diff options
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/fasta/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/fasta/fasta-36.3.5e.ebuild | 79 | ||||
| -rw-r--r-- | sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch | 74 |
3 files changed, 0 insertions, 154 deletions
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest index cff190468270..c0bd97106d3a 100644 --- a/sci-biology/fasta/Manifest +++ b/sci-biology/fasta/Manifest @@ -1,2 +1 @@ -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-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.5e.ebuild deleted file mode 100644 index c4c94d0e7f21..000000000000 --- a/sci-biology/fasta/fasta-36.3.5e.ebuild +++ /dev/null @@ -1,79 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit epatch flag-o-matic toolchain-funcs - -DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package" -HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml" -SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}36/${P}.tar.gz" - -LICENSE="fasta" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos" -IUSE="debug cpu_flags_x86_sse2 test" -RESTRICT="!test? ( test )" - -DEPEND="test? ( app-shells/tcsh )" -RDEPEND="" - -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="${ALT}" - - epatch "${FILESDIR}"/${P}-ldflags.patch - - sed \ - -e 's:-ffast-math::g' \ - -i make/Makefile* || die - -} - -src_compile() { - cd src || die - emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all -} - -src_test() { - cd test || die - FASTLIBS="../conf" bash test.sh || die -} - -src_install() { - local bin - dobin bin/* - - pushd bin > /dev/null || die - for bin in *36; do - dosym ${bin} /usr/bin/${bin%36} - done - popd - - 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-36.3.5e-ldflags.patch b/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch deleted file mode 100644 index a6eeabfdf46c..000000000000 --- a/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch +++ /dev/null @@ -1,74 +0,0 @@ - make/Makefile.pcom | 8 ++++---- - make/Makefile.pcom_s | 8 ++++---- - make/Makefile.pcom_t | 8 ++++---- - 3 files changed, 12 insertions(+), 12 deletions(-) - -diff --git a/make/Makefile.pcom b/make/Makefile.pcom -index 9c5f801..33fc001 100644 ---- a/make/Makefile.pcom -+++ b/make/Makefile.pcom -@@ -209,14 +209,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c - $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M) - - 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 -diff --git a/make/Makefile.pcom_s b/make/Makefile.pcom_s -index dc53001..8a45044 100644 ---- a/make/Makefile.pcom_s -+++ b/make/Makefile.pcom_s -@@ -143,14 +143,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c - $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M) - - 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 -diff --git a/make/Makefile.pcom_t b/make/Makefile.pcom_t -index 8a71438..5b08a50 100644 ---- a/make/Makefile.pcom_t -+++ b/make/Makefile.pcom_t -@@ -164,14 +164,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c - $(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M) - - 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 |