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updated module av overview authored by van Vliet's avatar van Vliet
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......@@ -383,45 +383,59 @@ Here below are some useful commands and examples:
module av
----------------------------------------------------------------------------------------------- /share/modulefiles ------------------------------------------------------------------------------------------------
container/singularity/3.5.3/gcc.8.3.1 library/cudnn/9.2/cudnn neuroImaging/fsl/5.0.11
cryogenicEM/chimera/1.14/gcc-8.3.1 library/fltk/1.3.5/gcc-8.3.1 neuroImaging/fsl/5.0.9
cryogenicEM/ctffind/4.1.13/gcc-8.3.1 library/ftgl/2.1.3/gcc-8.3.1 neuroImaging/fsl/6.0.0
cryogenicEM/eman2/2.31 library/gdal/2.4.4/gcc-8.3.1 neuroImaging/fsl/6.0.1
cryogenicEM/gctf/1.06 library/gdal/3.0.4/gcc-8.3.1 neuroImaging/fsl/6.0.2
cryogenicEM/imod/4.9.12 library/htslib/1.10.2/gcc-8.3.1 neuroImaging/fsl/6.0.3
cryogenicEM/motioncor2/1.31 library/java/OpenJDK-11.0.2 neuroImaging/fsl/fix/1.06.12
cryogenicEM/relion/3.0.8/gcc-8.3.1 library/java/OpenJDK-12.0.2 neuroImaging/mrtrix/3.0.0/gcc-8.3.1
cryogenicEM/relion/3.1-beta/gcc-8.3.1 library/java/OpenJDK-13.0.2 pharmaceutical/PsN/4.9.0
cryogenicEM/resmap/1.1.4 library/java/OpenJDK-14.0.1 (D) pharmaceutical/nonmem/7.4.4/gcc-8.3.1
genomics/hmmer/openmpi-3.1.5/3.3/gcc-8.3.1 library/lapack/3.9.0/gcc-8.3.1 pharmaceutical/pirana/2.9.7
genomics/ngs/bcftools/1.10.2/gcc-8.3.1 library/mpi/mpich/3.3.2/gcc-8.3.1 pharmaceutical/pirana/2.9.8 (D)
genomics/ngs/bcl2fastq/2.20.0 library/mpi/openmpi/3.1.5/gcc-8.3.1 statistical/MATLAB/R2016b
genomics/ngs/bedtools2/2.29.1/gcc-8.3.1 library/mpi/openmpi/4.0.2/gcc-8.3.1 statistical/MATLAB/R2018b
genomics/ngs/bwa/0.7.17/gcc-8.3.1 library/mpi/openmpi/4.0.3/gcc-8.3.1 (L) statistical/MATLAB/R2019b
genomics/ngs/samtools/1.10/gcc-8.3.1 library/pmi/openpmix/2.2.3/gcc-8.3.1 statistical/MATLAB/v93/MCR2017b
genomics/ngs/shapeit4/4.1.3/gcc-8.3.1 library/pmi/openpmix/3.1.4/gcc-8.3.1 statistical/MATLAB/v97/MCR2019b
genomics/ngs/vcftools/0.1.16/gcc-8.3.1 library/sparsehash/2.0.3/gcc-8.3.1 statistical/R/3.4.4/gcc.8.3.1
graphics/gnuplot/5.2.8/gcc-8.3.1 library/wxwidgets/3.1.3/gcc-8.3.1 statistical/R/3.5.3/gcc.8.3.1
graphics/graphicsmagick/1.3.35/gcc-8.3.1 mathematical/octave/5.2.0/gcc-8.3.1 statistical/R/3.6.2/gcc.8.3.1
gwas/depict/1.rel194 mathematical/octave/libs/SuiteSparse/5.7.2/gcc-8.3.1 statistical/R/4.0.2/gcc.8.3.1
gwas/plink/1.07 mathematical/octave/libs/arpack/3.7.0/gcc-8.3.1 statistical/RStudio/1.2.5033/gcc-8.3.1
gwas/plink/1.90b6.17 mathematical/octave/libs/gl2ps/1.4.2/gcc-8.3.1 system/go/1.13.7
gwas/plink/1.90p mathematical/octave/libs/glpk/4.65/gcc-8.3.1 system/hwloc/1.11.13/gcc-8.3.1
gwas/plink/2.00a3LM (D) mathematical/octave/libs/qhull/8.0.0/gcc-8.3.1 system/hwloc/2.1.0/gcc-8.3.1
library/blas/0.3.10/gcc-8.3.1 mathematical/octave/libs/qrupdate/1.1.2/gcc-8.3.1 system/knem/1.1.3/gcc-8.3.1
library/boost/1.72.0/gcc-8.3.1 mathematical/octave/libs/sundials/5.3.0/gcc-8.3.1 system/python/2.7.17
library/cuda/10.0/gcc.8.3.1 medicalImaging/minc-stuffs/0.1.25/gcc-8.3.1 system/python/3.7.6
library/cuda/10.1/gcc.8.3.1 medicalImaging/minc-toolkit-v2/1.9.17/gcc-8.3.1 system/python/3.8.1 (D)
library/cuda/10.2/gcc.8.3.1 medicalImaging/minc2-simple/2.2.30/gcc-8.3.1 system/qt/5.14.2/gcc-8.3.1
library/cuda/7.5/gcc.8.3.1 medicalImaging/pydpiper/2.0.9 system/swi-prolog/8.2.0
library/cuda/8.0/gcc.8.3.1 medicalImaging/pydpiper/2.0.14 (D) tools/biomake/0.1.5
library/cuda/9.0/gcc.8.3.1 medicalImaging/pyminc/0.52 tools/cmake/3.11.4
library/cuda/9.1/gcc.8.3.1 neuroImaging/Elastix/5.0.0/gcc-7.4.0 tools/gitlab-runner/12.8.0
library/cuda/9.2/gcc.8.3.1 neuroImaging/FSLeyes/0.32.3 tools/jupyterlab/4.3.1
library/cudnn/10.0/cudnn neuroImaging/SimpleElastix/0.10.0/python3.6.8 tools/luarocks/3.3.1/gcc-8.3.1
library/cudnn/10.1/cudnn neuroImaging/freesurfer/stable-pub-v6.0.0.patched tools/miniconda/python2.7/4.7.12
library/cudnn/10.2/cudnn neuroImaging/freesurfer/7.1.0 (D) tools/miniconda/python3.7/4.7.12
library/cudnn/9.0/cudnn neuroImaging/fsl/5.0.10 tools/websockify/0.9.0
bioimage/QuPath/0.2.3 library/cuda/11.0/gcc.8.3.1 neuroImaging/SimpleElastix/0.10.0/python3.6.8
bioinformatics/tools/SNP/flashpca/2.1/gcc-8.3.1 library/cuda/11.1/gcc.8.3.1 neuroImaging/freesurfer/stable-pub-v6.0.0.patched
bioinformatics/tools/assembly-stats/1.0.1/gcc-8.3.1 library/cuda/11.2/gcc.8.3.1 neuroImaging/freesurfer/7.1.0 (D)
bioinformatics/tools/ncbi/sra/2.10.8 library/cuda/7.5/gcc.8.3.1 neuroImaging/fsl/5.0.10
container/singularity/3.5.3/gcc.8.3.1 library/cuda/8.0/gcc.8.3.1 neuroImaging/fsl/5.0.11
container/singularity/3.6.1/gcc.8.3.1 library/cuda/9.0/gcc.8.3.1 neuroImaging/fsl/5.0.9
container/singularity/3.6.4/gcc.8.3.1 library/cuda/9.1/gcc.8.3.1 neuroImaging/fsl/6.0.0
container/singularity/3.7.0/gcc.8.3.1 library/cuda/9.2/gcc.8.3.1 neuroImaging/fsl/6.0.1
cryogenicEM/chimera/1.14/gcc-8.3.1 library/cudnn/10.0/cudnn neuroImaging/fsl/6.0.2
cryogenicEM/ctffind/4.1.13/gcc-8.3.1 library/cudnn/10.1/cudnn neuroImaging/fsl/6.0.3
cryogenicEM/eman2/2.31 library/cudnn/10.2/cudnn neuroImaging/fsl/6.0.4
cryogenicEM/gctf/1.06 library/cudnn/9.0/cudnn neuroImaging/fsl/fix/1.06.12
cryogenicEM/imod/4.9.12 library/cudnn/9.2/cudnn neuroImaging/mrtrix/3.0.0/gcc-8.3.1
cryogenicEM/motioncor2/1.31 library/fltk/1.3.5/gcc-8.3.1 pharmaceutical/PsN/4.9.0
cryogenicEM/relion/3.0.8/gcc-8.3.1 library/ftgl/2.1.3/gcc-8.3.1 pharmaceutical/PsN/5.0.0 (D)
cryogenicEM/relion/3.1-beta/gcc-8.3.1 library/gdal/2.4.4/gcc-8.3.1 pharmaceutical/nonmem/7.4.4/gcc-8.3.1
cryogenicEM/resmap/1.1.4 library/gdal/3.0.4/gcc-8.3.1 pharmaceutical/pirana/2.9.7
genomics/hmmer/openmpi-3.1.5/3.3/gcc-8.3.1 library/hdf5/1.10.5/gcc-8.3.1 pharmaceutical/pirana/2.9.8 (D)
genomics/ngs/aligners/bowtie2/2.4.2/gcc-8.3.1 library/htslib/1.10.2/gcc-8.3.1 statistical/MATLAB/R2016b
genomics/ngs/aligners/bwa/0.7.17/gcc-8.3.1 library/htslib/1.11/gcc-8.3.1 statistical/MATLAB/R2018b
genomics/ngs/aligners/minimap2/2.17/gcc-8.3.1 library/java/OpenJDK-11.0.2 statistical/MATLAB/R2019b
genomics/ngs/assembler/canu/2.2/gcc-8.3.1 library/java/OpenJDK-12.0.2 statistical/MATLAB/R2020b
genomics/ngs/assembler/flye/2.8.1/gcc-8.3.1 library/java/OpenJDK-13.0.2 statistical/MATLAB/v93/MCR2017b
genomics/ngs/assembler/miniasm/0.3/gcc-8.3.1 library/java/OpenJDK-14.0.1 statistical/MATLAB/v97/MCR2019b
genomics/ngs/assembler/trinityrnaseq/2.8.4/gcc-8.3.1 library/java/OracleJDK-1.8.0_251 (D) statistical/R/3.4.4/gcc.8.3.1
genomics/ngs/bcftools/1.10.2/gcc-8.3.1 library/lapack/3.9.0/gcc-8.3.1 statistical/R/3.5.3/gcc.8.3.1
genomics/ngs/bcftools/1.11/gcc-8.3.1 library/mpi/mpich/3.3.2/gcc-8.3.1 statistical/R/3.6.0/gcc.8.3.1
genomics/ngs/bcl2fastq/2.20.0 library/mpi/openmpi/3.1.5/gcc-8.3.1 statistical/R/3.6.2/gcc.8.3.1
genomics/ngs/bedtools2/2.29.1/gcc-8.3.1 library/mpi/openmpi/4.0.2/gcc-8.3.1 statistical/R/4.0.2/gcc.8.3.1
genomics/ngs/samtools/1.10/gcc-8.3.1 library/mpi/openmpi/4.0.3/gcc-8.3.1 statistical/RStudio/1.2.5033/gcc-8.3.1
genomics/ngs/samtools/1.11/gcc-8.3.1 library/mpi/openmpi/4.0.4/gcc-8.3.1 statistical/RStudio/1.3.959/gcc-8.3.1
genomics/ngs/shapeit4/4.1.3/gcc-8.3.1 library/mpi/openmpi/4.0.5/gcc-8.3.1 statistical/RStudio/1.3.959/server/gcc-8.3.1
genomics/ngs/tools/HISAT2/2.1.0/gcc-8.3.1 library/nlopt/2.6.2/gcc-8.3.1 system/go/1.13.7
genomics/ngs/tools/LTR_Finder/1.0.7/gcc-8.3.1 library/openslide/3.4.1/gcc-8.3.1 system/hwloc/1.11.13/gcc-8.3.1
genomics/ngs/tools/infernal/1.1.3/gcc-8.3.1 library/pmi/openpmix/2.2.3/gcc-8.3.1 system/hwloc/2.1.0/gcc-8.3.1
genomics/ngs/tools/liftoff/1.5.1/python-3.8 library/pmi/openpmix/3.1.4/gcc-8.3.1 system/knem/1.1.3/gcc-8.3.1
genomics/ngs/tools/pilon/1.23 library/sparsehash/2.0.3/gcc-8.3.1 system/knem/1.1.4/gcc-8.3.1
genomics/ngs/tools/stringtie/2.1.1/gcc-8.3.1 library/spectra/0.9.0 system/python/2.7.17
genomics/ngs/tools/transdecoder/5.0.2/gcc-8.3.1 library/wxwidgets/3.1.3/gcc-8.3.1 system/python/3.7.6
genomics/ngs/vcftools/0.1.16/gcc-8.3.1 mathematical/octave/5.2.0/gcc-8.3.1 system/python/3.8.1 (D)
graphics/gnuplot/5.2.8/gcc-8.3.1 mathematical/octave/libs/SuiteSparse/5.7.2/gcc-8.3.1 system/qt/5.14.2/gcc-8.3.1
graphics/graphicsmagick/1.3.35/gcc-8.3.1 mathematical/octave/libs/arpack/3.7.0/gcc-8.3.1 system/swi-prolog/8.2.0
gwas/depict/1.rel194 mathematical/octave/libs/gl2ps/1.4.2/gcc-8.3.1 tools/biomake/0.1.5
gwas/plink/1.07 mathematical/octave/libs/glpk/4.65/gcc-8.3.1 tools/cmake/3.11.4
gwas/plink/1.90b6.17 mathematical/octave/libs/qhull/8.0.0/gcc-8.3.1 tools/gitlab-runner/12.8.0
gwas/plink/1.90p mathematical/octave/libs/qrupdate/1.1.2/gcc-8.3.1 tools/hashdeep/4.3/gcc-8.3.1
gwas/plink/2.00a3LM (D) mathematical/octave/libs/sundials/5.3.0/gcc-8.3.1 tools/jupyterlab/4.3.1
library/blas/0.3.10/gcc-8.3.1 medicalImaging/minc-stuffs/0.1.25/gcc-8.3.1 tools/luarocks/3.3.1/gcc-8.3.1
library/boost/1.69.0/gcc-8.3.1 medicalImaging/minc-toolkit-v2/1.9.18 tools/miniconda/python2.7/4.7.12
library/boost/1.72.0/gcc-8.3.1 medicalImaging/minc2-simple/2.2.30/gcc-8.3.1 tools/miniconda/python3.8/4.8.5
library/cuda/10.0/gcc.8.3.1 medicalImaging/pydpiper/2.0.14 tools/miniconda/python3.8/4.9.2 (D)
library/cuda/10.1/gcc.8.3.1 neuroImaging/Elastix/5.0.0/gcc-7.4.0 tools/virtualgl/2.6.4/gcc-8.3.1
library/cuda/10.2/gcc.8.3.1 neuroImaging/FSLeyes/0.32.3 tools/websockify/0.9.0
-------------------------------------------------------------------------------------- /usr/share/lmod/lmod/modulefiles/Core --------------------------------------------------------------------------------------
lmod settarg
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