Dear EasyBuilders,
We're happy to announce the release of EasyBuild v4.8.0 [1].
This must be the best EasyBuild release so far...
Wait, hold on. Checking...
Yes, yes it is.
Don't be distracted by a bunch of guys pretending that riding a bike all
across a large European country in a couple of weeks, with an ugly shirt
as the main prize for the winner, is a sensible thing to do.
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.
(this information is also available at
https://github.com/easybuilders/easybuild/releases/tag/easybuild-v4.8.0)
## 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 at [4].
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 [5].
Two particularly easy options include:
* eb --install-latest-eb-release
* eb --from-pr 18282 # use easyconfig from PR #18282 [6]
Enjoy!
regards,
Kenneth & Miguel
[1] https://pypi.org/project/easybuild/4.8.0
[2] https://docs.easybuild.io/release-notes/#release_notes_eb480
[3]
https://docs.easybuild.io/partial-installations/#partial_installation_skip
[4] https://docs.easybuild.io/version-specific/supported-software
[5] https://docs.easybuild.io/installation/#updating
[6] https://github.com/easybuilders/easybuild-easyconfigs/pull/18282
