diff --git a/s/Salmon/Salmon-2.1.0-intel-2020b.eb b/s/Salmon/Salmon-2.1.0-intel-2020b.eb new file mode 100644 index 00000000..e7fec667 --- /dev/null +++ b/s/Salmon/Salmon-2.1.0-intel-2020b.eb @@ -0,0 +1,47 @@ +# IT4Innovations +# LK 2021 +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '2.1.0' + +homepage = 'https://github.com/COMBINE-lab/salmon' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimates from RNA-seq data.""" + +toolchain = {'name': 'intel', 'version': '2020b'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['http://salmon-tddft.jp/download/'] +sources = ['SALMON-v.%(version)s.tar.gz'] +checksums = ['95e1fabbbf161359ce6ec563cace99f4'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('pkg-config', '0.29.2'), + ('jemalloc', '5.2.1'), +] + +dependencies = [ + ('Boost', '1.74.0'), + ('tbb', '2020.3'), +] + +# Disable link-time optimizations (-flto) because it triggers a segfault/internal compiler error (ICE) with GCC 9.3.0 +# This problem might be solved with a newer version of either GCC or Salmon. +configopts = '-DJEMALLOC_ROOT=$EBROOTJEMALLOC -DNO_IPO=1' + +# need to unset the $LD_PRELOAD set be jemalloc to avoid hanging 'make test' +# since jemalloc is statically linked in Salmon (and hence only a build dep), +# this only affects the tests +pretestopts = "unset LD_PRELOAD && " +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["salmon --help"] + +moduleclass = 'bio' diff --git a/v/vaspkit/vaspkit-1.3.3-foss-2020b.eb b/v/vaspkit/vaspkit-1.3.3-foss-2020b.eb index 9d6457d2..3b426301 100644 --- a/v/vaspkit/vaspkit-1.3.3-foss-2020b.eb +++ b/v/vaspkit/vaspkit-1.3.3-foss-2020b.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = [SOURCEFORGE_SOURCE] sources = ['%(namelower)s.%(version)s.linux.x64.tar.gz'] -patches = ['vaspkit-1.3.3-foss-2020b-adjust-installation-process.patch'] +patches = ['vaspkit-1.3.3-foss-2020b-fix-install.patch'] checksums = [ 'a7d9e2cf011c424a8edadee7c893a34f2f886d0c450f803838a15b4c4a1561c9', # vaspkit.1.3.3.linux.x64.tar.gz '0ba8cadc06cc3d753bbd25fae99e5c52599a1cac2d793ccd6a1eb7adb2a9e0be', # vaspkit-1.3.3-foss-2020b-fix-install.patch