diff options
| -rw-r--r-- | .SRCINFO | 12 | ||||
| -rw-r--r-- | .gitignore | 1 | ||||
| -rw-r--r-- | PKGBUILD | 66 |
3 files changed, 30 insertions, 49 deletions
@@ -1,16 +1,22 @@ +# Generated by mksrcinfo v8 +# Fri Feb 24 10:24:48 UTC 2017 pkgbase = blasr-git pkgdesc = The PacBio long read aligner - pkgver = r122.9593a09 + pkgver = r507.f8bfa9c pkgrel = 1 url = https://github.com/PacificBiosciences/blasr arch = i686 arch = x86_64 license = custom - makedepends = python2 + makedepends = cmake depends = hdf5-cpp-fortran provides = blasr conflicts = blasr - source = blasr-git::git+https://github.com/PacificBiosciences/blasr + source = git+https://github.com/PacificBiosciences/blasr + source = git+https://github.com/PacificBiosciences/blasr_libcpp + source = git+https://github.com/PacificBiosciences/pbbam + md5sums = SKIP + md5sums = SKIP md5sums = SKIP pkgname = blasr-git diff --git a/.gitignore b/.gitignore new file mode 100644 index 000000000000..42ab3cf03f2d --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +*.pkg.tar* @@ -1,83 +1,57 @@ # Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com> pkgname=blasr-git -pkgver=r122.9593a09 +pkgver=r507.f8bfa9c pkgrel=1 pkgdesc="The PacBio long read aligner" arch=('i686' 'x86_64') url="https://github.com/PacificBiosciences/blasr" license=('custom') depends=('hdf5-cpp-fortran') -makedepends=('python2') +makedepends=('cmake') conflicts=('blasr') provides=('blasr') -source=("$pkgname::git+https://github.com/PacificBiosciences/blasr") +source=("git+https://github.com/PacificBiosciences/blasr" + "git+https://github.com/PacificBiosciences/blasr_libcpp" + "git+https://github.com/PacificBiosciences/pbbam") -md5sums=('SKIP') +md5sums=('SKIP' 'SKIP' 'SKIP') pkgver() { - cd $srcdir/$pkgname + cd $srcdir/blasr printf "r%s.%s" "$(git rev-list --count HEAD)" "$(git rev-parse --short HEAD)" } prepare() { - cd $srcdir/$pkgname + cd $srcdir/blasr git submodule init - git submodule update - sed -e 's|^#!/usr/bin/env python$|#!/usr/bin/env python2|' \ - -i configure.py \ - libcpp/configure.py + git config submodule.libcpp.url $srcdir/blasr_libcpp + git config submodule.pbbam.url $srcdir/pbbam - # 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|' \ - -i libcpp/unittest/normal.defines.mk \ - libcpp/unittest/common.mk + git submodule update - sed -e 's|DEP_LIBS += ${LIBPBDATA_LIB} ${HDF5_LIB} ${PBBAM_LIB} ${HTSLIB_LIB} ${ZLIB_LIB}|DEP_LIBS += ${LIBPBDATA_LIB} ${PBBAM_LIB} ${HTSLIB_LIB} ${ZLIB_LIB}|' \ - -i libcpp/alignment/makefile \ - libcpp/hdf/makefile + mkdir -p build } build() { - cd $srcdir/$pkgname - - export NOPBBAM= - export HDF5_INCLUDE=/usr/include - export HDF5_LIB=/usr/lib + cd $srcdir/blasr/build - cd libcpp - - ./configure.py \ - --no-pbbam \ - --submodules \ - --shared - - make - - cd .. - - ./configure.py \ - --no-pbbam \ - --submodules \ - --shared + cmake \ + -DCMAKE_INSTALL_PREFIX=/usr \ + -DCMAKE_BUILD_TYPE=Release \ + .. make } package() { - cd $srcdir/$pkgname - - for file in blasr utils/loadPulses utils/pls2fasta utils/samFilter utils/samtoh5 utils/samtom4 utils/sawriter utils/sdpMatcher utils/toAfg ; do - install -Dm755 $file $pkgdir/usr/bin/$(basename $file) - done + cd $srcdir/blasr/build - for file in libcpp/pbdata/libpbdata.so libcpp/hdf/libpbihdf.so libcpp/alignment/libblasr.so ; do - install -Dm755 $file $pkgdir/usr/lib/$(basename $file) - done + make DESTDIR=$pkgdir install - install -Dm644 LICENSES.txt $pkgdir/usr/share/licenses/$pkgname/LICENSE + install -Dm644 ../LICENSE $pkgdir/usr/share/licenses/$pkgname/LICENSE } |