module load application/ABySS/1.5.2

module load application/ABySS/1.3.2

module load application/allpathslg/43500

module load application/augustus/2.5.5

module load application/bcftools/1.3   

module load application/blast/2.2.31

module load application/blast/2.6.0

module load library/boost/1_49_0

module load library/boost/1_60_0

module load application/bowtie/1.0.0

module load application/bowtie2/2.2.2

module load application/bwa/0.7.12

(icc, module load compiler/ intel/12.1, loaded by default)

(gcc - module load compiler/gcc/4.5.0)

module load compiler/gcc/4.8.3

(pgCC - module load compiler/pgi/13.9)

pgCC
module load compiler/pgi/12.10

(g++)

module load application/cd-hit/v4.6.1-2012-08-27

module load application/wgs/7.0

module load application /chaste /release_3.1

The GCC 4.3.4 compilers are on the default command PATH.

Initialize your environment to use the GCC 4.8.3 compilers with

module load compiler/gcc/4.8.3

The Intel 12.1.5 compilers are on the default command PATH, but, you can also explicitly initialize your environment to use them with

module load compiler/intel/12.1

Initialize your environment to use the Portland Group 13.9-0 compilers with

module load compiler/pgi/13.9

module load application/cpmd/v3_15_3

Set up your environment to use Cufflinks 2.2.1 with:

module load application/cufflinks/2.2.1

module load application/estscan/2.1

module load application /dolfin/1.1.0

(gfortran - module load compiler/gcc/4.5.0)

module load compiler/gcc/4.8.3

ifort, module load compiler/ intel/12.1, loaded by default

module load application/freebayes/1.0.2

module load application/gatk/3.5

gatk.sh -Xmx1g -Xms1g --help

For U of A researchers only.  Initialize your environment with:

module load uofa/gaussian/g09-d1

See general gedit usage notes.

module load application/gmap/2017-04-13

module load library/gsl/1.16

module load application/hisat2/2.0.4

module load application/homer/4.8.3

Initialize your environment to use IQ-TREE 1.3.1 on Hungabee with:

module load application/iq_tree/1.3.1

module load application/julia/0.5.0

module load application/kraken/0.10.6-beta 

minikraken database in /global/software/kraken/db/minikraken_20141208

U of A only

module load uofa/Mathematica/8.0

module load application/megahit/1.1.1

module load application/mothur/1.39.5

module load application /nektar++/3.2.0

module load application/python/2.7.3

module load application/parallel/20150922

module load application/petsc/3.4.5

Set up your environment with:

module load application/picard-tools/1.98

This sets various aliases. To see them, type

module show application/picard-tools/1.98

module load application/picard-tools/2.9.0

module load application/python/3.4.2

(default)

module load application/R/3.1.2

Set up your environment to use R 3.2.5 on Hungabee with

module load application/R/3.2.5

module load application/R/3.3.2

module load application/relion/1.3

module load application/rmblastn/2.2.28

module load application/rsem/1.2.21

module load application/samtools/1.4

module load application/samtools/1.3

module load application/snap/2013-02-16

To use SPAdes 3.10.1 on Hungabee, initialize your environment with

module load application/SPAdes/3.10.1

module load application/SPAdes/3.6.1

Either one of

module load application/structure/2.3.4

or

application/structure-frontend/2.3.4

module load application/swig/2.0.9

module load application/tophat/2.0.14

module load application/Trans-ABySS/1.5.5

module load application/transdecoder/3.0.1

See instructions on the WestGrid Trimmomatic page.

Set up your enivronment to use Trinity 2.2.0 with

module load application/trinity/2.2.0

module load application/trinity/2.3.2

module load application/trinity/2.0.6

module load application/trinity/r2012-10-05

module load application/trinotate/2.0.2

module load  application/trinotate/3.0.1

Initialize your environment with

module load application/vcftools/0.1.10

Note, the VCFtools Perl utilities were not installed.

module load application/vtk/5.10.1