commit: 84e1af9d2932d855c6f05b3bda91a4dfedd2b0a4 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sat Mar 19 17:07:57 2022 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sat Mar 19 17:07:57 2022 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=84e1af9d
sci-biology/fasta: add 36.3.8h Bug: https://bugs.gentoo.org/648618 Bug: https://bugs.gentoo.org/828700 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/fasta/Manifest | 1 + sci-biology/fasta/fasta-36.3.8h.ebuild | 81 ++++++++++++++++++++++ .../fasta/files/fasta-36.3.8h-ldflags.patch | 63 +++++++++++++++++ 3 files changed, 145 insertions(+) diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest index 800c5b2628b4..cff190468270 100644 --- a/sci-biology/fasta/Manifest +++ b/sci-biology/fasta/Manifest @@ -1 +1,2 @@ DIST fasta-36.3.5e.tar.gz 943763 BLAKE2B 6234d0aee76af6614e6d25ebcfbdfae080db5bc5adf611aeb6edc53ed7c6cb6cef257bf852ed39bc286527cec4175c251765ce23ea5ff39d12ff8947dba97ac6 SHA512 ddfcae36dadd7e2ed5c8c8c0bda2eed077e9f6cd55e4ebf507690671af156358e9da4e7cb1406d2b8713c326c54a9d829fc25e668b16dfa6df48d18e3a009812 +DIST fasta-36.3.8h.tar.gz 1257682 BLAKE2B e6bd9087563150355fed6edf52a24a0b31ef0658b1e95c3df6d5b5711fc4d137ddd773fb8b3b2fa82fe3f5c310689b2f89668f5b51654eed41ed71f9ef140f99 SHA512 30d160ad083a605397c6c35d2b28f6064cd96f51f99b3664b424ec1dbbbd09772c72e89731a7257306ab58c4ad4b877e229873abd0e09407c64fae643bc04391 diff --git a/sci-biology/fasta/fasta-36.3.8h.ebuild b/sci-biology/fasta/fasta-36.3.8h.ebuild new file mode 100644 index 000000000000..cbe7a89c0383 --- /dev/null +++ b/sci-biology/fasta/fasta-36.3.8h.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic toolchain-funcs + +MY_PV="${PV}_04-May-2020" + +DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package" +HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"; +SRC_URI="https://github.com/wrpearson/fasta36/archive/refs/tags/v${MY_PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${PN}36-${MY_PV}" + +LICENSE="fasta" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos" +IUSE="debug cpu_flags_x86_sse2 test" +RESTRICT="!test? ( test )" + +BDEPEND="test? ( app-shells/tcsh )" + +src_prepare() { + CC_ALT= + CFLAGS_ALT= + ALT= + + use debug && append-flags -DDEBUG + + if [[ $(tc-getCC) == *icc* ]]; then + CC_ALT=icc + ALT="${ALT}_icc" + else + CC_ALT=$(tc-getCC) + use x86 && ALT="32" + use amd64 && ALT="64" + fi + + if use cpu_flags_x86_sse2 ; then + ALT="${ALT}_sse2" + append-flags -msse2 + [[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math + fi + + export CC_ALT="${CC_ALT}" + export ALT="${ALT}" + + eapply "${FILESDIR}"/${P}-ldflags.patch + + sed \ + -e 's:-ffast-math::g' \ + -i make/Makefile* || die + + eapply_user +} + +src_compile() { + emake -C src -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all +} + +src_test() { + cd test || die + FASTLIBS="../conf" bash test.sh || die +} + +src_install() { + dobin bin/* + + pushd bin >/dev/null || die + local i + for i in *36; do + dosym ${i} /usr/bin/${i%36} + done + popd >/dev/null || die + + insinto /usr/share/${PN} + doins -r conf/. data seq + + doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1} + dodoc FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*} +} diff --git a/sci-biology/fasta/files/fasta-36.3.8h-ldflags.patch b/sci-biology/fasta/files/fasta-36.3.8h-ldflags.patch new file mode 100644 index 000000000000..40070d50fe76 --- /dev/null +++ b/sci-biology/fasta/files/fasta-36.3.8h-ldflags.patch @@ -0,0 +1,63 @@ +--- a/make/Makefile.pcom ++++ b/make/Makefile.pcom +@@ -216,14 +216,14 @@ + $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c pssm_asn_subs.c $(LIB_M) $(LIB_DB) + + map_db : map_db.c uascii.h ncbl2_head.h +- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c + + list_db : list_db.c +- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c + + + lav2ps : lav2plt.o lavplt_ps.o +- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm + + lav2svg : lav2plt.o lavplt_svg.o +- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm +--- a/make/Makefile.pcom_s ++++ b/make/Makefile.pcom_s +@@ -149,14 +149,14 @@ + $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c pssm_asn_subs.c $(LIB_M) $(LIB_DB) + + map_db : map_db.c uascii.h ncbl2_head.h +- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c + + list_db : list_db.c +- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c + + + lav2ps : lav2plt.o lavplt_ps.o +- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm + + lav2svg : lav2plt.o lavplt_svg.o +- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm +--- a/make/Makefile.pcom_t ++++ b/make/Makefile.pcom_t +@@ -171,14 +171,14 @@ + $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c pssm_asn_subs.c $(LIB_M) $(LIB_DB) + + map_db : map_db.c uascii.h ncbl2_head.h +- $(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c + + list_db : list_db.c +- $(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c ++ $(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c + + + lav2ps : lav2plt.o lavplt_ps.o +- $(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm + + lav2svg : lav2plt.o lavplt_svg.o +- $(CC) -DUNIX -o $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm ++ $(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg lav2plt.o lavplt_svg.o -lm
