Software installed on Rocky 8: Difference between revisions
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Java/11.0.16 | Java/11.0.16 | ||
Java/13.0.2 | Java/13.0.2 | ||
Java/15.0.1 | Java/15.0.1 | ||
Java/17.0.6 | Java/17.0.6 | ||
Jellyfish/2.3.0-GCC-11.2.0 | Jellyfish/2.3.0-GCC-11.2.0 | ||
Jellyfish/2.3.0-GCC-11.3.0 | Jellyfish/2.3.0-GCC-11.3.0 | ||
Revision as of 13:22, 28 July 2023
As part of our August 29-31,2023 maintenance window, the GACRC will be upgrading the Sapelo2 cluster operating system from CentOS 7 to Rocky 8.
Because this is a major OS update, we need to recompile all the applications and ensure that they work with the new version of OS.
Below is a list of the modules already installed on the Rocky 8 system. More software packages continue to be installed. If the software you need is not in this list yet, please feel free to let us know, if you would like us to install it centrally on the updated cluster.
All singularity containers available in /apps/singularity-images on the current Sapelo2 (CentOS 7) will continue to be available after the maintenance.
List of software already installed centrally on the Rocky 8 system (new Sapelo2, available after the maintenance)
3D-DNA/201008-foss-2021b-Python-2.7.18 ABySS/2.3.5-foss-2021b ACTC/1.1-GCCcore-11.2.0 ADMIXTURE/1.3.0 AGAT/0.9.2-GCC-11.2.0 AGAT/1.1.0 AMOS/3.1.0-foss-2021b ANTLR/2.7.7-GCCcore-11.2.0-Java-11 ANTs/2.4.4-foss-2021b APR-util/1.6.1-GCCcore-11.2.0 APR/1.7.0-GCCcore-11.2.0 ART/2016.06.05-GCC-11.2.0 ASE/3.22.1-foss-2021b ASTRAL/5.7.8-Java-1.8.0_241 ATK/2.36.0-GCCcore-11.2.0 ATK/2.38.0-GCCcore-11.3.0 AUGUSTUS/3.4.0-foss-2021b Amber/22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1 Anaconda3/2022.10 Archive-Zip/1.68-GCCcore-11.2.0 Armadillo/11.4.3-foss-2021b Arrow/8.0.0-foss-2021b Autoconf/2.69-GCCcore-8.3.0 Autoconf/2.69-GCCcore-10.2.0 Autoconf/2.71-GCCcore-11.2.0 Autoconf/2.71-GCCcore-11.3.0 Autoconf/2.71-GCCcore-12.2.0 Automake/1.16.1-GCCcore-8.3.0 Automake/1.16.2-GCCcore-10.2.0 Automake/1.16.4-GCCcore-11.2.0 Automake/1.16.5-GCCcore-11.3.0 Automake/1.16.5-GCCcore-12.2.0 Autotools/20180311-GCCcore-8.3.0 Autotools/20200321-GCCcore-10.2.0 Autotools/20210726-GCCcore-11.2.0 Autotools/20220317-GCCcore-11.3.0 Autotools/20220317-GCCcore-12.2.0 BBMap/38.98-GCC-11.2.0 BCFtools/1.14-GCC-11.2.0 BEDOPS/2.4.41-foss-2021b BEDTools/2.30.0-GCC-11.2.0 BLAST+/2.2.31 BLAST+/2.12.0-gompi-2021b BLAST+/2.13.0-gompi-2021b BLAST+/2.13.0-gompi-2022a BLAST/2.2.26-Linux_x86_64 BLAT/3.5-GCC-11.2.0 BLAT/3.7-GCC-11.3.0 BLIS/0.8.1-GCC-11.2.0 BLIS/0.9.0-GCC-11.3.0 BRAKER/2.1.6-foss-2021b BRIG/0.95-gompi-2021b-Java-1.8.0_241 BUSCO/5.4.3-foss-2021b BWA/0.7.17-GCCcore-11.2.0 BamTools/2.5.2-GCC-11.2.0 BamUtil/1.0.15-foss-2021b Bandage/0.9.0-GCCcore-11.2.0 BayeScan/2.1-foss-2019b Bazel/3.7.2-GCCcore-11.2.0 Bazel/4.2.2-GCCcore-11.2.0 Bazel/5.1.1-GCCcore-11.3.0 Beagle/5.4.22Jul22.46e-Java-11 Beast/2.7.1-foss-2021b-CUDA-11.4.1 BigDFT/1.9.1-foss-2021b Bio-DB-HTS/3.01-GCC-11.2.0 BioPerl/1.7.8-GCCcore-11.2.0 Biopython/1.79-foss-2021b Biopython/1.79-foss-2022a Biopython/1.81-foss-2021b Bismark/0.23.1-foss-2021b Bison/3.3.2-GCCcore-8.3.0 Bison/3.3.2 Bison/3.7.1-GCCcore-10.2.0 Bison/3.7.6-GCCcore-11.2.0 Bison/3.8.2-GCCcore-11.3.0 Bison/3.8.2-GCCcore-12.2.0 Bison/3.8.2 Blosc/1.21.3-GCCcore-11.2.0 Boost.Python/1.77.0-GCC-11.2.0 Boost/1.75.0-GCC-11.2.0 Boost/1.77.0-GCC-11.2.0 Boost/1.79.0-GCC-11.3.0 Bowtie/1.3.1-GCC-11.2.0 Bowtie/1.3.1-GCC-11.3.0 Bowtie2/2.4.4-GCC-11.2.0 Bowtie2/2.4.5-GCC-11.2.0 Bowtie2/2.4.5-GCC-11.3.0 Bracken/2.7-GCCcore-11.2.0 Brotli/1.0.9-GCCcore-11.2.0 Brotli/1.0.9-GCCcore-11.3.0 CD-HIT/4.8.1-GCC-11.2.0 CD-HIT/4.8.1-GCC-11.3.0 CFITSIO/3.49-GCCcore-11.2.0 CGAL/4.14.3-gompi-2021b CGmapTools/0.1.2-foss-2021b CMake/3.12.1 CMake/3.21.1-GCCcore-11.2.0 CMake/3.22.1-GCCcore-11.2.0 CMake/3.23.1-GCCcore-11.3.0 CMake/3.24.3-GCCcore-11.3.0 CUDA/11.3.1 CUDA/11.4.1 CUDA/11.7.0 CUDA/12.0.0 CapnProto/0.9.1-GCCcore-11.2.0 CellRanger/7.0.0 Centrifuge/1.0.4-gompi-2021b Cereal/1.3.0 Check/0.15.2-GCCcore-11.2.0 CheckM/1.1.3-foss-2021b Chimera/1.16-linux_x86_64 Circos/0.69-9-GCCcore-11.2.0 Clang/13.0.1-GCCcore-11.2.0 Clustal-Omega/1.2.4-GCC-11.2.0 ClustalW2/2.1-GCC-11.2.0 Consed/29.0-foss-2021b CoordgenLibs/3.0.1-gompi-2021b CppUnit/1.15.1-GCCcore-11.2.0 Cufflinks/20190706-GCC-11.2.0 Cytoscape/3.9.1-Java-11 DB/18.1.32-GCCcore-8.3.0 DB/18.1.40-GCCcore-10.2.0 DB/18.1.40-GCCcore-11.2.0 DB/18.1.40-GCCcore-11.3.0 DB/18.1.40-GCCcore-12.2.0 DBD-mysql/4.050-GCC-11.2.0 DB_File/1.857-GCCcore-11.2.0 DBus/1.13.18-GCCcore-11.2.0 DBus/1.14.0-GCCcore-11.3.0 DIAMOND/2.0.13-GCC-11.2.0 DIAMOND/2.0.15-GCC-11.2.0 DIAMOND/2.1.0-GCC-11.3.0 DataWarrior/5.5.0 DendroPy/4.5.2-GCCcore-11.2.0 Deve-Size/0.83-GCCcore-11.2.0-Perl-5.34.0 DockQ/1.0-foss-2022a Doxygen/1.9.1-GCCcore-11.2.0 Doxygen/1.9.4-GCCcore-11.3.0 ELPA/2021.11.001-foss-2021b EMBOSS/6.6.0-foss-2021b ETE/3.1.2-foss-2021b EasyBuild/4.6.0 Eigen/3.3.9-GCCcore-11.2.0 Eigen/3.4.0-GCCcore-11.2.0 Eigen/3.4.0-GCCcore-11.3.0 EnTAP/0.10.8-beta-foss-2021b Exonerate/2.4.0-GCC-11.2.0 FASTX-Toolkit/0.0.14-GCC-11.2.0 FFTW.MPI/3.3.10-gompi-2022a FFTW/3.3.8-gompi-2019b FFTW/3.3.10-GCC-11.3.0 FFTW/3.3.10-gompi-2021b FFmpeg/4.3.2-GCCcore-11.2.0 FLAC/1.3.3-GCCcore-11.2.0 FLAC/1.3.4-GCCcore-11.3.0 FLASH/2.2.00-GCC-11.2.0 FLTK/1.3.7-GCCcore-11.2.0 FSL/6.0.5.1-foss-2021b FTGL/2.4.0-GCCcore-11.3.0 FastANI/1.33-GCC-11.2.0 FastME/2.1.6.1-GCC-11.2.0 FastQC/0.11.9-Java-11 FastTree/2.1.11-GCCcore-11.2.0 Flask/2.0.2-GCCcore-11.2.0 Flask/2.2.2-GCCcore-11.3.0 FlexiBLAS/3.0.4-GCC-11.2.0 FlexiBLAS/3.2.0-GCC-11.3.0 Flye/2.9.1-GCC-11.2.0 FragGeneScan/1.31-GCCcore-11.2.0 FreeImage/3.18.0-GCCcore-11.2.0 FreeSurfer/7.4.1-foss-2021b FriBidi/1.0.10-GCCcore-11.2.0 FriBidi/1.0.12-GCCcore-11.3.0 GATK/4.3.0.0-GCCcore-11.2.0-Java-11 GATK/4.3.0.0-GCCcore-11.2.0-Java-13.0.2 GATK/4.3.0.0-GCCcore-11.3.0-Java-11 GCC/8.3.0 GCC/10.2.0 GCC/11.2.0 GCC/11.3.0 GCC/12.2.0 GCCcore/8.3.0 GCCcore/10.2.0 GCCcore/11.2.0 GCCcore/11.3.0 GCCcore/12.2.0 GD/2.75-GCCcore-11.2.0 GDAL/3.3.2-foss-2021b GDAL/3.5.0-foss-2022a GDRCopy/2.3-GCCcore-11.2.0 GDRCopy/2.3-GCCcore-11.3.0 GEOS/3.9.1-GCC-11.2.0 GEOS/3.10.3-GCC-11.3.0 GLPK/5.0-GCCcore-11.2.0 GLPK/5.0-GCCcore-11.3.0 GLib/2.69.1-GCCcore-11.2.0 GLib/2.72.1-GCCcore-11.3.0 GLibmm/2.66.4-GCCcore-11.2.0 GMAP-GSNAP/2021-21-17-GCC-11.2.0 GMAP-GSNAP/2023-02-17-GCC-11.3.0 GMP/6.1.2-GCCcore-8.3.0 GMP/6.2.1-GCCcore-11.2.0 GMP/6.2.1-GCCcore-11.3.0 GObject-Introspection/1.68.0-GCCcore-11.2.0 GObject-Introspection/1.72.0-GCCcore-11.3.0 GROMACS/2021.5-foss-2021b-CUDA-11.4.1-PLUMED-2.8.0 GSL/2.7-GCC-11.2.0 GSL/2.7-GCC-11.3.0 GST-plugins-base/1.18.5-GCC-11.2.0 GStreamer/1.18.5-GCC-11.2.0 GTK+/3.24.23-GCCcore-11.3.0 GTK2/2.24.33-GCCcore-11.3.0 GTK3/3.24.31-GCCcore-11.2.0 GTS/0.7.6-GCCcore-11.2.0 Gdk-Pixbuf/2.42.6-GCCcore-11.2.0 Gdk-Pixbuf/2.42.8-GCCcore-11.3.0 GeneMark-ET/4.71-GCCcore-11.2.0 GeneMarkS-T/5.1-GCCcore-11.2.0 Genome/05012020-foss-2021b GenomeThreader/1.7.3-Linux_x86_64-64bit GenomeTools/1.6.2-GCC-11.2.0 GffCompare/0.12.6-GCC-11.2.0 Ghostscript/9.54.0-GCCcore-11.2.0 Ghostscript/9.56.1-GCCcore-11.3.0 GitPython/3.1.24-GCCcore-11.2.0 GlimmerHMM/3.0.4c-GCC-11.2.0 Globus-CLI/3.6.0-GCCcore-11.2.0 Go/1.17.6 Grace/5.1.25-foss-2021b Graphviz/2.50.0-GCCcore-11.2.0 Guile/3.0.7-GCCcore-11.2.0 HDF/4.2.15-GCCcore-11.2.0 HDF/4.2.15-GCCcore-11.3.0 HDF5/1.10.8-gompi-2021b HDF5/1.10.8-gompi-2022a HDF5/1.12.1-gompi-2021b HDF5/1.12.2-gompi-2022a HEC-RAS/6.10 HH-suite/3.3.0-gompi-2021b HISAT2/2.2.1-gompi-2021b HISAT2/2.2.1-gompi-2022a HMMER/3.3.2-gompi-2021b HMMER/3.3.2-gompi-2022a HPL/2.3-foss-2021b HTSeq/2.0.2-foss-2021b HTSlib/1.9-GCC-11.2.0 HTSlib/1.14-GCC-11.2.0 HTSlib/1.15.1-GCC-11.3.0 HarfBuzz/2.8.2-GCCcore-11.2.0 HarfBuzz/4.2.1-GCCcore-11.3.0 HyPhy/2.5.33-gompi-2021b ICU/69.1-GCCcore-11.2.0 ICU/71.1-GCCcore-11.3.0 IDBA-UD/1.1.3-GCC-11.2.0 IGV/2.16.1-Java-11 IPython/7.26.0-GCCcore-11.2.0 IQ-TREE/2.2.1-gompi-2021b ISA-L/2.30.0-GCCcore-11.2.0 ImageMagick/7.1.0-4-GCCcore-11.2.0 ImageMagick/7.1.0-37-GCCcore-11.3.0 Infernal/1.1.4-foss-2021b Infernal/1.1.4-foss-2022a InterProScan/5.62-94.0-foss-2021b JAGS/4.3.0-foss-2021b JasPer/2.0.33-GCCcore-11.2.0 JasPer/2.0.33-GCCcore-11.3.0 Java/1.7.0_80 Java/1.8.0_241 Java/11.0.16 Java/13.0.2 Java/15.0.1 Java/17.0.6 Jellyfish/2.3.0-GCC-11.2.0 Jellyfish/2.3.0-GCC-11.3.0 JsonCpp/1.9.4-GCCcore-11.2.0 JsonCpp/1.9.5-GCCcore-11.3.0 Judy/1.0.5-GCCcore-11.2.0 Judy/1.0.5-GCCcore-11.3.0 Julia/1.8.2-linux-x86_64 Kalign/3.3.2-GCCcore-11.2.0 Kent_tools/422-GCC-11.2.0 KronaTools/2.8.1-GCCcore-11.2.0 LAME/3.100-GCCcore-11.2.0 LAME/3.100-GCCcore-11.3.0 LAMMPS/23Jun2022-foss-2021b-kokkos LAPACK/3.10.1-GCC-11.2.0 LASTZ/1.04.15-foss-2021b LLVM/12.0.1-GCCcore-11.2.0 LLVM/14.0.3-GCCcore-11.3.0 LMDB/0.9.29-GCCcore-11.2.0 LMDB/0.9.29-GCCcore-11.3.0 LSD2/2.3-GCCcore-11.2.0 LTR_retriever/2.9.0-foss-2021b-RepeatMasker-4.1.4 LTR_retriever/2.9.0-foss-2021b LZO/2.10-GCCcore-11.2.0 LZO/2.10-GCCcore-11.3.0 LibTIFF/4.3.0-GCCcore-11.2.0 LibTIFF/4.3.0-GCCcore-11.3.0 LightGBM/3.3.5-foss-2021b-CUDA-11.4.1 LightGBM/3.3.5-foss-2021b LittleCMS/2.12-GCCcore-11.2.0 LittleCMS/2.13.1-GCCcore-11.3.0 LoFreq/2.1.3.1-foss-2021b-Python-2.7.18 Lua/5.4.3-GCCcore-11.2.0 M4/1.4.18-GCCcore-8.3.0 M4/1.4.18-GCCcore-10.2.0 M4/1.4.18 M4/1.4.19-GCCcore-11.2.0 M4/1.4.19-GCCcore-11.3.0 M4/1.4.19-GCCcore-12.2.0 M4/1.4.19 MACS2/2.2.7.1-foss-2021b MAFFT/7.490-GCC-11.2.0-with-extensions MAFFT/7.490-gompi-2021b-with-extensions MCL/14.137-GCCcore-11.2.0 MEGAN/6.24.23-Java-17 MEME/5.4.1-gompi-2021b MEME/5.5.0-gompi-2021b METIS/5.1.0-GCCcore-11.2.0 MMseqs2/13-45111-gompi-2021b MMseqs2/14-7e284-gompi-2021b MMseqs2/14-7e284-gompi-2022a MPFR/4.1.0-GCCcore-11.2.0 MPFR/4.1.0-GCCcore-11.3.0 MUMmer/4.0.0beta2-GCCcore-11.2.0 MUMmer/4.0.0rc1-GCCcore-11.2.0 MUSCLE/3.8.31-GCCcore-11.2.0 Make-Lastz-Chains/0.9.1 Mako/1.1.4-GCCcore-11.2.0 Mako/1.2.0-GCCcore-11.3.0 MariaDB/10.6.4-GCC-11.2.0 MariaDB/10.9.3-GCC-11.3.0 Mash/2.3-GCC-11.2.0 Mesa/21.1.7-GCCcore-11.2.0 Mesa/22.0.3-GCCcore-11.3.0 Meson/0.55.3-GCCcore-11.2.0 Meson/0.58.2-GCCcore-11.2.0 Meson/0.62.1-GCCcore-11.3.0 MetaEuk/6-GCC-11.2.0 Miniconda3/4.12.0 Mirage/2.0.0-GCCcore-11.2.0 MuTect/1.1.7-Java-1.7.0_80 MultiQC/1.12-foss-2021b MySQL/8.0.34-glibc2.28 NASM/2.15.05-GCCcore-11.2.0 NASM/2.15.05-GCCcore-11.3.0 NCCL/2.10.3-GCCcore-11.2.0-CUDA-11.4.1 NGS/2.10.9-GCCcore-11.2.0 NGS/2.11.2-GCCcore-11.2.0 NLopt/2.7.0-GCCcore-11.2.0 NLopt/2.7.1-GCCcore-11.3.0 NSPR/4.32-GCCcore-11.2.0 NSS/3.69-GCCcore-11.2.0 NVHPC/22.11-CUDA-11.7.0 NVHPC/23.1-CUDA-12.0.0 Nextflow/22.10.6 Ninja/1.10.2-GCCcore-11.2.0 Ninja/1.10.2-GCCcore-11.3.0 ORCA/5.0.3-gompi-2021b OpenBLAS/0.3.7-GCC-8.3.0 OpenBLAS/0.3.18-GCC-11.2.0 OpenBLAS/0.3.20-GCC-11.3.0 OpenBabel/3.1.1-gompi-2021b OpenCV/4.5.5-foss-2021b-contrib OpenEXR/3.1.1-GCCcore-11.2.0 OpenJPEG/2.4.0-GCCcore-11.2.0 OpenJPEG/2.5.0-GCCcore-11.3.0 OpenMM/7.5.1-foss-2021b-DeepMind-patch OpenMPI/4.1.2-GCC-11.2.0-pmi2 OpenMPI/4.1.2-GCC-11.2.0 OpenMPI/4.1.4-GCC-11.3.0 OpenMPI/4.1.4-GCC-12.2.0 OpenPGM/5.2.122-GCCcore-11.2.0 OpenSSL/1.1 OrthoFinder/2.5.4-foss-2021b PAML/4.9j-GCCcore-11.2.0 PCRE/8.45-GCCcore-11.2.0 PCRE/8.45-GCCcore-11.3.0 PCRE2/10.37-GCCcore-11.2.0 PCRE2/10.40-GCCcore-11.3.0 PLINK/2.00a4-GCC-11.2.0 PLUMED/2.7.3-foss-2021b PLUMED/2.8.0-foss-2021b PMIx/3.1.5-GCCcore-10.2.0 PMIx/4.1.0-GCCcore-11.2.0 PMIx/4.1.2-GCCcore-11.3.0 PMIx/4.2.2-GCCcore-12.2.0 PROJ/8.1.0-GCCcore-11.2.0 PROJ/9.0.0-GCCcore-11.3.0 PTarPmiR/0.1-foss-2021b-Python-3.9.6 Pango/1.48.8-GCCcore-11.2.0 Pango/1.50.7-GCCcore-11.3.0 Perl/5.30.0-GCCcore-8.3.0-minimal Perl/5.30.0-GCCcore-8.3.0 Perl/5.32.0-GCCcore-10.2.0-minimal Perl/5.32.0-GCCcore-10.2.0 Perl/5.34.0-GCCcore-11.2.0-minimal Perl/5.34.0-GCCcore-11.2.0 Perl/5.34.1-GCCcore-11.3.0-minimal Perl/5.34.1-GCCcore-11.3.0 Perl/5.36.0-GCCcore-12.2.0 Phobius/1.01-GCCcore-11.2.0-Perl-5.34.0 Phrap/0.990329-foss-2021b Phred/0.071220.c-foss-2021b Pillow/8.3.2-GCCcore-11.2.0 Pilon/1.23-Java-11 PnetCDF/1.12.3-gompi-2021b PyBioLib/1.1.988-GCCcore-11.3.0 PyQt5/5.15.4-GCCcore-11.2.0 PyRosetta/4.release-339-GCCcore-11.2.0-Python-3.9.6 PyTorch/1.12.1-foss-2021b-CUDA-11.4.1 PyYAML/5.4.1-GCCcore-11.2.0 PyYAML/6.0-GCCcore-11.2.0 PyYAML/6.0-GCCcore-11.3.0 Pysam/0.17.0-GCC-11.2.0 Python/2.7.18-GCCcore-11.2.0-bare Python/2.7.18-GCCcore-11.2.0 Python/3.7.4-GCCcore-8.3.0 Python/3.9.6-GCCcore-11.2.0-bare Python/3.9.6-GCCcore-11.2.0 Python/3.10.4-GCCcore-11.3.0-bare Python/3.10.4-GCCcore-11.3.0 QUAST/5.0.2-foss-2021b Qhull/2020.2-GCCcore-11.2.0 Qt5/5.15.2-GCCcore-11.2.0 QuantumESPRESSO/7.1-foss-2021b Qwt/6.2.0-GCCcore-11.2.0 R/4.1.2-foss-2021b R/4.2.1-foss-2021b R/4.2.1-foss-2022a RAxML/8.2.12-gompi-2021b-hybrid-avx2 RDKit/2022.03.5-foss-2021b RE2/2022-02-01-GCCcore-11.2.0 RECON/1.08-GCC-11.2.0 RMBlast/2.11.0-gompi-2021b RMBlast/2.13.0-gompi-2021b RSEM/1.3.3-foss-2021b RSEM/1.3.3-foss-2022a Racon/1.5.0-GCCcore-11.2.0 RapidJSON/1.1.0-GCCcore-11.2.0 RepeatMasker/4.1.2-p1-foss-2021b RepeatMasker/4.1.4-foss-2021b RepeatModeler/2.0.2a-foss-2021b RepeatModeler/2.0.3-foss-2021b RepeatModeler/2.0.4-foss-2021b RepeatProfiler/1.1-foss-2021b RepeatScout/1.0.6-GCC-11.2.0 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