diff options
| author | Christian Krause | 2015-07-21 11:03:46 +0200 |
|---|---|---|
| committer | Christian Krause | 2015-07-21 11:03:46 +0200 |
| commit | 08f5a1daf4739879925a088ebb3948a6480e423e (patch) | |
| tree | ae91e7c1fd1a8e8dad3e1d63b04cc2a5fc6d2ca8 | |
| parent | db42972ca5f8f0754ad12e3cdc822237897c4542 (diff) | |
| download | aur-08f5a1daf4739879925a088ebb3948a6480e423e.tar.gz | |
blasr-git-r114.b5b717f-1
| -rw-r--r-- | .SRCINFO | 2 | ||||
| -rw-r--r-- | PKGBUILD | 47 |
2 files changed, 28 insertions, 21 deletions
@@ -1,6 +1,6 @@ pkgbase = blasr-git pkgdesc = The PacBio long read aligner - pkgver = r98.caaf74a + pkgver = r114.b5b717f pkgrel = 1 url = https://github.com/PacificBiosciences/blasr arch = i686 @@ -1,7 +1,7 @@ # Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com> pkgname=blasr-git -pkgver=r98.caaf74a +pkgver=r114.b5b717f pkgrel=1 pkgdesc="The PacBio long read aligner" arch=('i686' 'x86_64') @@ -29,7 +29,8 @@ prepare() { git submodule update sed -e 's|^#!/usr/bin/env python$|#!/usr/bin/env python2|' \ - -i libcpp/configure.py + -i configure.py \ + 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 += $(LDFLAGS1) -lhdf5_cpp -lhdf5 -lpthread -lz -ldl|' \ @@ -43,29 +44,35 @@ prepare() { -e 's|$(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 + 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 } build() { cd $srcdir/$pkgname - make -j1 HDF5_LIB=/usr/lib/libhdf5.so HDF5_INC=/usr/include ZLIB_ROOT=/usr + export NOPBBAM= + export HDF5_INCLUDE=/usr/include + export HDF5_LIB=/usr/lib + + cd libcpp + + ./configure.py \ + --no-pbbam \ + --submodules \ + --shared + + make + + cd .. + + ./configure.py \ + --no-pbbam \ + --submodules \ + --shared + + make } package() { |