From 4dd95ec2c3e7986749fdd575e5551eb4a7041835 Mon Sep 17 00:00:00 2001
From: scimerman <sandi.cimerman@gmail.com>
Date: Fri, 1 Mar 2024 12:47:49 +0000
Subject: [PATCH] added SHAPEIT4: 4.2.0 & 4.2.2

---
 s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2022a.eb   | 46 +++++++++++++++++++++++
 s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2022a.eb   | 46 +++++++++++++++++++++++
 s/SHAPEIT4/SHAPEIT4_use_EB_settings.patch | 41 ++++++++++++++++++++
 3 files changed, 133 insertions(+)
 create mode 100644 s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2022a.eb
 create mode 100644 s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2022a.eb
 create mode 100644 s/SHAPEIT4/SHAPEIT4_use_EB_settings.patch

diff --git a/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2022a.eb b/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2022a.eb
new file mode 100644
index 0000000..75800f6
--- /dev/null
+++ b/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2022a.eb
@@ -0,0 +1,46 @@
+easyblock = "MakeCp"
+
+name = 'SHAPEIT4'
+version = '4.2.0'
+
+homepage = 'https://odelaneau.github.io/shapeit4/'
+description = """
+SHAPEIT4 is a fast and accurate method for estimation of haplotypes
+(aka phasing) for SNP array and high coverage sequencing data.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'opt': True, 'cstd': 'c++11'}
+
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['SHAPEIT4_%(version)s_use_EB_settings.patch']
+checksums = [
+    '329aa920be49b085c96b420d4f42ade7ba92eae8a202ecb2f71ca32a61955588',  # v4.2.0.tar.gz
+    'c4a5a5d280463a7e39435239284702e0d13feb2eb10f902434874176c884516e',  # SHAPEIT4_4.2.0_use_EB_settings.patch
+]
+
+github_account = 'odelaneau'
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.2.5'),
+    ('Boost', '1.79.0'),
+    ('HTSlib', '1.14'),
+]
+
+buildopts = 'HTSLIB_INC="$EBROOTHTSLIB/include" HTSLIB_LIB=-lhts '
+buildopts += 'BOOST_INC="$EBROOTBOOST/include" BOOST_LIB_IO=-lboost_iostreams BOOST_LIB_PO=-lboost_program_options '
+buildopts += 'CXX="$CXX" CXXFLAG="$CXXFLAGS" LDFLAG="$CXXFLAGS" '
+
+files_to_copy = [(['bin/shapeit4.2'], 'bin'), 'maps']
+
+sanity_check_paths = {
+    'files': ["bin/shapeit4.2"],
+    'dirs': ['maps']
+}
+
+sanity_check_commands = ['shapeit4.2 --help']
+
+moduleclass = 'bio'
+
diff --git a/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2022a.eb b/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2022a.eb
new file mode 100644
index 0000000..b249c82
--- /dev/null
+++ b/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2022a.eb
@@ -0,0 +1,46 @@
+easyblock = "MakeCp"
+
+name = 'SHAPEIT4'
+version = '4.2.2'
+
+homepage = 'https://odelaneau.github.io/shapeit4/'
+description = """
+SHAPEIT4 is a fast and accurate method for estimation of haplotypes
+(aka phasing) for SNP array and high coverage sequencing data.
+"""
+
+toolchain = {'name': 'foss', 'version': '2022a'}
+toolchainopts = {'opt': True, 'cstd': 'c++11'}
+
+source_urls = [GITHUB_SOURCE]
+sources = ['v%(version)s.tar.gz']
+patches = ['SHAPEIT4_%(version)s_use_EB_settings.patch']
+checksums = [
+    '9f109e307b5cc22ab68e7bf77de2429a9bbb2212d66303386e6a3dd81a5bc556',  # v4.2.2.tar.gz
+    '92ed45545bfcde7b1fbe079e6321ccae00865c8f0f66a924e872967d762df885',  # SHAPEIT4_4.2.2_use_EB_settings.patch
+]
+
+github_account = 'odelaneau'
+dependencies = [
+    ('zlib', '1.2.12'),
+    ('bzip2', '1.0.8'),
+    ('XZ', '5.2.5'),
+    ('Boost', '1.79.0'),
+    ('HTSlib', '1.14'),
+]
+
+buildopts = 'HTSLIB_INC="$EBROOTHTSLIB/include" HTSLIB_LIB=-lhts '
+buildopts += 'BOOST_INC="$EBROOTBOOST/include" BOOST_LIB_IO=-lboost_iostreams BOOST_LIB_PO=-lboost_program_options '
+buildopts += 'CXX="$CXX" CXXFLAG="$CXXFLAGS" LDFLAG="$CXXFLAGS" '
+
+files_to_copy = [(['bin/shapeit4.2'], 'bin'), 'maps']
+
+sanity_check_paths = {
+    'files': ["bin/shapeit4.2"],
+    'dirs': ['maps']
+}
+
+sanity_check_commands = ['shapeit4.2 --help']
+
+moduleclass = 'bio'
+
diff --git a/s/SHAPEIT4/SHAPEIT4_use_EB_settings.patch b/s/SHAPEIT4/SHAPEIT4_use_EB_settings.patch
new file mode 100644
index 0000000..a2492bd
--- /dev/null
+++ b/s/SHAPEIT4/SHAPEIT4_use_EB_settings.patch
@@ -0,0 +1,41 @@
+Don't use the hardcoded values in the makefile
+
+Åke Sandgren, 20200615
+diff --git a/makefile b/makefile
+index c0bd9d2..808b7cd 100644
+--- a/makefile
++++ b/makefile
+@@ -1,14 +1,14 @@
+ #COMPILER MODE C++11
+-CXX=g++ -std=c++11
++#CXX=g++ -std=c++11
+ 
+ #HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS]
+-HTSLIB_INC=$(HOME)/Tools/htslib-1.9
+-HTSLIB_LIB=$(HOME)/Tools/htslib-1.9/libhts.a
++#HTSLIB_INC=$(HOME)/Tools/htslib-1.9
++#HTSLIB_LIB=$(HOME)/Tools/htslib-1.9/libhts.a
+ 
+ #BOOST IOSTREAM & PROGRAM_OPTION LIBRARIES [SPECIFY YOUR OWN PATHS]
+-BOOST_INC=/usr/include
+-BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a
+-BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a
++#BOOST_INC=/usr/include
++#BOOST_LIB_IO=/usr/lib/x86_64-linux-gnu/libboost_iostreams.a
++#BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a
+ 
+ #HTSLIB LIBRARY [SPECIFY YOUR OWN PATHS]
+ #HTSLIB_INC=/software/UHTS/Analysis/samtools/1.4/include
+@@ -23,10 +23,10 @@ BOOST_LIB_PO=/usr/lib/x86_64-linux-gnu/libboost_program_options.a
+ #Best performance is achieved with this. Use it if running on the same plateform you're compiling, it's definitely worth it!
+ #CXXFLAG=-O3 -march=native
+ #Good performance and portable on most intel CPUs
+-CXXFLAG=-O3 -mavx2 -mfma 
++#CXXFLAG=-O3 -mavx2 -mfma 
+ #Portable version without avx2 (much slower)
+ #CXXFLAG=-O3
+-LDFLAG=-O3
++#LDFLAG=-O3
+ 
+ #DYNAMIC LIBRARIES
+ DYN_LIBS=-lz -lbz2 -lm -lpthread -llzma