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changes.mady.by.user Thomas Berger

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This will load all of the software and dependencies required to run Rversion 4.3.2. To see the list of software loaded when you run the above command you can run the module list command:

Code Block
$ module list

Currently Loaded Modules:
  1) GCCcore/12.3.0   ASReml/4.2.1.206                                  SQLite/3.42.0-GCCcore-12.3.0              (L)
   Apptainer/1.2.5                                   SWIG/3.0.8
   Arrow/14.0.1-GCC-12.3.0                  (L)      ScaLAPACK/2.2.0-gompi-2023a-fb            (L)
   BCL-Convert/4.2.4                                 Szip/2.1.1-GCCcore-12.3.0                 (L)
   BLASTDB/2024-04                                   Tcl/8.6.10-GCCcore-12.3.0
   BLIS/0.9.0-GCC-12.3.0                        19) ncurses/6.4     TeXLive/2022
   BLIS/4.1-GCC-12.3.0-amd                  (D)      Tk/8.6.10-GCCcore-12.3.0
   Boost/1.83.0-GCC-12.3.0                           UCC/1.2.0-GCCcore-12.3.0                  (L) zlib/1.2.13
   CMake/3.27.7                                      UCX/1.14.1-GCCcore-12.3.0                 (L)
   CUDA/11.8.0                                       UDUNITS/2.2.28-GCCcore-12.3.0             (L)
   Canu/2.2-GCC-12.3.0                               XZ/5.4.2-GCCcore-12.3.0                  20 (L)
libreadline/8.2-   EasyBuild/4.8.1                                   ZeroMQ/4.3.5-GCCcore-12.3.0
   EasyBuild/4.9.2                          (D)      ant/1.10.9-Java-17
   FFTW.MPI/3.3.10-gompi-2023a              (L)      binutils/2.40-GCCcore-12.3.0              (L)
   FFTW/3.3.10-GCC-12.3.0                   (L)      binutils/2.40                             (D)
   FlexiBLAS/3.3.1-GCC-12.3.0               (L)      bzip2/1.0.8-GCCcore-12.3.0                21(L)
   libpngFriBidi/1.6.40.0.12-GCC-12.3.0                         cURL/8.3.0-GCCcore-12.3.0                 4(L)
   GCC/12.3.0                               (L)      cuDNN/8.6.0.163-CUDA-11.8.0
   GCCcore/12.3.0                        22   (L) libxml2     expat/2.11.4-GCCcore.5.0-GCCcore-12.3.0                (L)
   GDAL/3.6.4-gompi-2023a                   (L)      fontconfig/2.14.2-GCCcore-12.3.0
   GEOS/3.11.3-GCC-12.3.0      5) numactl/2.0.16             (L)      foss/2023a                                (L)
   GLib/2.78.1-GCC-12.3.0                            freetype/2.13.2-GCCcore-12.3.0
  23) SQLite/3.42.0GMP/6.2.1-GCCcore-12.3.0                 (L)      gettext/0.21-GCCcore-12.3.0
   6) UCXGo/1.22.3                                         gompi/2023a                               (L)
   HDF5/1.14.3-gompi-2023a                  (L)      gperf/3.1-GCCcore-12.3.0       24) OpenSSL/1.1
  7) UCC/1.2.0-
   HarfBuzz/4.4.1-GCC-12.3.0                         gquery-dev/0.7.0
   IGV/2.17.4                                        gquery-dev/0.8.1
   IRkernel/1.3.2-foss-2023a-R-4.3.2                 gquery-dev/0.9.0
   IRkernel/1.3.2-foss-2023a-R-4.3.3        (D)      gquery-dev/0.9.1
   Java/17                                           gquery-dev/0.9.2                          (D)
   Java/20.0.2                              (L,D)    gquery-test/0.8.1
   Julia/1.10.1-GCC-12.3.0-VTune                     gquery-test/0.9.0
   JupyterLab/2023.11.0-foss-2023a-3.6.3             gquery-test/0.9.1
   JupyterLab/2024.05.0-foss-2023a-4.2.0    (D)      gquery-test/0.9.2                         (D)
   KEALib/1.5.2-gompi-2023a                 (L)      gquery/0.8.1
   LLVM/14.0.6-GCC-12.3.0-static                     gquery/0.9.0
   LibTIFF/4.4.0-GCCcore-12.3.0        25) cURL/8.3.0-GCCcore              gquery/0.9.1
   LibTIFF/4.5.1-GCCcore-12.3.0             (L,D)    gquery/0.9.2                              (D)
   Meson/0.62.1                                      graphite2/1.3.14
   Miniconda3/23.10.0-1                              json-c/0.17-GCC-12.3.0                    8(L)
  OpenMPI/4.1.5 NASM/2.15.05                                      libKML/1.3.0.2017-GCC-12.3.0        26)       (L)
   NLopt/2.7.1-GCC-12.3.0                   (L)      libffi/3.4.6
   NanoPlot/1.43.0-foss-2023a-Python-3.11.6          libgd/2.3.3-GCCcore-12.3.0
   Nextflow/24.04.2                                  libgeotiff/1.7.1-GCC-12.3.0-PROJ-9.3.0    (L)
   Ninja/1.11.1                                      libgit2/1.6.4-GCC-12.3.0                  (L)
   OpenBLAS/0.3.23-GCC-12.3.0               27(L) GMP/6.2     libjpeg-turbo/2.1.5.1-GCCcore-12.3.0      10(L)
 FlexiBLAS/3.3.1  OpenJPEG/2.5.0-GCCcore-12.3.0            (L)      libpng/1.6.40-GCCcore-12.3.0              (L)
   OpenMPI/4.1.5-GCC-12.3.0      28) Java/20.0.2
 11) FFTW/3.3.10-           (L)      libreadline/8.2-GCCcore-12.3.0            (L)
   OpenSSL/1.1                              (L)      libxml2/2.11.4-GCCcore-12.3.0             (L)
   OpenSSL/3.3.1-GCCcore-12.3.0             (D)      libxslt/1.1.38-GCCcore-12.3.0
   PCRE2/10.42-GCCcore-12.3.0               (L)      lz4/1.9.4-GCCcore-12.3.0                  (L)
   PROJ/9.3.0-GCC-12.3.0                 29   (L) libgit2/1.6.4     nanoget/1.19.3-foss-2023a-Python-3.11.6
   Perl/5.38.2-GCC-12.3.0                            ncurses/6.4-GCCcore-12.3.0                (L)
   PostgreSQL/14.12-GCC-12.3.0                       netCDF/4.9.2-gompi-2023a                  (L)
   Python/3.11.6-foss-2023a                         30) nodejs/18.18.2-GCCcore-12.3.0  13) FFTW.MPI/3.3.10-gompi-2023a           (L)
   R-Geo/4.3.2-foss-2023a                            nullarbor/2.0.20191013
   R/4.3.2-foss-2023a                  31) freetype     (D)      numactl/2.130.216-GCCcore-12.3.0             14(L)
 ScaLAPACK  R/24.23.03-gompi-2023a-fb  32) HarfBuzz/4.4.1foss-2023a                                pixman/0.42.2-GCC-12.3.0
  15) foss/2023a     R/4.4.0-foss-2023a                                snakemake/7.32.3-foss-2023a-Python-3.11.6
   R/4.4.1-foss-2023a                  33) FriBidi/1.0.12-GCC     (L)      snakemake/8.14.0-foss-2023a-Python-3.11.6 (D)
   RStudio-Server/2023.12.0-369                      snappy/1.1.10-GCCcore-12.3.0              16(L) bzip2/1.
   RStudio-Server/2024.04.2-764             (D)      yaml-cpp/0.8-GCCcore.0-GCC-12.3.0
   Rust/1.73.0-GCC-12.3.0                       34) LibTIFF/4.4.0     zlib/1.2.13-GCCcore-12.3.0           17     (L)
XZ/5.4.2   SAMtools/0.1.19-GCCcore-12.3.0                      35) R/4.3.2-foss-2023a
 18) PCRE2/10.42zlib/1.2.13                               (D)
   SOCI/4.0.3-GCC-12.3.0                             zstd/1.5.5-GCCcore-12.3.0                 (L)
   SPAdes/4.0.0-foss-2023a-Python-3.11.6

Working with containers

Singularity

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