gentoo auto-resync : 18:04:2025 - 08:46:04nextedge

4 files changed, 102 insertions, 0 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 57b35dde5f02..746806a270f2 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
index e2d6df08a8af..52c6f36eccc2 100644
--- a/sci-biology/fasta/Manifest
+++ b/sci-biology/fasta/Manifest
@@ -1,6 +1,8 @@
 AUX fasta-36.3.8h-ldflags.patch 2291 BLAKE2B 61c0b7d82a4c138e82148f354576fbeadf38362337ae6d2ecdb23aea5c4dbb3719f3889a0479ea2b48de8e2c3e19c5b61a7b9508507fd7f61289205b93e899ed SHA512 a34021b398e077a409bd31508b0736e7a0fda533d86b26efe998227ce628414796a0dfd88b0010154e25ef79148b1b9acac4cd94cb7aa72a59fbcbd1fbbb6726
+AUX fasta-36.3.8i-musl-build-fix.patch 855 BLAKE2B 0d6568babc44a310514cbf11b5fb7214b7915902c9023c75492edecca939c8fabacf7b5ff36c3db0a47dcf59980032225b46288e77f287325bed7bcdede50189 SHA512 b13613543e18f8037647fa50771de2e344bb38028fae38741696d9598bb652496b54029426ff3c97d05f46bc4a5dc570f91e4ba36a4bfabcf60d175785c77399
 DIST fasta-36.3.8h.tar.gz 1257682 BLAKE2B e6bd9087563150355fed6edf52a24a0b31ef0658b1e95c3df6d5b5711fc4d137ddd773fb8b3b2fa82fe3f5c310689b2f89668f5b51654eed41ed71f9ef140f99 SHA512 30d160ad083a605397c6c35d2b28f6064cd96f51f99b3664b424ec1dbbbd09772c72e89731a7257306ab58c4ad4b877e229873abd0e09407c64fae643bc04391
 DIST fasta-36.3.8i.tar.gz 1402674 BLAKE2B 5653ae18d38a8f99ac1a76235ebad7189faeaacf9a043ab81ec56036e851d45fcc47435413f81f989efc6dfbccd6e3235c9cd14a6f129719d978ffc69e5def0f SHA512 6f34bd1a5f74362fd569d9c8e7ca7c9fcb0648ea7e861c3d0b54bbdc32ba0caad4beb2aad204122178ee6bcefd579d824412a863163050c305da0a661d55c234
 EBUILD fasta-36.3.8h-r1.ebuild 1770 BLAKE2B 77f3ebcfa44b0dd96b73909ea5cfe772366985e688df007aed3205a159d5896c6be20e88ab9e294920e55452014db1f73c2fc9d0d0763c7e5bba53e89e99dc44 SHA512 d55d8345400033078b9d7e634bbf4881f2e69bb3e3c4f048f840cc44ac90af844496070836b21fd208203f98ef4cb80b0b256ccdd9a0674d83d8fef2f3398b18
+EBUILD fasta-36.3.8i-r1.ebuild 1784 BLAKE2B b4f8961302c01963ba3c51e7f4d6917a689078aa99b3d45d43faaea246be0e5183c20668d0d947b247e7e0e3f974b6943c827b89dc6d9b4c807f4f265a9ceca7 SHA512 d367e876e0ff4b6f30278a07336565e6b6d916d018d47ab7c525ac2283810577ff5a9a082760c7ffaacd8eca91ed6dcba11960f9a12463de81293ee99f2578ed
 EBUILD fasta-36.3.8i.ebuild 1725 BLAKE2B 28655f72b4eccad925599f3811ba2ff86e5ea5a9d9eb90a37f1545269dea5549a47972044e41bf5e515faca12d2c42856d64439c4077419d69051bcdee168076 SHA512 0c4320a3238c93743e111864dccf73312abadd84f51a4ca8793c4d98a28e5b95185ce0f15d3c7c37ab4962e25898e8234acca1c27d4467bc9a9439ffdfd7df16
 MISC metadata.xml 344 BLAKE2B 75f42620d20abfbba91acae49acb672fe1b42fccf6227e358c1d94101c894226f51e9c2efe4014dd263b55a2940894eee9d8c96fb5ac6ff64c3c4ae6a426cc74 SHA512 13001db79cb9763ee83f1701e316287efdaef1ac5c4eab1249a1815df5ac6a34ff6b0f76e1706684058966b2201c642a2f8bda1d6d36473c0cdfbe00ca1d094a
diff --git a/sci-biology/fasta/fasta-36.3.8i-r1.ebuild b/sci-biology/fasta/fasta-36.3.8i-r1.ebuild
new file mode 100644
index 000000000000..6fa29e9baed1
--- /dev/null
+++ b/sci-biology/fasta/fasta-36.3.8i-r1.ebuild
@@ -0,0 +1,85 @@
+# Copyright 1999-2025 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit flag-o-matic toolchain-funcs
+
+MY_PV="${PV}_14-Nov-2020"
+
+DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
+HOMEPAGE="https://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
+SRC_URI="https://github.com/wrpearson/fasta36/archive/refs/tags/v${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"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-36.3.8i-musl-build-fix.patch"
+)
+
+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="${ALT}"
+
+	# -Werror=lto-type-mismatch
+	# https://bugs.gentoo.org/862267
+	# https://github.com/wrpearson/fasta36/issues/63
+	filter-lto
+
+	sed \
+		-e 's:-ffast-math::g' \
+		-i make/Makefile* || die
+
+	default
+}
+
+src_compile() {
+	emake -C src -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS}" 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*,readme*,fasta*,changes*}
+}
diff --git a/sci-biology/fasta/files/fasta-36.3.8i-musl-build-fix.patch b/sci-biology/fasta/files/fasta-36.3.8i-musl-build-fix.patch
new file mode 100644
index 000000000000..1ce5e0089611
--- /dev/null
+++ b/sci-biology/fasta/files/fasta-36.3.8i-musl-build-fix.patch
@@ -0,0 +1,15 @@
+https://patch-diff.githubusercontent.com/raw/wrpearson/fasta36/pull/64.patch
+--- a/make/Makefile.linux64_sse2
++++ b/make/Makefile.linux64_sse2
+@@ -28,7 +28,7 @@ LIB_DB=
+ 
+ # standard options
+ 
+-CFLAGS += -DPOSIX_C_SOURCE=2 -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit  -DM10_CONS  -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP  -D_LARGEFILE64_SOURCE  -DBIG_LIB64
++CFLAGS += -DPOSIX_C_SOURCE=2 -D_GNU_SOURCE -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit  -DM10_CONS  -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP  -D_LARGEFILE64_SOURCE  -DBIG_LIB64
+ 
+ # -I/usr/include/mysql -DMYSQL_DB
+ # -DSUPERFAMNUM -DSFCHAR="'|'" 
+-- 
+2.46.0
+