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-rw-r--r--sci-biology/Manifest.gzbin19002 -> 19016 bytes
-rw-r--r--sci-biology/amap/Manifest2
-rw-r--r--sci-biology/amap/amap-2.2-r6.ebuild (renamed from sci-biology/amap/amap-2.2-r5.ebuild)30
-rw-r--r--sci-biology/bowtie/Manifest2
-rw-r--r--sci-biology/bowtie/bowtie-2.5.1.ebuild2
-rw-r--r--sci-biology/fasta/Manifest4
-rw-r--r--sci-biology/fasta/fasta-36.3.8h-r1.ebuild12
-rw-r--r--sci-biology/fasta/fasta-36.3.8i.ebuild81
8 files changed, 107 insertions, 26 deletions
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 13cd984b5e49..3cd5396be933 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
Binary files differ
diff --git a/sci-biology/amap/Manifest b/sci-biology/amap/Manifest
index c97246215a2f..13fa0fcaf898 100644
--- a/sci-biology/amap/Manifest
+++ b/sci-biology/amap/Manifest
@@ -1,5 +1,5 @@
AUX amap-2.2-includes.patch 1088 BLAKE2B 3b870c229f3efb9819d9f176b59b014ad4bae3034ed4fe9f8c8474ebf8ce7c8373efef66c3c61c8f6fe04a645243f09639aa4a4c95ee75f692e504f4478fcf77 SHA512 e9c2ae7ea75f059b816a8562c9ac79e343d73b9a3d63ac1182fe41b3634bf0b949738a4bdd90c09f61bb4505a721e2faa98334b81ad17c0d7360a2e3f37f9044
AUX amap-2.2-makefile.patch 1089 BLAKE2B 5ed09060ebc9c0c5748d1bdd1517bc6d5e7989d8125db1dff13a221f13e69e717508ac30410ae0c38a4e126f490179ac68ee7e501f7c7d61888993c850f6fbf8 SHA512 cd08a7a71eb85521c60e522d3a8ea0b2bbe4dfb93c0f4d6f0e2e4c35787a0836f23f51f50c4c9344eeda6533a7d689c4b246c700f7d37b8b3666f4904bd625d6
DIST amap.2.2.tar.gz 102861 BLAKE2B 7f9b1cb747946232db0b5b469896cc4f83ef78d190e929e28f37df790dfac342e6e7f913797bc9ff00191253318db2d42f79577dc72128d62a21d0e241bfb0e1 SHA512 a297b6eb1b52d5deab65db5bb1344b06a85c7ef6fa4b550798501041091357e605543eaadd85c053a74e857ebdd7b846dca4b226c5c61bedc329bf93c886c18f
-EBUILD amap-2.2-r5.ebuild 1104 BLAKE2B 120ae0dd66942b77dc7acc28d05b6f76c9dc1152dea85b419f2a84cab1a7ef2be373575bdd0f0edabfba1765c3a4db83b699c25ae0855c7e162d19d13f6b404f SHA512 60ad29cc9bb1698ff04eec6fa719f66a9fe0ebc57698f6986abc7b401a4781248140a73d36828d9592dae3176148fc0ee27e6baf0d302e461387b13b98ff9530
+EBUILD amap-2.2-r6.ebuild 1081 BLAKE2B abfa680a1d4f14cbb4fcffb646a781d59ad65022f0f75257e372cd0ca49e4de33da02447dbc7312f6c62a2ae561dfdc4ad406e546c84ecfe5ed790eceb440cf8 SHA512 df5007ef8960c066b9b6b49a2d2272b959d81a70835173afc1c456154d4b6394720e974db756f0e67fa78f661f2c8c403cf0dc1a74ce11fc995da661ff13cc37
MISC metadata.xml 258 BLAKE2B 51009df26b3682090e316b4cf4a3afad84001705063be6c74a28fb11bacde48b758dc280bf9d4d049c69e728d9660e737072674ad5ff8068da4f6a49f1f4e203 SHA512 05153e39b77e8b1437a0ba80b66b6bb1b4837d719765cb157b23d5425a625ddb4056422dcbf28d182e039583a0b3863e8429efe80da85a035c96f4c4788ced6d
diff --git a/sci-biology/amap/amap-2.2-r5.ebuild b/sci-biology/amap/amap-2.2-r6.ebuild
index 949749969c27..487616726fc4 100644
--- a/sci-biology/amap/amap-2.2-r5.ebuild
+++ b/sci-biology/amap/amap-2.2-r6.ebuild
@@ -1,24 +1,26 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
-inherit java-pkg-opt-2 java-ant-2 toolchain-funcs
+JAVA_PKG_IUSE="doc source"
-MY_P=${PN}.${PV}
+inherit java-pkg-opt-2 java-pkg-simple toolchain-funcs
DESCRIPTION="Protein multiple-alignment-based sequence annealing"
HOMEPAGE="https://wiki.gentoo.org/wiki/No_homepage"
-SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz"
-S="${WORKDIR}/${PN}-align"
+SRC_URI="http://baboon.math.berkeley.edu/amap/download/${P/-/.}.tar.gz"
+S="${WORKDIR}/amap-align"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="java"
+DEPEND="java? ( >=virtual/jdk-1.8:* )"
RDEPEND="java? ( >=virtual/jre-1.8:* )"
-BDEPEND="${RDEPEND}"
+
+DOCS=( align/{README,PROBCONS.README} )
PATCHES=(
"${FILESDIR}"/${P}-makefile.patch
@@ -27,7 +29,7 @@ PATCHES=(
src_prepare() {
default
- java-pkg-opt-2_src_prepare
+ use java && java-pkg-opt-2_src_prepare && java-pkg_clean
}
src_configure() {
@@ -36,24 +38,18 @@ src_configure() {
src_compile() {
emake -C align
-
if use java; then
- pushd display >/dev/null || die
- eant -Ddisplay all || die
- popd >/dev/null || die
+ JAVA_JAR_FILENAME="amapdisplay.jar"
+ JAVA_SRC_DIR="display/src"
+ java-pkg-simple_src_compile
fi
}
src_install() {
dobin align/${PN}
- dodoc align/{README,PROBCONS.README}
-
insinto /usr/share/${PN}
doins -r examples
- if use java; then
- java-pkg_newjar display/AmapDisplay.jar amapdisplay.jar
- java-pkg_dolauncher amapdisplay --jar amapdisplay.jar
- fi
+ use java && java-pkg-simple_src_install
}
diff --git a/sci-biology/bowtie/Manifest b/sci-biology/bowtie/Manifest
index d8a1aac4fceb..147f1a2052f5 100644
--- a/sci-biology/bowtie/Manifest
+++ b/sci-biology/bowtie/Manifest
@@ -1,5 +1,5 @@
DIST bowtie2-2.4.4-source.zip 10515984 BLAKE2B be4ceb9d3155d2a9a1f580e5032251b04b89ce0c8c9c89fc3551b34fe3bd71a683362488be7aad6daef24734c6f95c19223f20e67f198f745c4432381243039c SHA512 1b5dadd7e41b90bb9b05f50bfa171fe219cfd03aa8bb6f800de4baaffeb975eef6efc4fb8b49cb0d18833f74a1741cbe1556b87388f59188e04a55dcee6a02da
DIST bowtie2-2.5.1-source.zip 10528859 BLAKE2B 9dc22bfef4b3a1cfaa606cb235acd1d7688015678d82e8ca80d3d7cf269e1f45d6cb60bc29eb334fb6f0c25d5afd8202e83a83e53668c8965857b8885d2692c8 SHA512 31cc642e318ab50e7ef6035a9c2095024d46d92a317011ed0c3ac3ccb3d427a13bf724d0158d29a4f1e07115ddcb85229b95bcb2d4351164fcadd6568293565f
EBUILD bowtie-2.4.4.ebuild 1215 BLAKE2B 4d88c3ff6149289019301cbdf5b682da576feabe5a51f2a83fceccf2b2475e81ae69a9318e64453d16c4c2b713dc7858bf4f5c3e9306004e418d34f10099ac71 SHA512 2da6db5d4d96ea3e5eba3fb992e8ef350becdbd24ba4d0844a2c6127a357f458fb709ea833bb06bf464001872f45530f9fdc6b5682801aab7ac400641c42e1b1
-EBUILD bowtie-2.5.1.ebuild 1542 BLAKE2B b927f815c929a324c607df93479833079a0e5a8dd9b723755ad19d528e35601b796cdb0618c5d7787ce591c0d8e5c0be5b5d7217fc1a0393f070049451c3d9db SHA512 1ea410f3b1c0b5be41369f1f001f92f366cd3fec9f1518bfc9da32bda8f88c9b2bb57b73e6f2ec71e9144844cca7db47c747e4193ff243c78ca1304d4897b176
+EBUILD bowtie-2.5.1.ebuild 1542 BLAKE2B 313f1f87d691a258d7bd3e6e2cea1d7de49dbbb12ae1c380648a69eb4aaae2b593b263b25107cfe367adc9971f8aa49e2e540e7dda4c9f7158d8367a5f5184b2 SHA512 94635590d0ec1d31ae520d2e231735834f03c6b25d2dbc1613fc98a2055dc6be4f596b57f7ec3e0a27f1c25ac6686ab14f5d7ad8051244a4535f5bba6ecbf0bb
MISC metadata.xml 342 BLAKE2B 7f98f1707e3f53e7c2e532427d6935c692cdcf45304701d28d245ba13b62e752d14d5c3a96925fdf5bceb87a9c291edad0ce715339a5bf92ca6de7ee839adced SHA512 b7f0359b22f70ab25737565bda08e500f6a79bf33052d39fe2013b085c3f636122d0f373430ce3f0b56f95051db9571cb6c79b6f58e30658f45ef752ec708df6
diff --git a/sci-biology/bowtie/bowtie-2.5.1.ebuild b/sci-biology/bowtie/bowtie-2.5.1.ebuild
index b30a2b920f4e..a2b75d6b9880 100644
--- a/sci-biology/bowtie/bowtie-2.5.1.ebuild
+++ b/sci-biology/bowtie/bowtie-2.5.1.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_COMPAT=( python3_{10..12} )
inherit python-single-r1 toolchain-funcs
diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
index 1626943dfb25..e2d6df08a8af 100644
--- a/sci-biology/fasta/Manifest
+++ b/sci-biology/fasta/Manifest
@@ -1,4 +1,6 @@
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 1713 BLAKE2B de1276ea990e856cf562a5f970d180c3872c3ce6d3d8f73a50b398ff1408f7840872d90e690a9511cdbb14c586627c061389ad307c85b1a2662130aea66d0b33 SHA512 059b00c917565477765897b03656dfe8e67c2879ac8a78b2187edd0a5f0199f52dca45886dd8d2ac300ee0995697458fffa69e7704df951837b1c50d7ad92f9d
+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.ebuild 1725 BLAKE2B 28655f72b4eccad925599f3811ba2ff86e5ea5a9d9eb90a37f1545269dea5549a47972044e41bf5e515faca12d2c42856d64439c4077419d69051bcdee168076 SHA512 0c4320a3238c93743e111864dccf73312abadd84f51a4ca8793c4d98a28e5b95185ce0f15d3c7c37ab4962e25898e8234acca1c27d4467bc9a9439ffdfd7df16
MISC metadata.xml 344 BLAKE2B 75f42620d20abfbba91acae49acb672fe1b42fccf6227e358c1d94101c894226f51e9c2efe4014dd263b55a2940894eee9d8c96fb5ac6ff64c3c4ae6a426cc74 SHA512 13001db79cb9763ee83f1701e316287efdaef1ac5c4eab1249a1815df5ac6a34ff6b0f76e1706684058966b2201c642a2f8bda1d6d36473c0cdfbe00ca1d094a
diff --git a/sci-biology/fasta/fasta-36.3.8h-r1.ebuild b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
index 1cd7ca60dcde..b811765e502e 100644
--- a/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
+++ b/sci-biology/fasta/fasta-36.3.8h-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2024 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -15,10 +15,7 @@ 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 )"
+IUSE="debug cpu_flags_x86_sse2"
src_prepare() {
CC_ALT=
@@ -45,6 +42,11 @@ src_prepare() {
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
+
eapply "${FILESDIR}"/${P}-ldflags.patch
sed \
diff --git a/sci-biology/fasta/fasta-36.3.8i.ebuild b/sci-biology/fasta/fasta-36.3.8i.ebuild
new file mode 100644
index 000000000000..6363b4b56f2d
--- /dev/null
+++ b/sci-biology/fasta/fasta-36.3.8i.ebuild
@@ -0,0 +1,81 @@
+# Copyright 1999-2024 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"
+
+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="${ALT}"
+
+ # -Werror=lto-type-mismatch
+ # https://bugs.gentoo.org/862267
+ # https://github.com/wrpearson/fasta36/issues/63
+ filter-lto
+
+ sed \
+ -e 's:-ffast-math::g' \
+ -i make/Makefile* || die
+
+ eapply_user
+}
+
+src_compile() {
+ emake -C src -f ../make/Makefile.linux${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*}
+}
generated by cgit v1.2.3 (git 2.25.1) at 2024-09-03 20:31:38 +0000