new(github.com/pachterlab/kallisto): kallisto 0.52.0#13465
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RNA-seq quantification (C++/CMake). HDF5+zlib; explicit HDF5_LIBRARIES (find_package commented upstream); COMPILATION_ARCH=OFF for arm64; companion transcripts.fa.
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Adds kallisto — near-optimal RNA-seq quantification. C++/CMake. Links HDF5 (
-DUSE_HDF5=ON) + zlib. Upstream comments outfind_package(HDF5), so the recipe injects-DHDF5_INCLUDE_DIRS/-DHDF5_LIBRARIES(full .so/.dylib path) — load-bearing, else the link breaks.-DCOMPILATION_ARCH=OFFdrops-march=native(and must NOT setENABLE_AVX2=OFF, which injects x86-only-mno-avx2that gcc rejects on aarch64).CMAKE_POLICY_VERSION_MINIMUM=3.5(env, so the bundled bifrost ExternalProject inherits it under cmake 4). gcc 14 build + libstdcxx runtime on linux (gcc 16 fails bifrost templates; darwin = Apple clang). Verified on linux/arm64:lddshows libhdf5 linked,kallisto version-> 0.52.0,kallisto index+inspecton a shippedtranscripts.fa.