Internalized jellyfish v1 dependency

1 files changed, 43 insertions, 11 deletions

diff --git a/PKGBUILD b/PKGBUILD
index af3ee9e593b6..6d610b772f8a 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,27 +1,55 @@
 # Maintainer: Clint Valentine <valentine.clint@gmail.com>
 
+_jellyfishver=1.1.11
 pkgname=kraken
 pkgver=1.1
-pkgrel=2
+pkgrel=3
 pkgdesc="Kraken taxonomic sequence classification system"
-arch=('i686' 'x86_64')
+arch=('x86_64')
 url=https://github.com/DerrickWood/"${pkgname}"
 license=('GPL3')
 depends=('perl')
-optdepends=('jellyfish<=1: for building Kraken databases')
-source=("${pkgname}"-"${pkgver}".tar.gz::https://github.com/DerrickWood/"${pkgname}"/archive/v"${pkgver}".tar.gz)
-sha256sums=('a4ac74c54c10920f431741c80d8a172670be12c3b352912000030fb5ea4c87a7')
+source=(
+  "${pkgname}"-"${pkgver}".tar.gz::https://github.com/DerrickWood/"${pkgname}"/archive/v"${pkgver}".tar.gz
+  jellyfish-"${_jellyfishver}".tar.gz::http://www.cbcb.umd.edu/software/jellyfish/jellyfish-"${_jellyfishver}".tar.gz
+)
+sha256sums=(
+  'a4ac74c54c10920f431741c80d8a172670be12c3b352912000030fb5ea4c87a7'
+  '496645d96b08ba35db1f856d857a159798c73cbc1eccb852ef1b253d1678c8e2'
+)
 _installation_dir=/usr/share/"${pkgname}"-"${pkgver}"
 
 prepare() {
-  cd "${srcdir}"/"${pkgname}"-"${pkgver}"
+  pushd "${srcdir}"/"${pkgname}"-"${pkgver}"
   sed -i "s#\$(KRAKEN_DIR)#${pkgdir}${_installation_dir}#g" src/Makefile
   make -C src clean
+
+  for script in scripts/*; do
+    sed -i "s|#####=KRAKEN_DIR=#####|${_installation_dir}|g" "${script}"
+    sed -i "s|#####=VERSION=#####|${pkgver}|g" "${script}"
+  done
+
+  sed -i "s#  check_for_jellyfish.sh##g" scripts/build_kraken_db.sh
+  sed -i "s#jellyfish#${_installation_dir}/jellyfish#g" scripts/build_kraken_db.sh
+  popd
+
+  pushd "${srcdir}"/jellyfish-"${_jellyfishver}"
+  ./configure --prefix="${_installation_dir}"
+  make clean
+  popd
 }
 
 build() {
   cd "${srcdir}"/"${pkgname}"-"${pkgver}"
   make -C src
+
+  cd "${srcdir}"/jellyfish-"${_jellyfishver}"
+  make
+}
+
+check() {
+  cd "${srcdir}"/jellyfish-"${_jellyfishver}"
+  # make check
 }
 
 package() {
@@ -31,11 +59,8 @@ package() {
 
   make -C src install
 
-  for scripts in scripts/*; do
-    sed -i "s|#####=KRAKEN_DIR=#####|${_installation_dir}|g" "${scripts}"
-    sed -i "s|#####=VERSION=#####|${pkgver}|g" "${scripts}"
-
-    install -Dm775 "${scripts}" "${pkgdir}""${_installation_dir}"/
+  for script in scripts/*; do
+    install -Dm775 "${script}" "${pkgdir}""${_installation_dir}"/
   done
 
   install -D -m644 LICENSE "${pkgdir}"/usr/share/licenses/"${pkgname}"_v"${pkgver}"/LICENSE
@@ -49,4 +74,11 @@ package() {
   for file in "${pkgdir}${_installation_dir}"/kraken*; do
     install -Dm775 "${file}" "${pkgdir}"/usr/bin/$( basename "${file}" )
   done
+
+  cd "${srcdir}"/jellyfish-"${_jellyfishver}"
+  install -D -m644 LICENSE "${pkgdir}"/usr/share/licenses/jellyfish_"${_jellyfishver}"/LICENSE
+  install -D -m644 HalfLICENSE "${pkgdir}"/usr/share/licenses/jellyfish_"${_jellyfishver}"/HalfLICENSE
+  install -D -m644 README "${pkgdir}"/usr/share/doc/jellyfish-"${_jellyfishver}"/README
+
+  install -Dm775 bin/jellyfish  "${pkgdir}${_installation_dir}"/jellyfish
 }