Merge pull request #72 from scimerman/main

Shape-it latest update
molgenis · Mar 11, 2024 · 1044a3e · 1044a3e
2 parents e6f66ed + c9f5d61
commit 1044a3e
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Showing 4 changed files with 51 additions and 14 deletions.
diff --git a/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2022a.eb b/s/SHAPEIT4/SHAPEIT4-4.2.0-foss-2022a.eb
@@ -17,7 +17,7 @@ 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
+    '526ec38647a7a2605e1dafdc3e54f2b1693c036e6e356c85c5810ecee7296452',  # SHAPEIT4_4.2.0_use_EB_settings.patch
 ]
 
 github_account = 'odelaneau'

diff --git a/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2022a.eb b/s/SHAPEIT4/SHAPEIT4-4.2.2-foss-2022a.eb
@@ -17,7 +17,7 @@ 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
+    'b9d5753b49a3d7c046366e7ddadc4f2833f61ac8f75c3b46e69bfca418a1ac53',  # SHAPEIT4_4.2.2_use_EB_settings.patch
 ]
 
 github_account = 'odelaneau'

diff --git a/s/SHAPEIT4/SHAPEIT4_use_EB_settings.patch → ...EIT4/SHAPEIT4_4.2.0_use_EB_settings.patch b/s/SHAPEIT4/SHAPEIT4_use_EB_settings.patch → ...EIT4/SHAPEIT4_4.2.0_use_EB_settings.patch
@@ -1,10 +1,5 @@
-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
+--- shapeit4-4.2.0/makefile   2021-01-21 08:05:26.000000000 +0000
++++ shapeit4-4.2.0.new/makefile  2021-02-19 17:32:01.321128179 +0000
 @@ -1,14 +1,14 @@
  #COMPILER MODE C++11
 -CXX=g++ -std=c++11
@@ -26,16 +21,20 @@ index c0bd9d2..808b7cd 100644
 
  #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!
+@@ -25,12 +25,14 @@
  #CXXFLAG=-O3 -march=native
- #Good performance and portable on most intel CPUs
+
+ #Good performance and portable on most CPUs
 -CXXFLAG=-O3 -mavx2 -mfma 
 +#CXXFLAG=-O3 -mavx2 -mfma 
+
  #Portable version without avx2 (much slower)
  #CXXFLAG=-O3
+
 -LDFLAG=-O3
-+#LDFLAG=-O3
++#CXXFLAG=${CXXFLAGS}
++
++#LDFLAG=${OPTFLAGS}
+
 
  #DYNAMIC LIBRARIES
- DYN_LIBS=-lz -lbz2 -lm -lpthread -llzma
diff --git a/s/SHAPEIT4/SHAPEIT4_4.2.2_use_EB_settings.patch b/s/SHAPEIT4/SHAPEIT4_4.2.2_use_EB_settings.patch
@@ -0,0 +1,38 @@
+--- shapeit4-4.2.2/makefile   2021-09-07 13:08:23.000000000 +0100
++++ shapeit4-4.2.2.new/makefile  2021-10-06 17:34:49.006112748 +0100
+@@ -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=$(HOME)/Tools/htslib-1.11
+-HTSLIB_LIB=$(HOME)/Tools/htslib-1.11/libhts.a
++#HTSLIB_INC=$(HOME)/Tools/htslib-1.11
++#HTSLIB_LIB=$(HOME)/Tools/htslib-1.11/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
+@@ -25,12 +25,12 @@
+ #CXXFLAG=-O3 -march=native
+
+ #Good performance and portable on most CPUs
+-CXXFLAG=-O3 -mavx2 -mfma 
++#CXXFLAG=-O3 -mavx2 -mfma 
+
+ #Portable version without avx2 (much slower)
+ #CXXFLAG=-O3
+
+-LDFLAG=-O3
++#LDFLAG=-O3
+
+
+ #DYNAMIC LIBRARIES