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48 lines
1.3 KiB
Plaintext
48 lines
1.3 KiB
Plaintext
# IT4Innovations
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# LK 2021
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easyblock = 'CMakeMake'
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name = 'Salmon'
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version = '2.1.0'
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homepage = 'https://github.com/COMBINE-lab/salmon'
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description = """Salmon is a wicked-fast program to produce a highly-accurate,
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transcript-level quantification estimates from RNA-seq data."""
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toolchain = {'name': 'intel', 'version': '2020b'}
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toolchainopts = {'pic': True, 'openmp': True}
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source_urls = ['http://salmon-tddft.jp/download/']
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sources = ['SALMON-v.%(version)s.tar.gz']
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checksums = ['95e1fabbbf161359ce6ec563cace99f4']
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builddependencies = [
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('CMake', '3.18.4'),
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('pkg-config', '0.29.2'),
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('jemalloc', '5.2.1'),
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]
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dependencies = [
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('Boost', '1.74.0'),
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('tbb', '2020.3'),
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]
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# Disable link-time optimizations (-flto) because it triggers a segfault/internal compiler error (ICE) with GCC 9.3.0
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# This problem might be solved with a newer version of either GCC or Salmon.
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configopts = '-DJEMALLOC_ROOT=$EBROOTJEMALLOC -DNO_IPO=1'
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# need to unset the $LD_PRELOAD set be jemalloc to avoid hanging 'make test'
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# since jemalloc is statically linked in Salmon (and hence only a build dep),
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# this only affects the tests
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pretestopts = "unset LD_PRELOAD && "
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runtest = 'test'
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sanity_check_paths = {
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'files': ['bin/%(namelower)s'],
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'dirs': [],
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}
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sanity_check_commands = ["salmon --help"]
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moduleclass = 'bio'
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