init

2 files changed, 108 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..875ead086339
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,19 @@
+# Generated by mksrcinfo v8
+# Mon Feb  8 16:05:55 UTC 2016
+pkgbase = seqan-git
+	pkgdesc = C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data
+	pkgver = r.fcad60a
+	pkgrel = 1
+	url = http://www.seqan.de/
+	arch = i686
+	arch = x86_64
+	license = custom
+	makedepends = cmake
+	depends = bash
+	depends = bzip2
+	depends = zlib
+	conflicts = seqan
+	conflicts = seqan2
+
+pkgname = seqan-git
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..db56ceb802a0
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,89 @@
+# Maintainer: zfo <zfoofz1@gmail.com>
+# Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
+
+pkgname=seqan-git
+_pkgname=seqan
+pkgver=r.fcad60a
+pkgrel=1
+pkgdesc='C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data'
+arch=('i686' 'x86_64')
+url="http://www.seqan.de/"
+license=('custom')
+depends=('bash' 'bzip2' 'zlib')
+makedepends=('cmake')
+conflicts=('seqan' 'seqan2')
+source=()
+md5sums=()
+
+_gitroot=https://github.com/seqan/seqan
+_gitname=seqan
+
+update_git(){
+  cd "$srcdir"
+  msg "Connecting to GIT server...."
+
+  if [[ -d "$_gitname" ]]; then
+    cd "$_gitname" && git pull origin > /dev/null
+    msg "The local files are updated."
+  else
+    git -q clone --depth 1 "$_gitroot" "$_gitname"
+  fi
+
+  msg "GIT checkout done or server timeout"
+}
+
+pkgver() {
+  update_git
+  cd "${srcdir}/${_gitname}"
+  printf "r.%s" "$(git rev-parse --short HEAD)"
+}
+
+build() {
+  msg "Starting build..."
+
+  #zfo: this seems to me unnecessary
+  #rm -rf "$srcdir/$_gitname-build"
+  if [[ -d "$_gitname" ]]; then
+  	cd "$srcdir/$_gitname-build" && git pull origin
+  else
+  	git clone "$srcdir/$_gitname" "$srcdir/$_gitname-build"
+  fi
+  cd "$srcdir/$_gitname-build"
+
+  # common patching (aka prepare)
+  mkdir -p build
+
+  sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \
+      -i $(grep -rl '/usr/bin/env python')
+  ###
+
+  cd "$srcdir/$_gitname-build"/build
+
+  cmake \
+    -DCMAKE_INSTALL_PREFIX=/usr \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DPYTHON_EXECUTABLE=/usr/bin/python2 \
+    -DSEQAN_BUILD_SYSTEM=SEQAN_RELEASE \
+    ..
+
+  make
+}
+
+package() {
+  cd "$srcdir/$_gitname-build"/build
+
+  make prefix=/usr DESTDIR=$pkgdir install
+
+  install -Dm644 $pkgdir/usr/share/doc/sak/man/sak.1 $pkgdir/usr/share/man/man1/sak.1
+  rm $pkgdir/usr/share/doc/sak/man/sak.1
+  rmdir $pkgdir/usr/share/doc/sak/man
+
+  install -Dm644 ../LICENSE $pkgdir/usr/share/licenses/$pkgname/LICENSE
+
+  # install popular apps
+  files=("mason_frag_sequencing" "mason_genome" "mason_materializer" "mason_methylation"
+	"mason_simulator" "mason_splicing" "mason_tests" "mason_variator")
+  for file in "${files[@]}" ; do
+  	install -Dm644 bin/$file $pkgdir/usr/bin/$file
+  done
+}