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authorV3n3RiX <venerix@koprulu.sector>2022-03-20 00:40:44 +0000
committerV3n3RiX <venerix@koprulu.sector>2022-03-20 00:40:44 +0000
commit4cbcc855382a06088e2f016f62cafdbcb7e40665 (patch)
tree356496503d52354aa6d9f2d36126302fed5f3a73 /sci-biology/fasta
parentfcc5224904648a8e6eb528d7603154160a20022f (diff)
gentoo resync : 20.03.2022
Diffstat (limited to 'sci-biology/fasta')
-rw-r--r--sci-biology/fasta/Manifest6
-rw-r--r--sci-biology/fasta/fasta-36.3.8h-r1.ebuild (renamed from sci-biology/fasta/fasta-36.3.5e.ebuild)36
-rw-r--r--sci-biology/fasta/files/fasta-36.3.8h-ldflags.patch (renamed from sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch)23
3 files changed, 28 insertions, 37 deletions
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
index a9a197a0cebd..bdbbddf97625 100644
--- a/sci-biology/fasta/Manifest
+++ b/sci-biology/fasta/Manifest
@@ -1,4 +1,4 @@
-AUX fasta-36.3.5e-ldflags.patch 2781 BLAKE2B e6d4e0984b4dadfc9d38504ab215d769084edc6c79cfe641b6b3fba8264a40add1665027295ec4afa19d26277036bfe1a5103ecdf72ef91a1139542ac8272954 SHA512 5424bb8385def72ff75701c2da153f697520cbec82f36cbed8de0e98f93d399de660e79da7700ab0ff688fd5388cf9f42a30ccc4359335ae02042bf8cbb3aae7
-DIST fasta-36.3.5e.tar.gz 943763 BLAKE2B 6234d0aee76af6614e6d25ebcfbdfae080db5bc5adf611aeb6edc53ed7c6cb6cef257bf852ed39bc286527cec4175c251765ce23ea5ff39d12ff8947dba97ac6 SHA512 ddfcae36dadd7e2ed5c8c8c0bda2eed077e9f6cd55e4ebf507690671af156358e9da4e7cb1406d2b8713c326c54a9d829fc25e668b16dfa6df48d18e3a009812
-EBUILD fasta-36.3.5e.ebuild 1632 BLAKE2B 6165b7f1fc3440d94b337c13c0d520e5848d14b95720a27d941594355d70233af1c9db75e30603e4ae817ba2d2f3b1f5f7711dbcf37a2881effaade2608bc175 SHA512 f4c5cf2cb35e653d14c6afc8fd56743c8f7afb6302dd6227aec04bd8cb3efa9846fe32b6078b1b3dda94359857a214ec1580a2905aacb4ea9ed5234e2667b51c
+AUX fasta-36.3.8h-ldflags.patch 2291 BLAKE2B 61c0b7d82a4c138e82148f354576fbeadf38362337ae6d2ecdb23aea5c4dbb3719f3889a0479ea2b48de8e2c3e19c5b61a7b9508507fd7f61289205b93e899ed SHA512 a34021b398e077a409bd31508b0736e7a0fda533d86b26efe998227ce628414796a0dfd88b0010154e25ef79148b1b9acac4cd94cb7aa72a59fbcbd1fbbb6726
+DIST fasta-36.3.8h.tar.gz 1257682 BLAKE2B e6bd9087563150355fed6edf52a24a0b31ef0658b1e95c3df6d5b5711fc4d137ddd773fb8b3b2fa82fe3f5c310689b2f89668f5b51654eed41ed71f9ef140f99 SHA512 30d160ad083a605397c6c35d2b28f6064cd96f51f99b3664b424ec1dbbbd09772c72e89731a7257306ab58c4ad4b877e229873abd0e09407c64fae643bc04391
+EBUILD fasta-36.3.8h-r1.ebuild 1707 BLAKE2B 73197e61355b74a56ded2f3ff9feb3301d5831fc732419a8450db33a60b78473e6875ae6fff33e86996b255ddf9a6383e28ca66a1bfef105fab31320a6f8a554 SHA512 f3525c06e2937462f66dadda89c43cd4dd4b57b9b8ac0d37d34c3d4b8addd3f515f973af23644ea44f823e1855edecf98e94f1350acbe96e81b5aac57dd9e680
MISC metadata.xml 268 BLAKE2B a4d67334cdad8626d60e46b677ee1c83f569e5e20b3739a7664bb33be1829f8478af35e135bf734a6ff151b8543ea6c4ecafbf822cee8189f7e7096bd9698711 SHA512 59d3d8213b1a219396b74b6f4188c01e1cb4eb1c63e6792ce1e7fdb8000d1a4625919337ff77288ca7f7e07d9753f481d2381a06f554012633cd678194c980de
diff --git a/sci-biology/fasta/fasta-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
index c4c94d0e7f21..1c396edf4586 100644
--- a/sci-biology/fasta/fasta-36.3.5e.ebuild
+++ b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
@@ -1,13 +1,16 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=8
-inherit epatch flag-o-matic toolchain-funcs
+inherit flag-o-matic toolchain-funcs
+
+MY_PV="${PV}_04-May-2020"
DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
-SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}36/${P}.tar.gz"
+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"
@@ -15,8 +18,7 @@ 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=""
+BDEPEND="test? ( app-shells/tcsh )"
src_prepare() {
CC_ALT=
@@ -43,17 +45,17 @@ src_prepare() {
export CC_ALT="${CC_ALT}"
export ALT="${ALT}"
- epatch "${FILESDIR}"/${P}-ldflags.patch
+ eapply "${FILESDIR}"/${P}-ldflags.patch
sed \
-e 's:-ffast-math::g' \
-i make/Makefile* || die
+ eapply_user
}
src_compile() {
- cd src || die
- emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all
+ emake -C src -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all
}
src_test() {
@@ -62,18 +64,18 @@ src_test() {
}
src_install() {
- local bin
dobin bin/*
- pushd bin > /dev/null || die
- for bin in *36; do
- dosym ${bin} /usr/bin/${bin%36}
- done
- popd
+ 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
+ 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*}
+ dodoc FASTA_LIST README* doc/{README*,readme*,fasta*,changes*}
}
diff --git a/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch b/sci-biology/fasta/files/fasta-36.3.8h-ldflags.patch
index a6eeabfdf46c..40070d50fe76 100644
--- a/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch
+++ b/sci-biology/fasta/files/fasta-36.3.8h-ldflags.patch
@@ -1,14 +1,7 @@
- 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)
+@@ -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
@@ -26,12 +19,10 @@ index 9c5f801..33fc001 100644
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)
+@@ -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
@@ -49,12 +40,10 @@ index dc53001..8a45044 100644
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)
+@@ -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
generated by cgit v1.2.3 (git 2.25.1) at 2024-09-29 15:05:34 +0000