------------------------------------------

vcftools

module load bioinformatics/vcftools/0.1.9
module display bioinformatics/vcftools/0.1.9
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/vcftools/0.1.9:

module-whatis    adds vcftools directories to PATH etc.
module           load perl/5.15.8
prepend-path     PATH /sw/bioinformatics/vcftools/0.1.9/bin
prepend-path     PERL5LIB /sw/bioinformatics/vcftools/0.1.9/lib
-------------------------------------------------------------------

bedtools

 module load bioinformatics/bedtools/2.16.2

 module display bioinformatics/bedtools/2.16.2
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/bedtools/2.16.2:

prepend-path     PATH /sw/bioinformatics/BEDTools/2.16.2/bin
-------------------------------------------------------------------

bfast

module load bioinformatics/bfast/0.7.0a

 module display bioinformatics/bfast/0.7.0a
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/bfast/0.7.0a:

module-whatis    adds BFAST directories to PATH etc.
prepend-path     PATH /sw/bioinformatics/bfast/0.7.0a/bin
-------------------------------------------------------------------

repeatmasker

module load bioinformatics/repeatmasker/3.3.0-p1

 module display bioinformatics/repeatmasker/3.3.0-p1
-------------------------------------------------------------------
/sw/com/modulefiles/bioinformatics/repeatmasker/3.3.0-p1:

module-whatis    adds repeatmasker directories to PATH etc.
module           load bioinformatics/rmblast/2.2.23
module           load bioinformatics/trf/4.04
prepend-path     PATH /sw/bioinformatics/repeatmasker/3.3.0-p1
-------------------------------------------------------------------

libgtextutils

To be done

 
 

ParsInsert

module  load    bioinformatics/ParsInsert/1.04

userach

 module load bioinformatics/usearch/5.2.32

rtax

module load bioinformatics/rtax/0.983

pplacer

module load bioinformatics/pplacer/1.1

 

impute2

module load bioinformatics/impute2/2.3.2static

 

shapeit

module load bioinformatics/shapeit/2.r837.static

 

admixture

module load bioinformatics/admixture/1.3.0

 

rsem

module load bioinformatics/rsem/1.3.1 (gowonda)
module load bioinformatics/rsem/1.3.1-gu (awoonga)