vep: add v110-v112 #44251
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vep: add v110-v112 #44251
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…e addressed and HAIL's requirements can be met
…ned requirements for HAIL
…. Py4J will call Java to start a Java sub process and will fail at runtime if it is not available
e2fsprogs: adding version 1.47.0 and fuse2fs variant fuse-overlayfs: adding version 1.13 squashfuse: adding version 0.5.1 and 0.5.2 e2fsprogs: fixing audit errors apptainer: expanding deps to cover more versions, fix binary_path logic. apptainer: add go version deps, fix e2fsprogs patch sums, rework dep paths fuse-overlayfs: tightening up the libfuse dep Signed-off-by: Shane Nehring <snehring@iastate.edu>
* update * Apply suggestions from code review Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> --------- Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Adding gmsh 4.11.1 * Becoming a maintainer --------- Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Spglib: add version 2.4.0 * DLA-Future: fix +test option * update * [@spackbot] updating style on behalf of RMeli * Apply suggestions from code review Co-authored-by: Wouter Deconinck <wdconinc@gmail.com> --------- Co-authored-by: RMeli <RMeli@users.noreply.github.com> Co-authored-by: Wouter Deconinck <wdconinc@gmail.com>
* Add GASNet v 2024.5.0 * cosmetic fix to info output * Add a missing dependency * Ensure GASNet detects the provided ROCm/CUDA dependency * [@spackbot] updating style on behalf of bonachea --------- Co-authored-by: bonachea <bonachea@users.noreply.github.com>
* Now need to explicitly depend on libfabric for Cray EX * Ensure build uses the selected CUDA and ROCm versions * Correct spelling on `configure --with-ldflags` * Patch a defect regarding `configure --with-ldflags` * Default to Spack's copy of GASNet-EX, which is newer than embedded
teaguesterling
changed the title
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Once the other recent pull requests are merged this can be rebased and will be ready to go. The handling of the cache still needs some consideration however. |
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This was split up into multiple PRs |
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This is a draft. The VEP install process is built around a custom perl script that we're currently wrapping. Ideally we could download the dependencies as either resources or (ideally) by creating additional
perl-bio-ensembl-...packages to install the appropriate dependencies.The
veppackage installs the core tools and perl scripts as well as the VEP installer that is also used to download caches.The
vep-cachepackage uses VEP installer to download requisite resources and allow them to be selected (with appropriate spack-based paths) as an additional package that sets up runtime environment variables.