From 79f3238d0637faec3dd99858744137336a6350dd Mon Sep 17 00:00:00 2001
From: Lukas Krupcik <lukas.krupcik@vsb.cz>
Date: Tue, 24 May 2022 12:07:13 +0200
Subject: [PATCH] new file: s/Salmon/Salmon-2.1.0-intel-2020b.eb
modified: v/vaspkit/vaspkit-1.3.3-foss-2020b.eb
---
s/Salmon/Salmon-2.1.0-intel-2020b.eb | 47 +++++++++++++++++++++++++++
v/vaspkit/vaspkit-1.3.3-foss-2020b.eb | 2 +-
2 files changed, 48 insertions(+), 1 deletion(-)
create mode 100644 s/Salmon/Salmon-2.1.0-intel-2020b.eb
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