* [gentoo-commits] proj/sci:master commit in: sci-biology/wise/
@ 2017-01-10 17:13 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2017-01-10 17:13 UTC (permalink / raw
To: gentoo-commits
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"
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/wise/
@ 2017-01-10 17:13 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2017-01-10 17:13 UTC (permalink / raw
To: gentoo-commits
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
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/wise/
@ 2015-05-09 22:55 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2015-05-09 22:55 UTC (permalink / raw
To: gentoo-commits
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"
+}
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