commit: 989059eec92c6fda0890e076cb9fc70fc994ed3f Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Jun 26 08:15:28 2018 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Tue Jun 26 08:15:28 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=989059ee
sci-biology/stringtie: keep modified bundled copy of samtools-0.1.18 https://github.com/gpertea/stringtie/issues/185#issuecomment-400128090 https://github.com/gpertea/stringtie/issues/186#issuecomment-400131844 Therefore, keep local copy of gclib and samtools. Still it does not compile for me with gcc-7.3.0 Package-Manager: Portage-2.3.40, Repoman-2.3.9 sci-biology/stringtie/files/Makefile.patch | 6 +++--- sci-biology/stringtie/stringtie-1.2.2.ebuild | 18 +++++++----------- 2 files changed, 10 insertions(+), 14 deletions(-) diff --git a/sci-biology/stringtie/files/Makefile.patch b/sci-biology/stringtie/files/Makefile.patch index 7db068985..a7ca43c39 100644 --- a/sci-biology/stringtie/files/Makefile.patch +++ b/sci-biology/stringtie/files/Makefile.patch @@ -2,9 +2,9 @@ +++ stringtie-1.2.2/Makefile 2018-06-26 00:46:43.406712302 +0200 @@ -1,13 +1,15 @@ -BAM := ./samtools-0.1.18 -+BAM_INC = -I$(EPREFIX)/usr/include/bam-0.1-legacy -+BAM_LIB = # or -L/some/path -+BAM_LIBS = -lbam-0.1-legacy ++BAM_INC = -I./samtools-0.1.18 ++BAM_LIB = -L./samtools-0.1.18 ++BAM_LIBS = -lbam #path to the directory where the samtools package was built (in place) #so libbam.a and *.h files MUST be in here diff --git a/sci-biology/stringtie/stringtie-1.2.2.ebuild b/sci-biology/stringtie/stringtie-1.2.2.ebuild index 37c0f26cf..953999e87 100644 --- a/sci-biology/stringtie/stringtie-1.2.2.ebuild +++ b/sci-biology/stringtie/stringtie-1.2.2.ebuild @@ -8,25 +8,21 @@ HOMEPAGE="https://ccb.jhu.edu/software/stringtie https://github.com/gpertea/stringtie"; SRC_URI="http://ccb.jhu.edu/software/stringtie/dl/${P}.tar.gz"; -LICENSE="Artistic-2" +LICENSE="Artistic-2 MIT" # MIT from bundled samtools-0.1.18 SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="" -# contains bundled gclib (0.9.8?), well they are just headers -DEPEND=" - sci-biology/gclib - sci-biology/samtools:0.1-legacy" # bundled samtools-0.1.18 +# contains bundled and modified samtools-0.1.18 +# https://github.com/gpertea/stringtie/issues/185#issuecomment-400128090 +# +# contains bundled gclib (0.9.8?), a modified version? +# https://github.com/gpertea/stringtie/issues/186#issuecomment-400131844 +DEPEND="" RDEPEND="${DEPEND}" PATCHES=( "${FILESDIR}"/Makefile.patch ) -src_prepare(){ - default - rm -r samtools-0.1.18 || die - # TODO: `rm -rf ./gclib' and fix Makefile -} - src_compile(){ emake release }
