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EasyBuild v4.8.0
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@boegel boegel released this 07 Jul 21:04
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easybuild-v4.8.0
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EasyBuild v4.8.0 is primarily a feature release, but it also includes various minor bug fixes, enhancements, and updates.

The executive summary for this release:

  • Easyconfigs for the 2023a update of the foss + intel common toolchains;

  • 2 new easyblocks: a generic PerlBundle easyblock, and a custom easyblock for Rust;

  • Easyconfigs for various recent software versions, including elastix 5.0.0, GROMACS 2023.1, PyTorch 1.13.1, VTK 9.2.6, ...;

  • Support for installing 76 new software applications and libraries;

Highlights for this release are listed below. More details are available in the release notes [2] which includes links to the respective pull requests for more detailed information.

Highlighted enhancements & updates

(enhancements or updates that (may) warrant updating existing installations are marked with (***))

  • add PerlBundle generic easyblock for installing a bundle of Perl modules;

  • add custom easyblock for Rust, which makes sure that all shared libraries use RPATH rather than RUNPATH if --rpath is used;

  • add support for install_cmds in Binary easyblock;

  • update OpenBLAS easyblock since make shared is necessary and sufficient with OpenBLAS 0.3.23 + recent parallel build fixes;

  • (***) add extra packages to recent R easyconfigs;

  • (***) add extra packages to recent R-bundle-Bioconductor easyconfigs;

  • (***) enable building static libs and check for libexslt.* in libxslt;

Prominent bug fixes & changes

(bug fixes or changes that (may) warrant reinstalling easyconfigs are marked with (***))

  • fix regex for extracting glibc version from output of 'ldd --version' in Gentoo Linux;

  • stop running tests with Python 2.7 since it is no longer supported in GitHub Actions;

  • patch CMake's UnixPaths.cmake script if --sysroot is set;

  • use upstream patch for symbol compatibility in XZ 5.2.5;

  • (***) change base compiler for intel/2023.03 to GCCcore/12.3.0 (required to use it as intel/2023a);

  • (***) use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2;

  • (***) stick to FFmpeg 4.4.2 as dependency for SoX 14.4.2;

  • (***) fix exec permissions for all binaries & scripts of L_RNA_scaffolder 20190530;

  • (***) update SUNDIALS dependency for Cantera v2.6.0 to v6.5.1 + add missing dependencies;

  • (***) fix incorrect version for GMAP-GSNAP 2021-12-17 (was 2021-21-17);

  • (***) fix toolchain for networkx-3.0 (foss/2022b -> gfbf/2022b);

  • (***) bump OpenSSL 1.1 wrapper fallback to 1.1.1u;

Supported software

Support for installing 76 new software packages has been added, including (but not limited to):

  • alleleIntegrator
  • BayesPrism
  • Circuitscape
  • DALI
  • DaliLite
  • ecFlow
  • FragPipe
  • GLIMPSE
  • KerasTuner
  • mannkendall
  • MONAI-Label
  • NanoStat
  • pastml
  • Perl-bundle-CPAN
  • PyBioLib
  • PyWBGT
  • Sniffles
  • Tapenade
  • timm
  • wrapt
  • xclip

This brings the total number of supported software packages to 3,161 (excluding extensions)!
An up-to-date list of supported software is available here.

Various software updates have been added, including (but not limited to):

  • alleleCount 4.2.1
  • BayesTraits 3.0.2
  • Bowtie2 2.5.1
  • Cellpose 2.2.2
  • CUDA 12.1.1 + 12.2.0
  • CVXOPT 1.3.1
  • deepTools 3.5.2
  • DMTCP 3.0.0
  • dorado 0.3.0 + 0.3.1
  • duplex-tools 0.3.3
  • fastp 0.23.4
  • FreeSurfer 7.4.0
  • GATK 4.4.0.0
  • GCC 11.4.0
  • Geant4 11.1.2
  • GROMACS 2023.1
  • Horovod 0.25.0
  • Julia 1.9.0
  • LibLZF 3.6
  • MAGeCK 0.5.9.5
  • MaxQuant 2.4.2.0
  • MMseqs2 14-7e284
  • MuJoCo 2.2.2
  • ncbi-vdb 3.0.5
  • ont-fast5-api 4.1.1
  • openpyxl 3.1.2
  • ParaView 5.11.1
  • Perl 5.36.1
  • PSI4 1.7
  • Pysam 0.21.0
  • Python 3.11.3
  • PyTorch 1.13.1
  • Rust 1.70.0
  • seqtk 1.4
  • SUNDIALS 6.5.1
  • TransDecoder 5.5.0
  • Transformers 4.29.2 + 4.30.2
  • VTK 9.2.6
  • xarray 2023.4.2
  • zlib-ng 2.0.7

These changes result from various contributions, made by 25 different contributors:

  • 9 merged pull requests for EasyBuild framework
  • 13 merged pull requests for easyblocks
  • 301 merged pull requests for easyconfigs

Thanks to everyone who contributed to this release in one way or another!

To upgrade to EasyBuild v4.8.0, there are several options.
Two particularly easy options include:

  • eb --install-latest-eb-release

  • eb --from-pr 18282 # use easyconfig from PR #18282

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