blasr-git-r98.caaf74a-1

2 files changed, 38 insertions, 14 deletions

diff --git a/.SRCINFO b/.SRCINFO
index d9bb5cd6f278..c433c57280f5 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,12 +1,16 @@
 pkgbase = blasr-git
 	pkgdesc = The PacBio long read aligner
-	pkgver = r70.463a369
+	pkgver = r98.caaf74a
 	pkgrel = 1
 	url = https://github.com/PacificBiosciences/blasr
 	arch = i686
 	arch = x86_64
 	license = custom
+	makedepends = python2
 	depends = hdf5-cpp-fortran
+	depends = htslib
+	provides = blasr
+	conflicts = blasr
 	source = blasr-git::git+https://github.com/PacificBiosciences/blasr
 	md5sums = SKIP
 
diff --git a/PKGBUILD b/PKGBUILD
index 70c79574ad1d..bdf3d66eebc6 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,13 +1,16 @@
 # Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com>
 
 pkgname=blasr-git
-pkgver=r70.463a369
+pkgver=r98.caaf74a
 pkgrel=1
 pkgdesc="The PacBio long read aligner"
 arch=('i686' 'x86_64')
 url="https://github.com/PacificBiosciences/blasr"
 license=('custom')
-depends=('hdf5-cpp-fortran')
+depends=('hdf5-cpp-fortran' 'htslib')
+makedepends=('python2')
+conflicts=('blasr')
+provides=('blasr')
 
 source=("$pkgname::git+https://github.com/PacificBiosciences/blasr")
 
@@ -22,18 +25,11 @@ pkgver() {
 prepare() {
   cd $srcdir/$pkgname
 
-  # with the git@github.com: url you would need to have both a github account and have set it up for ssh
-  # so we use https instead
-  sed -e 's|git@github.com:|https://github.com/|' \
-      -i .gitmodules
-
   git submodule init
   git submodule update
 
-  # otherwise there would be this error:
-  # Makefile:42: *** recipe commences before first target.  Stop.
-  sed -e 's|    INCLUDES +=|\tINCLUDES +=|' \
-      -i libcpp/pbdata/Makefile
+  sed -e 's|^#!/usr/bin/env python$|#!/usr/bin/env python2|' \
+      -i libcpp/configure.py
 
   # we want to link against shared libs
   sed -e 's|LDFLAGS   := $(LDFLAGS1) $(HDF5_LIB)/libhdf5_cpp.a $(HDF5_LIB)/libhdf5.a -lpthread -lz -ldl|LDFLAGS   += $(LDFLAGS1) -lhdf5_cpp -lhdf5 -lpthread -lz -ldl|' \
@@ -41,6 +37,26 @@ prepare() {
       -i common.mk \
          libcpp/unittest/common.mk
 
+  # use system provided htslib
+  sed -e 's|HTSLIB_INCLUDE    := $(PBBAM)/../htslib/htslib|HTSLIB_INCLUDE    := /usr/include|' \
+      -e 's|HTSLIB_LIB    := $(PBBAM)/../htslib|HTSLIB_LIB    := /usr/lib|' \
+      -e 's|$(HTSLIB_LIB)/libhts.a|$(HTSLIB_LIB)/libhts.so|' \
+      -i common.mk
+
+  # PBINCROOT fix
+  sed -e '1 i top_srcdir := $(PWD)' \
+      -e '1 i PBINCROOT := $(top_srcdir)/libcpp' \
+      -i Makefile
+
+  # moar PBINCROOT fixes
+  sed -e '1 i PBINCROOT := ../libcpp' \
+      -e 's|pblib: $(PBINCROOT)/Makefile|pblib: $(PBINCROOT)/makefile|' \
+      -i utils/Makefile
+
+  # this is neither included nor needed
+  sed -e 's|-lpbbam||' \
+      -i common.mk
+
   # don't link statically
   sed -e 's|-static||' \
       -i common.mk
@@ -49,7 +65,7 @@ prepare() {
 build() {
   cd $srcdir/$pkgname
 
-  make HDF5_LIB=/usr/lib HDF5_INC=/usr/include ZLIB_ROOT=/usr
+  make -j1 HDF5_LIB=/usr/lib/libhdf5.so HDF5_INC=/usr/include ZLIB_ROOT=/usr
 }
 
 package() {
@@ -59,5 +75,9 @@ package() {
     install -Dm755 $file $pkgdir/usr/bin/$(basename $file)
   done
 
-  install -Dm644 <(echo unknown) $pkgdir/usr/share/licenses/$pkgname/LICENSE
+  for file in libcpp/pbdata/libpbdata.so libcpp/hdf/libpbihdf.so libcpp/alignment/libblasr.so ; do
+    install -Dm755 $file $pkgdir/usr/lib/$(basename $file)
+  done
+
+  install -Dm644 LICENSES.txt $pkgdir/usr/share/licenses/$pkgname/LICENSE
 }