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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:
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$ 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 TeXLive/2022 19) ncurses/6.4-GCCcoreBLIS/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) libreadlineEasyBuild/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) libpng/1.6.40 (L) FriBidi/1.0.12-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) libxml2/2.11.4-GCCcore- (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 Go/1.22.3 gompi/2023a 6(L) UCXHDF5/1.14.3-gompi-2023a (L) gperf/3.1 HarfBuzz/4.4.1-GCCcoreGCC-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 24) OpenSSL/1.1 7) UCC/1.2.0(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) 25) cURL/8.3.0-GCCcoregquery/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) OpenMPINASM/4.1.52.15.05 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) 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) libgit2/1.6.4 (L) 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 31) freetype/2.13.2(L) R-Geo/4.3.2-foss-2023a nullarbor/2.0.20191013 R/4.3.2-foss-2023a (D) numactl/2.0.16-GCCcore-12.3.0 14(L) ScaLAPACKR/24.23.03-gompi-2023a-fb 32) HarfBuzz/4.4.1foss-2023a pixman/0.42.2-GCC-12.3.0 R/4.4.0 15) foss/2023a-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) bzip2/1.0.8-GCCcore (L) RStudio-Server/2024.04.2-764 (D) yaml-cpp/0.8.0-GCC-12.3.0 Rust/1.73.0-GCC-12.3.0 34) LibTIFFzlib/41.42.013-GCCcore-12.3.0 17) XZ/5.4.2 (L) SAMtools/0.1.19-GCCcore-12.3.0 zlib/1.2.13 35(D) RSOCI/4.0.3.2-foss-2023a 18) PCRE2/10.42GCC-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
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
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# QIIME1
module purge
module load Apptainer/1.2.5
# 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 |