Add new recipe for Alder (#13390)

New recipe for Alder software

recipes/alder/bioconda.patch

@@ -0,0 +1,49 @@
+diff --git a/Alder.cpp b/Alder.cpp
+index 2b64c09..b621c22 100644
+--- a/Alder.cpp
++++ b/Alder.cpp
+@@ -40,7 +40,7 @@ namespace ALD {
+
+   double sq(double x) { return x*x; }
+
+-  Alder::AffineData::AffineData(int n=0, int _num_refs=0) {
++  Alder::AffineData::AffineData(int n, int _num_refs) {
+     count = 0;
+     ws = ss = s2 = 0.0;
+     wg = gg = gs = vector <double> (n);
+diff --git a/Alder.hpp b/Alder.hpp
+index 9e9b6f6..eb5457b 100644
+--- a/Alder.hpp
++++ b/Alder.hpp
+@@ -36,7 +36,7 @@ namespace ALD {
+       vector <double> wg, gg, gs;
+       vector < vector <double> > gigj;
+       int num_refs;
+-      AffineData(int n, int _num_refs);
++      AffineData(int n=0, int _num_refs=0);
+     };
+
+     // constants for determining LD correlation extent
+diff --git a/AlderParams.cpp b/AlderParams.cpp
+index d4e44db..47bd92a 100644
+--- a/AlderParams.cpp
++++ b/AlderParams.cpp
+@@ -172,7 +172,7 @@ namespace ALD {
+     phandle *ph ;
+
+     int i;
+-    while ((i = getopt (argc, argv, "p:vV")) != -1) {
++    while ((i = getopt (argc, argv, "hp:vV")) != -1) {
+       switch (i)
+ 	{
+ 	case 'p':
+@@ -184,6 +184,9 @@ namespace ALD {
+ 	case 'V':
+ 	  verbose = YES ;
+ 	  break; 
++  case 'h':
++    printf ("Usage: alder -p <parameter file> \n") ;
++    exit(0);
+ 	case '?':
+ 	  printf ("Usage: bad params.... \n") ;
+ 	  fatalx("bad params\n") ;

recipes/alder/build.sh

@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+
+if [[ $(uname -s) == Darwin ]]; then
+	make CXX=clang++ \
+		 CXXFLAGS="-Wall -Wno-return-type -Wno-write-strings -I$PREFIX/include -Iadmixtools_src -Iadmixtools_src/nicksrc" \
+		 CFLAGS="-c -O2 -Wimplicit -Wno-return-type -Wno-write-strings -I$PREFIX/include -I. -I./nicksrc" \
+		 L="-L$PREFIX/lib -lfftw3 -llapack -fopenmp"
+else
+	make CXXFLAGS="-Wall -Wno-return-type -Wno-write-strings -I$PREFIX/include -Iadmixtools_src -Iadmixtools_src/nicksrc" \
+		 CFLAGS="-c -O2 -Wimplicit -Wno-return-type -Wno-write-strings -I$PREFIX/include -I. -I./nicksrc" \
+		 L="-L$PREFIX/lib -lfftw3 -llapack -fopenmp"
+fi
+
+mkdir -p $PREFIX/bin
+cp alder $PREFIX/bin/

recipes/alder/license.txt

@@ -0,0 +1,5 @@
+This software is licensed for academic and non-profit use only.  The
+source code included in the admixtools_src/ subdirectory is derived
+from Nick Patterson's ADMIXTOOLS software suite:
+
+  http://genetics.med.harvard.edu/reich/Reich_Lab/Software.html

recipes/alder/meta.yaml

@@ -0,0 +1,44 @@
+package:
+  name: alder
+  version: "1.03"
+
+build:
+  number: 0
+
+source:
+  url: http://cb.csail.mit.edu/cb/alder/alder_v1.03.tar.gz
+  sha256: aae68848dc444946aefe171322e0d98b1a0cc0c82f3669007ad9608d331b7241
+  patches:
+    - bioconda.patch
+
+requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - patch
+  host:
+    - fftw
+    - lapack
+    - clangdev     # [osx]
+    - libcxx 4.0.* # [osx]
+    - openmp 4.0.* # [osx]
+  run:
+    - fftw
+    - lapack
+    - libcxx 4.0.* # [osx]
+    - openmp 4.0.* # [osx]
+
+test:
+  commands:
+    - alder -h > /dev/null 2>&1
+
+about:
+  home: http://cb.csail.mit.edu/cb/alder/
+  license: Custom OSS
+  license_file: license.txt
+  summary: The ALDER software computes the weighted linkage disequilibrium (LD) statistic for making inference about population admixture
+
+extra:
+  identifiers:
+    - biotools:alder
+    - doi:10.1534/genetics.112.147330