[gentoo-commits] proj/sci:master commit in: sci-biology/wise/

[gentoo-commits] proj/sci:master commit in: sci-biology/wise/

[Martin Mokrejs]

commit:     a4f1661dd0ed743fd5ea4e21edc558c83fbc5dd6
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat May  9 22:55:35 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat May  9 22:55:35 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a4f1661d

sci-biology/wise: version bump, new HOMEPAGE, SRC_URI, does not compile, the former patches need to be updated as well

Package-Manager: portage-2.2.18

 sci-biology/wise/ChangeLog         | 10 ++++++
 sci-biology/wise/metadata.xml      |  5 +++
 sci-biology/wise/wise-2.4.1.ebuild | 74 ++++++++++++++++++++++++++++++++++++++
 3 files changed, 89 insertions(+)

diff --git a/sci-biology/wise/ChangeLog b/sci-biology/wise/ChangeLog
new file mode 100644
index 0000000..7bbe629
--- /dev/null
+++ b/sci-biology/wise/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/wise
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*wise-2.4.1 (09 May 2015)
+
+  09 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+  +wise-2.4.1.ebuild:
+  sci-biology/wise: version bump, new HOMEPAGE, SRC_URI, does not compile, the
+  former patches need to be updated as well

diff --git a/sci-biology/wise/metadata.xml b/sci-biology/wise/metadata.xml
new file mode 100644
index 0000000..f17a827
--- /dev/null
+++ b/sci-biology/wise/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+</pkgmetadata>

diff --git a/sci-biology/wise/wise-2.4.1.ebuild b/sci-biology/wise/wise-2.4.1.ebuild
new file mode 100644
index 0000000..d7d88b6
--- /dev/null
+++ b/sci-biology/wise/wise-2.4.1.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/wise/wise-2.4.0_alpha.ebuild,v 1.6 2015/04/19 10:02:55 ago Exp $
+
+EAPI=5
+
+inherit eutils toolchain-funcs versionator
+
+DESCRIPTION="Genewise, promoterwise: align protein HMMs to DNA for CDS predictions"
+HOMEPAGE="http://www.ebi.ac.uk/~birney/wise2"
+SRC_URI="http://www.ebi.ac.uk/~birney/${PN}2/${PN}$(delete_version_separator 3).tar.gz"
+#SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS=""
+IUSE="doc static-libs"
+
+RDEPEND="~sci-biology/hmmer-2.3.2"
+DEPEND="
+	${RDEPEND}
+	app-shells/tcsh
+	dev-lang/perl
+	virtual/latex-base"
+
+S="${WORKDIR}"/${PN}$(delete_version_separator 3)
+
+#src_prepare() {
+#	epatch \
+#		"${FILESDIR}"/${P}-glibc-2.10.patch \
+#		"${FILESDIR}"/${P}-cflags.patch
+#	cd "${S}"/docs || die
+#	cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die
+#	cat wise2api.tex temp.tex apiend.tex > api.tex || die
+#	epatch "${FILESDIR}"/${PN}-api.tex.patch
+#}
+
+src_compile() {
+	emake \
+		-C src \
+		CC="$(tc-getCC)" \
+		all
+	if use doc; then
+		cd "${S}"/docs || die
+		for i in api appendix dynamite wise2 wise3arch; do
+			latex ${i} || die
+			latex ${i} || die
+			dvips ${i}.dvi -o || die
+		done
+	fi
+}
+
+src_test() {
+	cd "${S}"/src || die
+	WISECONFIGDIR="${S}/wisecfg" emake test
+}
+
+src_install() {
+	dobin "${S}"/src/bin/* "${S}"/src/dynlibsrc/testgendb
+	use static-libs && \
+		dolib.a \
+			"${S}"/src/base/libwisebase.a \
+			"${S}"/src/dynlibsrc/libdyna.a \
+			"${S}"/src/models/libmodel.a
+
+	insinto /usr/share/${PN}
+	doins -r "${S}"/wisecfg
+
+	if use doc; then
+		insinto /usr/share/doc/${PF}
+		doins "${S}"/docs/*.ps
+	fi
+	newenvd "${FILESDIR}"/${PN}-env 24wise || die "Failed to install env file"
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/wise/

[Martin Mokrejs]

commit:     7490080c8499c8762691ecd64e6ba8bc9f2dc3cd
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 10 17:13:10 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 10 17:13:10 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7490080c

sci-biology/wise: fix slot operator

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/wise/wise-2.4.1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/wise/wise-2.4.1.ebuild b/sci-biology/wise/wise-2.4.1.ebuild
index 95cd6ad..5471606 100644
--- a/sci-biology/wise/wise-2.4.1.ebuild
+++ b/sci-biology/wise/wise-2.4.1.ebuild
@@ -16,7 +16,7 @@ SLOT="0"
 KEYWORDS=""
 IUSE="doc static-libs"
 
-RDEPEND="~sci-biology/hmmer-2.3.2"
+RDEPEND="sci-biology/hmmer:2"
 DEPEND="
 	${RDEPEND}
 	dev-lang/perl

[gentoo-commits] proj/sci:master commit in: sci-biology/wise/

[Martin Mokrejs]

commit:     96bd0833fd10983de60beb60ff8b1267348fe8bb
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 10 17:13:50 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 10 17:13:50 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=96bd0833

sci-biology/wise: add keywords

Package-Manager: Portage-2.3.3, Repoman-2.3.1

 sci-biology/wise/wise-2.4.1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/wise/wise-2.4.1.ebuild b/sci-biology/wise/wise-2.4.1.ebuild
index 5471606..5d299ca 100644
--- a/sci-biology/wise/wise-2.4.1.ebuild
+++ b/sci-biology/wise/wise-2.4.1.ebuild
@@ -13,7 +13,7 @@ SRC_URI="http://www.ebi.ac.uk/~birney/${PN}2/${PN}$(delete_version_separator 3).
 
 LICENSE="BSD"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64 ~x86"
 IUSE="doc static-libs"
 
 RDEPEND="sci-biology/hmmer:2"