diff options
Diffstat (limited to 'sci-biology/dialign-tx')
4 files changed, 82 insertions, 2 deletions
diff --git a/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild new file mode 100644 index 000000000000..123977916f06 --- /dev/null +++ b/sci-biology/dialign-tx/dialign-tx-1.0.2-r2.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2017 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=6 + +inherit toolchain-funcs + +MY_P=${PN^^}_${PV} + +DESCRIPTION="Greedy and progressive approaches for segment-based multiple sequence alignment" +HOMEPAGE="http://dialign-tx.gobics.de/" +SRC_URI="http://dialign-tx.gobics.de/${MY_P}.tar.gz" + +LICENSE="LGPL-2.1" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +S=${WORKDIR}/${MY_P} +PATCHES=( + "${FILESDIR}"/${P}-fix-build-system.patch + "${FILESDIR}"/${P}-implicits.patch + "${FILESDIR}"/${P}-modernize.patch + "${FILESDIR}"/${P}-gnu89-inline.patch +) + +src_configure() { + tc-export CC +} + +src_compile() { + emake -C source clean + emake -C source +} + +src_install() { + dobin source/dialign-tx + insinto /usr/$(get_libdir)/${PN}/conf + doins -r conf/. +} + +pkg_postinst() { + einfo "The configuration directory is" + einfo "${EROOT%/}/usr/$(get_libdir)/${PN}/conf" + einfo "You will need to pass this to ${PN} on every run." +} diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch new file mode 100644 index 000000000000..cbfd458043c5 --- /dev/null +++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-fix-build-system.patch @@ -0,0 +1,24 @@ +--- a/source/Makefile ++++ b/source/Makefile +@@ -1,4 +1,3 @@ +-CC=gcc
+ # debug
+ #CPPFLAGS=-g -O0 -Q -v -da
+ #CPPFLAGS=-g -O0 -fstack-check -Q -v -da
+@@ -8,7 +7,6 @@ + # THIS IS FOR THE OPTIMIZED ONE
+ #CPPFLAGS=-g
+ #CPPFLAGS=-O3 -march=i686 -funroll-loops
+-CPPFLAGS=-O3 -funroll-loops -march=i686 -mfpmath=sse -msse -mmmx
+ #CPPFLAGS=-march=athlon-mp -g -O0 -Wall -D_USE_XOPEN -D__unix__
+
+ OBJ_DIR=.
+@@ -33,7 +31,7 @@ +
+ museq: $(OBJ)
+ rm -f $(TARGET)/$@
+- $(CC) -o $(TARGET)/$@ \
++ $(CC) $(LDFLAGS) -o $(TARGET)/$@ \
+ $(OBJ) \
+ -pipe -Wall -lm
+ mv museq dialign-tx
diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch new file mode 100644 index 000000000000..21f576f07052 --- /dev/null +++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-gnu89-inline.patch @@ -0,0 +1,11 @@ +--- a/source/diag.c ++++ b/source/diag.c +@@ -958,7 +958,7 @@ + * The pointer returned (and the ones included in the struct) + * has to be deallocted explicitely from memory. + */ +-inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix, ++static inline struct simple_diag_col* find_diags_dialign(struct scr_matrix *smatrix, + struct prob_dist *pdist, struct seq* seq1, + struct seq* seq2, struct alignment *algn, + long double **tmp_dist, int round) { diff --git a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch index a8388d03232f..d82a5bf4be33 100644 --- a/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch +++ b/sci-biology/dialign-tx/files/dialign-tx-1.0.2-implicits.patch @@ -1,5 +1,5 @@ ---- source/museq.c -+++ source/museq.c +--- a/source/museq.c ++++ b/source/museq.c @@ -38,6 +38,7 @@ //extern void calc_weight(struct diag* dg, struct scr_matrix* smatrix, // struct prob_dist *pdist); |