diff options
Diffstat (limited to 'sci-biology/clustalw-mpi')
| -rw-r--r-- | sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild (renamed from sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild) | 19 | ||||
| -rw-r--r-- | sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch | 13 | ||||
| -rw-r--r-- | sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch (renamed from sci-biology/clustalw-mpi/files/0.13-gentoo.patch) | 0 | ||||
| -rw-r--r-- | sci-biology/clustalw-mpi/metadata.xml | 18 |
4 files changed, 32 insertions, 18 deletions
diff --git a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild index 76d3b80cde32..334c34e78ce6 100644 --- a/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r2.ebuild +++ b/sci-biology/clustalw-mpi/clustalw-mpi-0.13-r3.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 inherit toolchain-funcs @@ -12,28 +12,31 @@ SRC_URI="http://web.bii.a-star.edu.sg/~kuobin/${PN}/${P}.tar.gz" LICENSE="public-domain" SLOT="0" KEYWORDS="~amd64 ~x86" -IUSE="mpi_njtree static_pairalign" +IUSE="mpi-njtree static-pairalign" DEPEND="virtual/mpi" RDEPEND="${DEPEND}" -PATCHES=( "${FILESDIR}"/${PV}-gentoo.patch ) +PATCHES=( + "${FILESDIR}"/${P}-makefile.patch + "${FILESDIR}"/${P}-fno-common.patch +) src_prepare() { default - if use mpi_njtree; then + if use mpi-njtree; then sed -e "s/TREES_FLAG/#TREES_FLAG/" -i Makefile || \ die "Failed to configure MPI code for NJ trees" fi - if use static_pairalign; then + if use static-pairalign; then sed -e "s/DDYNAMIC_SCHEDULING/DSTATIC_SCHEDULING/" -i Makefile || \ die "Failed to configure static scheduling for pair alignments" fi } src_install() { - dobin ${PN} - newdoc README.${PN} README + dobin clustalw-mpi + newdoc README.clustalw-mpi README } diff --git a/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch new file mode 100644 index 000000000000..da74f0ba172d --- /dev/null +++ b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-fno-common.patch @@ -0,0 +1,13 @@ +--- a/parallel_compare.c ++++ b/parallel_compare.c +@@ -74,8 +74,8 @@ + static sint **accum; + static sint *diag_index; + static char *slopes; +-sint ktup,window,wind_gap,signif; +-sint *zza, *zzb, *zzc, *zzd; ++extern sint ktup,window,wind_gap,signif; ++extern sint *zza, *zzb, *zzc, *zzd; + extern Boolean percent; + static void make_p_ptrs(sint *tptr, sint *pl, sint naseq, sint l); + static void make_n_ptrs(sint *tptr, sint *pl, sint naseq, sint len); diff --git a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch index 6e36061cbb39..6e36061cbb39 100644 --- a/sci-biology/clustalw-mpi/files/0.13-gentoo.patch +++ b/sci-biology/clustalw-mpi/files/clustalw-mpi-0.13-makefile.patch diff --git a/sci-biology/clustalw-mpi/metadata.xml b/sci-biology/clustalw-mpi/metadata.xml index 8ab4494152c8..ffe2c4efec87 100644 --- a/sci-biology/clustalw-mpi/metadata.xml +++ b/sci-biology/clustalw-mpi/metadata.xml @@ -1,14 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> -<maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> -</maintainer> -<use> - <flag name="mpi_njtree">Use MPI (as opposed to serial) code for computing - neighbor-joining trees</flag> - <flag name="static_pairalign">Use static (as opposed to dynamic) scheduling - for pair alignments</flag> -</use> + <maintainer type="project"> + <email>sci-biology@gentoo.org</email> + <name>Gentoo Biology Project</name> + </maintainer> + <use> + <flag name="mpi-njtree">Use MPI (as opposed to serial) code for computing neighbor-joining trees</flag> + <flag name="static-pairalign">Use static (as opposed to dynamic) scheduling for pair alignments</flag> + </use> </pkgmetadata> |