[gentoo-commits] repo/gentoo:master commit in: sci-biology/augustus/
commit: 82f595247fbc8571fad2518a444f8b57f573e5bd
Author: Petr Vaněk atlas cz>
AuthorDate: Mon Feb 6 09:17:17 2023 +
Commit: Sam James gentoo org>
CommitDate: Mon Feb 6 17:43:55 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=82f59524
sci-biology/augustus: move remote-id inside upstream block
Fixes: f203a8487a2f ("sci-biology/augustus: add github remote-id")
Signed-off-by: Petr Vaněk atlas.cz>
Closes: https://github.com/gentoo/gentoo/pull/29448
Signed-off-by: Sam James gentoo.org>
sci-biology/augustus/metadata.xml | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/sci-biology/augustus/metadata.xml
b/sci-biology/augustus/metadata.xml
index 20555ec8076a..a4352248acda 100644
--- a/sci-biology/augustus/metadata.xml
+++ b/sci-biology/augustus/metadata.xml
@@ -5,5 +5,7 @@
sci-biol...@gentoo.org
Gentoo Biology Project
- Gaius-Augustus/Augustus
+
+Gaius-Augustus/Augustus
+
[gentoo-commits] repo/gentoo:master commit in: sci-biology/augustus/
commit: f203a8487a2f5ba0e5285d9aa05cd6d85548cb24 Author: Sam James gentoo org> AuthorDate: Sat Feb 4 17:21:51 2023 + Commit: Sam James gentoo org> CommitDate: Sat Feb 4 17:22:59 2023 + URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f203a848 sci-biology/augustus: add github remote-id Signed-off-by: Sam James gentoo.org> sci-biology/augustus/metadata.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/sci-biology/augustus/metadata.xml b/sci-biology/augustus/metadata.xml index ccdff086e20b..20555ec8076a 100644 --- a/sci-biology/augustus/metadata.xml +++ b/sci-biology/augustus/metadata.xml @@ -5,4 +5,5 @@ sci-biol...@gentoo.org Gentoo Biology Project + Gaius-Augustus/Augustus
[gentoo-commits] repo/gentoo:master commit in: sci-biology/augustus/
commit: 25774a0a53557d280b9519cd6b85cf7da886e95f
Author: Sam James gentoo org>
AuthorDate: Sat Feb 4 17:19:53 2023 +
Commit: Sam James gentoo org>
CommitDate: Sat Feb 4 17:22:58 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=25774a0a
sci-biology/augustus: add lpsolve subslot dep
Bug: https://bugs.gentoo.org/614866
Signed-off-by: Sam James gentoo.org>
.../augustus/{augustus-3.4.0-r2.ebuild => augustus-3.4.0-r3.ebuild} | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/augustus/augustus-3.4.0-r2.ebuild
b/sci-biology/augustus/augustus-3.4.0-r3.ebuild
similarity index 93%
rename from sci-biology/augustus/augustus-3.4.0-r2.ebuild
rename to sci-biology/augustus/augustus-3.4.0-r3.ebuild
index 30b3d7d0a6f8..7c662aead62f 100644
--- a/sci-biology/augustus/augustus-3.4.0-r2.ebuild
+++ b/sci-biology/augustus/augustus-3.4.0-r3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
@@ -26,7 +26,7 @@ RDEPEND="
sci-libs/gsl:=
sci-libs/htslib:=
sci-libs/suitesparse
- sci-mathematics/lpsolve
+ sci-mathematics/lpsolve:=
sys-libs/zlib
"
DEPEND="${RDEPEND}"
[gentoo-commits] repo/gentoo:master commit in: sci-biology/augustus/
commit: 405d411472329b890d43b44367b7874514c30379
Author: Sam James gentoo org>
AuthorDate: Sat Sep 3 22:04:43 2022 +
Commit: Sam James gentoo org>
CommitDate: Sat Sep 3 22:09:19 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=405d4114
sci-biology/augustus: fix Boost dep
Closes: https://bugs.gentoo.org/864773
Signed-off-by: Sam James gentoo.org>
.../{augustus-3.4.0-r1.ebuild => augustus-3.4.0-r2.ebuild} | 12 ++--
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/sci-biology/augustus/augustus-3.4.0-r1.ebuild
b/sci-biology/augustus/augustus-3.4.0-r2.ebuild
similarity index 86%
rename from sci-biology/augustus/augustus-3.4.0-r1.ebuild
rename to sci-biology/augustus/augustus-3.4.0-r2.ebuild
index 56c2f49baebc..abd32ec0ac0c 100644
--- a/sci-biology/augustus/augustus-3.4.0-r1.ebuild
+++ b/sci-biology/augustus/augustus-3.4.0-r2.ebuild
@@ -18,13 +18,13 @@ KEYWORDS="~amd64 ~x86"
RDEPEND="
dev-db/sqlite:3
- dev-db/mysql++
- dev-db/mysql-connector-c
- dev-libs/boost:=
- sci-biology/bamtools
+ dev-db/mysql++:=
+ dev-db/mysql-connector-c:=
+ dev-libs/boost:=[zlib]
+ sci-biology/bamtools:=
sci-biology/samtools:0
- sci-libs/gsl
- sci-libs/htslib
+ sci-libs/gsl:=
+ sci-libs/htslib:=
sci-libs/suitesparse
sci-mathematics/lpsolve
sys-libs/zlib
[gentoo-commits] repo/gentoo:master commit in: sci-biology/augustus/
commit: 792d8f2c5fe18c131fc63df1dda88c4d791eb5bf
Author: Sam James gentoo org>
AuthorDate: Sat Sep 3 22:09:15 2022 +
Commit: Sam James gentoo org>
CommitDate: Sat Sep 3 22:09:19 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=792d8f2c
sci-biology/augustus: respect CC, CXX
Closes: https://bugs.gentoo.org/832187
Signed-off-by: Sam James gentoo.org>
sci-biology/augustus/augustus-3.4.0-r2.ebuild | 7 +--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/sci-biology/augustus/augustus-3.4.0-r2.ebuild
b/sci-biology/augustus/augustus-3.4.0-r2.ebuild
index abd32ec0ac0c..30b3d7d0a6f8 100644
--- a/sci-biology/augustus/augustus-3.4.0-r2.ebuild
+++ b/sci-biology/augustus/augustus-3.4.0-r2.ebuild
@@ -5,7 +5,7 @@ EAPI=8
DOCS_BUILDER="doxygen"
DOCS_CONFIG_NAME="doxygen.conf"
-inherit docs
+inherit docs toolchain-funcs
DESCRIPTION="Eukaryotic gene predictor"
HOMEPAGE="https://bioinf.uni-greifswald.de/augustus/;
@@ -32,7 +32,10 @@ RDEPEND="
DEPEND="${RDEPEND}"
src_compile() {
- default
+ tc-export CC CXX
+
+ emake LINK.cc="$(tc-getCXX)"
+
docs_compile
}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/augustus/
commit: c974dd2172656250d7e432b3619652ea68b1e723
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Fri Jan 28 21:48:40 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Fri Jan 28 21:49:14 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c974dd21
sci-biology/augustus: add forgotten runtime dependency
Closes: https://bugs.gentoo.org/832186
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan gentoo.org>
sci-biology/augustus/{augustus-3.4.0.ebuild => augustus-3.4.0-r1.ebuild} | 1 +
1 file changed, 1 insertion(+)
diff --git a/sci-biology/augustus/augustus-3.4.0.ebuild
b/sci-biology/augustus/augustus-3.4.0-r1.ebuild
similarity index 97%
rename from sci-biology/augustus/augustus-3.4.0.ebuild
rename to sci-biology/augustus/augustus-3.4.0-r1.ebuild
index 0608d11dee6c..56c2f49baebc 100644
--- a/sci-biology/augustus/augustus-3.4.0.ebuild
+++ b/sci-biology/augustus/augustus-3.4.0-r1.ebuild
@@ -22,6 +22,7 @@ RDEPEND="
dev-db/mysql-connector-c
dev-libs/boost:=
sci-biology/bamtools
+ sci-biology/samtools:0
sci-libs/gsl
sci-libs/htslib
sci-libs/suitesparse
[gentoo-commits] repo/gentoo:master commit in: sci-biology/augustus/
commit: aea4f8147ac23b904f17d3890b398d5fb30c9eee
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Thu Jan 27 19:08:10 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Thu Jan 27 19:08:36 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=aea4f814
sci-biology/augustus: add version 3.4.0
Closes: https://bugs.gentoo.org/515996
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan gentoo.org>
sci-biology/augustus/Manifest | 1 +
sci-biology/augustus/augustus-3.4.0.ebuild | 47 ++
2 files changed, 48 insertions(+)
diff --git a/sci-biology/augustus/Manifest b/sci-biology/augustus/Manifest
index 7d0b1e3689b4..7ddb67b5c888 100644
--- a/sci-biology/augustus/Manifest
+++ b/sci-biology/augustus/Manifest
@@ -1 +1,2 @@
+DIST augustus-3.4.0.tar.gz 221652100 BLAKE2B
dfc8c98107f5a955f688f3d2976ca936faf2ef7004095f6b9d7c1902a36ca5d3c9aef59cab1b82b56cd5c2abc7b67195c5030111ed68557d53128814b1bf6bab
SHA512
ca1df1016589f55527a883429edd5024cbc32c1b32036c81f9df5e0967a7d194f5b7a82109e924f380627427d9731caa478e63cad8cd804c01521aed76d8c4a6
DIST augustus.2.5.5.tar.gz 70826249 BLAKE2B
3f3f1537c5c614f00298e1835eeb7bbe968987c3e0dee13299e1e26b4abf198d8635a93121b11722d2c90b63ff54cf153c72716d01c3ca033481bb54357b7bcf
SHA512
33eb05d5c90200d2fc17026743d3a25e73aa3e217b8546f0bed4c94bcb460597d853377a67896e52e45ead5d736d13ed3b2c91b31fed8216da2920c825e8c20f
diff --git a/sci-biology/augustus/augustus-3.4.0.ebuild
b/sci-biology/augustus/augustus-3.4.0.ebuild
new file mode 100644
index ..0608d11dee6c
--- /dev/null
+++ b/sci-biology/augustus/augustus-3.4.0.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DOCS_BUILDER="doxygen"
+DOCS_CONFIG_NAME="doxygen.conf"
+inherit docs
+
+DESCRIPTION="Eukaryotic gene predictor"
+HOMEPAGE="https://bioinf.uni-greifswald.de/augustus/;
+SRC_URI="https://github.com/Gaius-Augustus/Augustus/archive/refs/tags/v${PV}.tar.gz
-> ${P}.tar.gz"
+S="${WORKDIR}/${P^}"
+
+LICENSE="Artistic"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-db/sqlite:3
+ dev-db/mysql++
+ dev-db/mysql-connector-c
+ dev-libs/boost:=
+ sci-biology/bamtools
+ sci-libs/gsl
+ sci-libs/htslib
+ sci-libs/suitesparse
+ sci-mathematics/lpsolve
+ sys-libs/zlib
+"
+DEPEND="${RDEPEND}"
+
+src_compile() {
+ default
+ docs_compile
+}
+
+src_install() {
+ einstalldocs
+ # from upstream Makefile install:
+ dodir "opt/${P}"
+ cp -a config bin scripts "${ED}/opt/${P}" || die
+ local file
+ for file in bin/*; do
+ dosym "../${P}/${file}" "/opt/${file}"
+ done
+}
[gentoo-commits] repo/gentoo:master commit in: sci-biology/augustus/
commit: c5138c7f261799f62b944004c108f7a01b138be7
Author: David Seifert gentoo org>
AuthorDate: Tue Dec 10 23:48:28 2019 +
Commit: David Seifert gentoo org>
CommitDate: Tue Dec 10 23:48:28 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c5138c7f
sci-biology/augustus: Port to EAPI 7
Package-Manager: Portage-2.3.81, Repoman-2.3.20
Signed-off-by: David Seifert gentoo.org>
sci-biology/augustus/augustus-2.5.5.ebuild | 19 ++-
1 file changed, 10 insertions(+), 9 deletions(-)
diff --git a/sci-biology/augustus/augustus-2.5.5.ebuild
b/sci-biology/augustus/augustus-2.5.5.ebuild
index ff4dfd6cc7e..5bf36e85cb9 100644
--- a/sci-biology/augustus/augustus-2.5.5.ebuild
+++ b/sci-biology/augustus/augustus-2.5.5.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=4
+EAPI=7
-inherit eutils toolchain-funcs
+inherit toolchain-funcs
DESCRIPTION="Eukaryotic gene predictor"
HOMEPAGE="http://augustus.gobics.de/;
@@ -15,30 +15,31 @@ KEYWORDS="amd64 x86"
IUSE="examples"
S="${WORKDIR}/${PN}.${PV}"
+PATCHES=( "${FILESDIR}"/${P}-sane-build.patch )
-src_prepare() {
- epatch "${FILESDIR}"/${P}-sane-build.patch
+src_configure() {
tc-export CC CXX
}
src_compile() {
- emake clean && emake
+ emake clean
+ default
}
src_install() {
dobin bin/*
-# dobin
src/{augustus,etraining,consensusFinder,curve2hints,fastBlockSearch,prepareAlign}
exeinto /usr/libexec/${PN}
doexe scripts/*.p*
+
insinto /usr/libexec/${PN}
doins scripts/*.conf
insinto /usr/share/${PN}
doins -r config
- echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > "${S}/99${PN}"
- doenvd "${S}/99${PN}"
+ echo "AUGUSTUS_CONFIG_PATH=\"/usr/share/${PN}/config\"" > 99${PN} || die
+ doenvd 99${PN}
dodoc -r README.TXT HISTORY.TXT docs/*.{pdf,txt}
