Bio-informatics Helper Modulefile
The following modulefiles (and app installs) are old, and unlikely to work on the CSF3 (Slurm) cluster.
If you have previously used these modules but find that they no longer work, please consider installing the app yourself using Conda – MiniForge (in the case of a python app) or contact us to request help. Note that we are unlikely to install very old versions of applications – now is an opportunity to upgrade to a recent version of an app.
As part of the DPSF merger in to the CSF3, many bio-informatics applications were copied from the DPSF to the CSF3. These are not documented individually. To access these applications, please run the following command on the login node, and also in your jobscripts, if you load modulefiles from within jobscripts:
module load apps/bioinf # Same as loading the apps/dpsf modulefile
Listing the available module files using module avail or searching for modulefiles using module search name will display more modulefile names.
To use the required software you will need to load both the bioinf modulefile and the specific one for the software. For example to use module load apps/bioinf
module load apps/bioinf module load apps/picard/2.1.0/bin
If you have moved from CSF2 and cannot find the application you require then please try loading this modulefile as it may be that what you require is available, but has a slightly different modulefile name on CSF3.
The following list of applications is available as of 3-Jan-2019. We will not frequently update this list so please use module search as above to check whether what you need may have been installed recently.
--- /opt/gridware/legacy-dpsf/el7/etc/modules --- apps/bamtools/2.3.0/gcc-4.8.5 apps/bbmap/36.32/gcc-4.8.5 apps/bcftools/1.2/gcc-4.8.5 apps/bcftools/1.3/gcc-4.8.5 apps/bcftools/1.4/gcc-4.8.5 apps/bcl2fastq/1.8.4/gcc-4.8.5 apps/bcl2fastq/2.17/gcc-4.8.5+boost-1.55.0 apps/bedtools/2.22.0/gcc-4.8.5 apps/bedtools/2.25.0/gcc-4.8.5 apps/bedtools/2.27.1/gcc-4.8.5 apps/bismark/0.16.3/noarch apps/bismark/0.17.0/noarch apps/bitseq/0.7.5/gcc-4.8.5 apps/bowtie/1.1.0/gcc-4.8.5 apps/bowtie2/2.2.3/gcc-4.8.5 apps/bowtie2/2.2.6/gcc-4.8.5 apps/bowtie2/2.3.0/gcc-4.8.5 apps/breakdancer/1.3.5.1/gcc-4.8.5+samtools-0.1.18+boost-1.60.0 apps/bwa/0.7.12/gcc-4.8.5 apps/bwa/0.7.15/gcc-4.8.5 apps/bwa/0.7.7/gcc-4.8.5+perl-5.20.2 apps/chromhmm/1.2/noarch apps/cmake/3.5.2/gcc-4.8.5 apps/cpanminus/1.5017/perl-5.20.2 apps/cufflinks/2.2.2.20150701/gcc-4.8.5+boost-1.55.0+samtools-0.1.19+eigen-3.2.4 apps/cutadapt/1.14/gcc-4.8.5+python-2.7.8+setuptools-15.1 apps/cutadapt/1.8/gcc-4.8.5+python-2.7.8 apps/cython/0.23.4/gcc-4.8.5+python-2.7.8 apps/cython_python3/0.23.4/gcc-4.8.5+python3-3.3.3 apps/cython_python34/0.23.4/gcc-4.8.5+python3-3.4.3 apps/delly/0.6.5/gcc-4.8.5+htslib-1.3+bamtools-2.3.0+boost-1.60.0 apps/diaumpire/2.0.0/noarch apps/diffreps/20150410/gcc-4.8.5+perl-5.20.2 apps/ensemblvep/84/perl-5.20.2+htslib-1.3 apps/fastlowess/20130915/gcc-4.8.5+atlas-3.11.36+numpy-1.9.2+cython-0.23.4+python-2.7.8 apps/fastml/3.1/noarch apps/fastqc/0.11.3/noarch apps/fastqscreen/0.4.1/noarch apps/fastqscreen/0.6.1/gcc-4.8.5+perl-5.20.2 apps/faststructure/1.0/gcc-4.8.5+python-2.7.8+numpy-1.9.2+scipy-0.17.0+cython-0.23.4+gsl-1.16+setuptools-15.1 apps/fasttree/2.1.3/gcc-4.8.5 apps/freebayes/1.0.2/gcc-4.8.5+bamtools-2.3.0+cmake-3.5.2 apps/freebayes/1.1.0/gcc-4.8.5+cmake-3.5.2 apps/gatk/3.5.0/noarch apps/gatk/3.6.0/noarch apps/gatk/3.8.0/noarch [CSF(Slurm): Add -jdk_inflater -jdk_deflater to your GATK command-line] apps/gatk/4.0.4.0/noarch apps/gatkqueue/3.5.0/noarch apps/gatkqueue/3.6.0/noarch apps/gemini/0.18.3/gcc-4.8.5+setuptools-15.1+python-2.7.8+numpy-1.9.2+numexpr-2.4.4+pysam-0.8.3+cython-0.23.4+pybedtools-0.7.4+scipy-0.17.0+pandas-0.17.0+bcolz-1.1.0+ipython-4.2.1 apps/genomicsbcftbx/0.99.12/gcc-4.8.5+setuptools-15.1+python-2.7.8 apps/ghc/7.8.2/bin apps/ginkgo/20180103/gcc-4.8.5+R-3.3.1+bioconductor-2.14 apps/gnuplot/5.0.2/gcc-4.8.5 apps/gubbins/1.4.9/python3-3.4.3+setuptools_python34-15.1+fasttree-2.1.3+fastml-3.1+raxml-8.1.16 apps/hdf5_mpi/1.8.9/gcc-4.8.5+openmpi-1.8.5 apps/hdf5_serial/1.8.9/gcc-4.8.5 apps/hicpro/2.10.0/gcc-4.8.5+python-2.7.8+pip-8.1.2+numpy-1.9.2+scipy-0.17.0+pysam-0.8.3+R-3.1.1+bowtie2-2.3.0+samtools-1.4 apps/htseq/0.6.1p1/gcc-4.8.5+python-2.7.8+numpy-1.9.2 apps/htseq/0.9.1/gcc-4.8.5+python-2.7.8+setuptools-15.1+numpy-1.9.2+matplotlib-1.4.3 apps/htslib/1.3/gcc-4.8.5 apps/htslib/1.3.2/gcc-4.8.5 apps/idr_python34/2.0.2/python3-3.4.3+numpy_python34-1.9.2+setuptools_python34-15.1+matplotlib_python34-1.4.3+scipy_python34-0.17.0 apps/imb/4.0/gcc-4.8.5+openmpi-1.8.5 apps/ipython/4.2.1/gcc-4.8.5+python-2.7.8+numpy-1.9.2+matplotlib-1.4.3 apps/kallisto/0.43.0/gcc-4.8.5+hdf5_serial-1.8.9 apps/kent/303.1/gcc-4.8.5 apps/khmer/2.0/gcc-4.8.5+python-2.7.8+screed-0.9 apps/khmer_python3/2.0/gcc-4.8.5+python3-3.3.3+screed_python3-0.9 apps/khmer_python34/2.0/gcc-4.8.5+python3-3.4.3+screed_python34-0.9 apps/luciphor2/20141023/noarch apps/macs/2.1.0/gcc-4.8.5+numpy-1.9.2 apps/macs/2.1.0.20150420/gcc-4.8.5+numpy-1.9.2 apps/macs/2.1.0.20150731/gcc-4.8.5+numpy-1.9.2 apps/macs/2.1.1.20160309/gcc-4.8.5+numpy-1.9.2 apps/mats/3.2.2b/noarch apps/mats/4.0.1/noarch apps/memesuite/4.11.2/gcc-4.8.5+perl-5.20.2+python-2.7.8 apps/memesuite_mpi/4.11.2/gcc-4.8.5+perl-5.20.2+python-2.7.8+openmpi-1.8.5 apps/memtester/4.3.0/gcc-4.8.5 apps/minimap2/2.2/gcc-4.8.5+python-2.7.8+cython-0.23.4 apps/misopy/0.5.4/gcc-4.8.5+python-2.7.8+numpy-1.9.2+scipy-0.17.0 apps/mono/4.0.4.1/gcc-4.8.5 apps/msproteomicstools/0.3.3/gcc-4.8.5+python-2.7.8+cython-0.23.4+numpy-1.9.2+biopython-1.63+scipy-0.17.0+pil-1.1.7+pyqwt_qt46-5.2.1+pyqt-4.9.6 apps/msproteomicstools/0.4.3/gcc-4.8.5+python-2.7.8+cython-0.23.4+numpy-1.9.2+biopython-1.63+scipy-0.17.0+sip-4.16.3+pil-1.1.7+pyqt-4.11.2+pyqwt_qt48-5.2.1 apps/multiqc/1.0/gcc-4.8.5+python-2.7.8+setuptools-15.1+numpy-1.9.2+matplotlib-1.4.3 apps/multiqc/1.1/gcc-4.8.5+python-2.7.8+setuptools-15.1+numpy-1.9.2+matplotlib-1.4.3 apps/ncbiblast/2.2.30/gcc-4.8.5 apps/novobreak/1.1/noarch apps/openms/2.0.0/gcc-4.8.5+boost-1.60.0+eigen-3.2.4+seqan-1.4.1+libsvm-3.21.0+qt-4.8.4 apps/openms/2.0.1/gcc-4.8.5+boost-1.60.0+eigen-3.2.4+seqan-1.4.1+libsvm-3.21.0+qt-4.8.4 apps/openms/2.2.0/gcc-4.8.5+boost-1.60.0+eigen-3.2.4+seqan-1.4.1+libsvm-3.21.0+qt-4.8.4 apps/openms_python/2.0.0/gcc-4.8.5+boost-1.60.0+eigen-3.2.4+seqan-1.4.1+libsvm-3.21.0+qt-4.8.4+python-2.7.8+numpy-1.9.2+cython-0.23.4 apps/pandaseq/2.8.1/gcc-4.8.5 apps/parallel/20151222/gcc-4.8.5 apps/patchelf/0.9/gcc-4.8.5 apps/percolator/3.2/gcc-4.8.5+boost-1.60.0+xsd-4.0.0 apps/perl/5.20.2/gcc-4.8.5 apps/phantompeakqualtools/1.1/gcc-4.8.5+R-3.2.3+boost-1.60.0 apps/picard/2.1.0/bin apps/pip/8.1.2/python-2.7.8 apps/plink/1.07/gcc-4.8.5 apps/plink/1.90.150618/gcc-4.8.5+atlas-3.11.36+patchelf-0.9 apps/plinkseq/0.10/gcc-4.8.5 apps/proteowizard/3.0.9844/gcc-4.8.5+boost-1.60.0 apps/pycogent/1.5.3/gcc-4.8.5+numpy-1.9.2+python-2.7.8 apps/pynast/1.2.2/python-2.7.8+pycogent-1.5.3 apps/pyprophet/0.18.3/gcc-4.8.5+python-2.7.8+numpy-1.9.2+pandas-0.17.0+numexpr-2.4.4+scipy-0.17.0+matplotlib-1.4.3+seaborn-0.7.0+scikitlearn-0.17.1+setuptools-15.1 apps/pyprophet/0.22.0/gcc-4.8.5+python-2.7.8+numpy-1.9.2+pandas-0.17.0+numexpr-2.4.4+scipy-0.17.0+matplotlib-1.4.3+seaborn-0.7.0+scikitlearn-0.17.1+setuptools-15.1 apps/python/2.7.8/gcc-4.8.5 apps/python3/3.3.3/gcc-4.8.5 apps/python3/3.4.3/gcc-4.8.5 apps/qiime/1.9.1/python-2.7.8+numpy-1.9.2+scipy-0.17.0+pycogent-1.5.3+pandas-0.17.0+biomformat-2.1.4+matplotlib-1.4.3+ghc-7.8.2+pynast-1.2.2 apps/quast/2.3/gcc-4.8.5+python-2.7.8+matplotlib-1.4.3 apps/quast/4.6.3/gcc-4.8.5+python-2.7.8+matplotlib-1.4.3 apps/R/3.1.1/gcc-4.8.5+lapack-3.5.0+blas-3.6.0 apps/R/3.2.3/gcc-4.8.5+lapack-3.5.0+blas-3.6.0 apps/R/3.3.1/gcc-4.8.5+lapack-3.5.0+blas-3.6.0 apps/raxml/8.1.16/gcc-4.8.5+openmpi-1.8.5 apps/rcount/20150128/gcc-4.8.5 apps/rdpclassifier/2.2/noarch apps/repeatmasker/4.0.5/gcc-4.8.5+trf-4.07b+rmblast-2.2.27 apps/rmblast/2.2.27/gcc-4.8.5 apps/rnachipintegrator/1.0.1/gcc-4.8.5+setuptools-15.1+python-2.7.8 apps/rnaseqc/1.1.8/noarch apps/rsem/1.2.19/gcc-4.8.5 apps/salmon/0.8.2/gcc-4.8.5+boost-1.60.0+tbb-4.4.20160128 apps/samtools/0.1.18/gcc-4.8.5 apps/samtools/0.1.19/gcc-4.8.5 apps/samtools/1.2/gcc-4.8.5 apps/samtools/1.3.1/gcc-4.8.5+htslib-1.3.2 apps/samtools/1.4/gcc-4.8.5 apps/screed/0.9/gcc-4.8.5+python-2.7.8 apps/screed_python3/0.9/gcc-4.8.5+python3-3.3.3 apps/screed_python34/0.9/gcc-4.8.5+python3-3.4.3 apps/seqprep/1.2/gcc-4.8.5 apps/seqtk/1.0/gcc-4.8.5 apps/setuptools/15.1/python-2.7.8 apps/setuptools/24.0.1/python-2.7.8 apps/setuptools_python3/15.1/python3-3.3.3 apps/setuptools_python34/15.1/python3-3.4.3 apps/sip/4.14.2/gcc-4.8.5+python-2.7.8 apps/sip/4.16.3/gcc-4.8.5+python-2.7.8 apps/sra/2.3.5-2/gcc-4.8.5 apps/star/2.4.2a/gcc-4.8.5 apps/star/2.5.1a/gcc-4.8.5 apps/star/2.5.3a/gcc-4.8.5 apps/star_long/2.4.2a/gcc-4.8.5 apps/star_long/2.5.3a/gcc-4.8.5 apps/stringtie/1.3.3b/gcc-4.8.5 apps/subread/1.5.0-p3/gcc-4.8.5 apps/subread/1.6.0/gcc-4.8.5 apps/swathprophet/20150223/noarch apps/tabix/0.2.6/gcc-4.8.5 apps/tax2tree/1.0/python-2.7.8+pycogent-1.5.3 apps/tophat/2.1.0/gcc-4.8.5+boost-1.60.0 apps/tpp/4.8.0/gcc-4.8.5+gnuplot-5.0.2 apps/trf/4.07b/bin apps/trimgalore/0.4.2/noarch apps/trimgalore/0.4.4/noarch apps/trimmomatic/0.32/noarch apps/trimmomatic/0.35/noarch apps/trimmomatic/0.36/noarch apps/vcftools/0.1.14/gcc-4.8.5+perl-5.20.2 apps/vcftools/0.1.9/gcc-4.8.5 apps/virtualenv/13.1.2/python-2.7.8 apps/virtualenv_python3/13.1.2/python3-3.3.3 apps/virtualenv_python34/13.1.2/python3-3.4.3 apps/vt/0.577/gcc-4.8.5 apps/xtandem/20151215/gcc-4.8.5 compilers/gcc/4.8.2 compilers/gcc/system *default* libs/atlas/3.10.3/gcc-4.8.5+openmp+haswell *default* libs/atlas/3.10.3/gcc-4.8.5+openmp+ivybridge libs/atlas/3.11.36/gcc-4.8.5 libs/bcolz/1.1.0/gcc-4.8.5+setuptools-24.0.1+python-2.7.8+numpy-1.9.2 libs/bioconductor/2.14/gcc-4.8.5+R-3.2.3 libs/bioconductor/3.3/gcc-4.8.5+R-3.3.1 libs/biomformat/2.1.4/gcc-4.8.5+python-2.7.8+numpy-1.9.2+scipy-0.17.0 libs/bioperl/1.6.923/gcc-4.8.5+samtools-0.1.19 libs/biopython/1.63/gcc-4.8.5+python-2.7.8+numpy-1.9.2 libs/biopython_python3/1.63/gcc-4.8.5+python3-3.3.3+numpy_python3-1.9.2 libs/blas/3.6.0/gcc-4.8.5 libs/boost/1.55.0/gcc-4.8.5+openmpi-1.8.5+python-2.7.8 libs/boost/1.60.0/gcc-4.8.5+openmpi-1.8.5+python-2.7.8 libs/eigen/3.2.4/gcc-4.8.5 libs/gcc/4.8.2 libs/gcc/system libs/gsl/1.16/gcc-4.8.5 libs/imagemagick/6.9.4/gcc-4.8.5 libs/lapack/3.5.0/gcc-4.8.5 libs/libsvm/3.21.0/gcc-4.8.5 libs/matplotlib/1.4.3/gcc-4.8.5+python-2.7.8+numpy-1.9.2 *default* libs/matplotlib/1.4.3/ivy libs/matplotlib_python3/1.4.3/gcc-4.8.5+python3-3.3.3+numpy_python3-1.9.2 libs/matplotlib_python34/1.4.3/gcc-4.8.5+python3-3.4.3+numpy_python34-1.9.2 libs/netcdf/4.3.0/gcc-4.8.5+hdf5_serial-1.8.9 libs/numexpr/2.4.4/gcc-4.8.5+python-2.7.8+numpy-1.9.2 libs/numpy/1.9.2/gcc-4.8.5+atlas-3.10.3+python-2.7.8 libs/numpy/1.9.2/gcc-4.8.5+atlas-3.11.36+python-2.7.8 *default* libs/numpy_python3/1.9.2/gcc-4.8.5+atlas-3.11.36+python3-3.3.3 libs/numpy_python34/1.9.2/gcc-4.8.5+atlas-3.11.36+python3-3.4.3 libs/pandas/0.17.0/gcc-4.8.5+python-2.7.8+numpy-1.9.2 libs/pil/1.1.7/gcc-4.8.5+python-2.7.8 libs/pybedtools/0.7.4/gcc-4.8.5+python-2.7.8+pysam-0.8.3 libs/pyqt/4.11.2/gcc-4.8.5+python-2.7.8+qt-4.8.4 libs/pyqt/4.9.6/gcc-4.8.5+python-2.7.8+qt-4.6.4 libs/pyqwt_qt46/5.2.1/gcc-4.8.5+python-2.7.8+numpy-1.9.2+sip-4.14.2+pyqt-4.9.6+qt-4.6.4 libs/pyqwt_qt48/5.2.1/gcc-4.8.5+python-2.7.8+numpy-1.9.2+sip-4.16.3+pyqt-4.11.2+qt-4.8.4 libs/pysam/0.8.3/gcc-4.8.5+python-2.7.8 libs/qt/4.6.4/gcc-4.8.5 libs/qt/4.8.4/gcc-4.8.5 libs/rpy2/2.8.2/gcc-4.8.5+setuptools-15.1+python-2.7.8+R-3.2.3 libs/scikitlearn/0.17.1/gcc-4.8.5+python-2.7.8+matplotlib-1.4.3+numpy-1.9.2+scipy-0.17.0 libs/scikit-learn/0.17.1/gcc-4.8.5+python-2.7.8+matplotlib-1.4.3+numpy-1.9.2+scipy-0.17.0 libs/scikit-learn_python3/0.17.1/gcc-4.8.5+python3-3.3.3+matplotlib_python3-1.4.3+numpy_python3-1.9.2+scipy_python3-0.17.0 libs/scikit-learn_python34/0.17.1/gcc-4.8.5+python3-3.4.3+matplotlib_python34-1.4.3+numpy_python34-1.9.2+scipy_python34-0.17.0 libs/scipy/0.17.0/gcc-4.8.5+atlas-3.10.3+python-2.7.8+numpy-1.9.2 libs/scipy/0.17.0/gcc-4.8.5+atlas-3.11.36+python-2.7.8+numpy-1.9.2 *default* libs/scipy_python3/0.17.0/gcc-4.8.5+atlas-3.11.36+python3-3.3.3+numpy_python3-1.9.2 libs/scipy_python34/0.17.0/gcc-4.8.5+atlas-3.11.36+python3-3.4.3+numpy_python34-1.9.2 libs/seaborn/0.7.0/gcc-4.8.5+python-2.7.8+scipy-0.17.0+matplotlib-1.4.3+pandas-0.17.0 libs/seqan/1.4.1/noarch libs/tbb/4.4.20160128/gcc-4.8.5 libs/xsd/4.0.0/bin