add: seqlib

prepare/freebayes/PKGBUILD

@@ -18,7 +18,9 @@ prepare() {
   cd "$pkgname"
   git submodule update --init --recursive
   # find vcflib
-  sed -i "s|dependency('libvcflib'|cc.find_library('libvcflib'" CMakeLists.txt
+  sed -i "s|dependency('libvcflib'|cc.find_library('libvcflib'|g" meson.build
+  sed -i "s|dependency('libseqlib'|cc.find_library('libseqlib'|g" meson.build
+  # sed -i "167c include_directories : [ seqlib_inc]," meson.build
 }
 build() {
   cd "$pkgname"

prepare/seqlib/PKGBUILD

@@ -0,0 +1,45 @@
+pkgname=seqlib
+pkgver=1.2.0
+pkgrel=1
+pkgdesc="C++ htslib/bwa-mem/fermi interface for interrogating sequence data"
+arch=('i686' 'x86_64')
+url="https://github.com/walaj/SeqLib"
+license=('Apache')
+depends=('htslib')
+# Do NOT add 'bwa' to depends, this package uses a flavored version of bwa.
+makedepends=('autoconf' 'git')
+source=("${pkgname}::git+https://github.com/walaj/SeqLib.git#tag=${pkgver}"
+"fermi-lite::git+https://github.com/walaj/fermi-lite.git"
+)
+
+prepare(){
+    cd $srcdir/${pkgname}
+    git submodule update --init --recursive
+    sed -i '33c extern const uint8_t rle_auxtab[8];' bwa/rle.h fermi-lite/rle.h
+}
+build() {
+  cd ${pkgname}
+  ./configure LDFLAGS='-lcurl -lcrypto' CFLAGS='-fPIC' CXXFLAGS='-fPIC'
+  make
+  make seqtools
+}
+
+package() {
+  cd ${pkgname}
+  make install
+  install -d ${pkgdir}/usr
+  mv bin lib ${pkgdir}/usr
+  cd ${pkgdir}/usr/lib
+  # {bwa,fml,hts,seqlib};
+  for mylib in {seqlib,};
+  do
+    ar -x lib${mylib}.a
+    gcc  -shared *.o -o lib${mylib}.so
+    rm -rf *.o
+  done
+
+  mkdir -p ${pkgdir}/usr/include/
+  cp -rf SeqLib ${pkgdir}/usr/include/
+}
+sha256sums=('SKIP'
+            'SKIP')