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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) libreadline/8.2-           (L)
   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)
libpng   FriBidi/1.6.40.0.12-GCC-12.3.0                         cURL/8.3.0-GCCcore-12.3.0               4)   (L)
   GCC/12.3.0                      22) libxml2/2.11.4-GCCcore         (L)      cuDNN/8.6.0.163-CUDA-11.8.0
   GCCcore/12.3.0                           (L)      expat/2.5.0-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) UCX/1.14.1-GCCcore-12.3.0       24) OpenSSL/1.1
  7) UCC/1.2.0-GCCcore-12.3.0        25) cURL/8.3.0-GCCcore-12.3.0
  8) OpenMPI/4.1.5Go/1.22.3                                         gompi/2023a                               (L)
   HDF5/1.14.3-gompi-2023a                  (L)      gperf/3.1
   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                      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                    (L)
   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) GMP/6.2         (L)      libjpeg-turbo/2.1.5.1-GCCcore-12.3.0      10(L)
   FlexiBLAS/3.3.1OpenJPEG/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(L) Java/20.0.2
 11) FFTW/3.3.10-      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) libgit2(L)      nanoget/1.19.3-foss-2023a-Python-3.11.6.4
   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(L) FFTW.MPI/3.3.10-gompi-2023a
   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) ScaLAPACK/2.2.0-gompi-2023a-fb  32) HarfBuzz/4.4.1-GCC   (L)
   R/4.3.3-foss-2023a                                pixman/0.42.2-GCC-12.3.0
   R/4.4.0-foss-2023a                                snakemake/7.32.3-foss-2023a-Python-3.11.6
   R/4.4.1-foss-2023a                       (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      15) foss/2023a        (L)
   RStudio-Server/2024.04.2-764             (D)      yaml-cpp/0.8.0-GCC-12.3.0
  33) FriBidiRust/1.73.0.12-GCC-12.3.0  16) bzip2/1.0.8                          zlib/1.2.13-GCCcore-12.3.0                (L)
   SAMtools/0.1.19-GCCcore-12.3.0      34) LibTIFF/4.4.0-GCCcore              zlib/1.2.13                               (D)
   SOCI/4.0.3-GCC-12.3.0                            17) XZzstd/1.5.4.25-GCCcore-12.3.0                 35(L)
   RSPAdes/4.30.20-foss-2023a-Python-3.11.6

Working with containers

Singularity

Available as Apptainer and aliasing enabled, both apptainer --version and singularity --version will work. There are NeSI/Mahuika based notes on building containers HERE


Example

Code Block
# QIIME1
module purge
module 18)load PCRE2Apptainer/10.42-GCCcore-12.3.01.2.5

# recent Apptainer modules set APPTAINER_BIND, which typically breaks
# container builds, so unset it here
unset APPTAINER_BIND

# create a build and cache directory on scratch storage
export APPTAINER_CACHEDIR="/agr/scratch/projects/<YOURPROJECT>/$USER/apptainer_cache"
export APPTAINER_TMPDIR="/agr/scratch/projects/<YOURPROJECT>/$USER/apptainer_tmpdir"
mkdir -p $APPTAINER_CACHEDIR $APPTAINER_TMPDIR
setfacl -b $APPTAINER_TMPDIR

# pull the container
apptainer pull docker://mgrast/qiime:1.0

# execute the container
apptainer exec qiime_1.0.sif align_seqs.py -h