Merge branch 'master' of ssh://github.com/gentoo-science/sci

5 files changed, 36 insertions, 11 deletions

diff --git a/sci-biology/discrover/ChangeLog b/sci-biology/discrover/ChangeLog
index 8994dda11..d81ca8c9f 100644
--- a/sci-biology/discrover/ChangeLog
+++ b/sci-biology/discrover/ChangeLog
@@ -1,7 +1,25 @@
 # ChangeLog for sci-biology/discrover
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*discrover-1.4.1 (05 Jan 2015)
+
+  05 Jan 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.4.1.ebuild,
+  -discrover-1.4.0.ebuild:
+  Bump patch version
+
+*discrover-1.4.0 (04 Jan 2015)
+
+  04 Jan 2015; Jonas Maaskola <jonas@maaskola.de> +discrover-1.4.0.ebuild,
+  -discrover-1.3.1.ebuild, discrover-9999.ebuild, metadata.xml:
+  Bump minor version to 1.4.0.  Introduces a new USE flag: 'cairo'.
+  x11-libs/cairo is used to generate sequence logos.  The USE flag 'logo' has
+  been renamed to 'tikzlogo'. The tikzlogo Ruby script served the purpose that
+  is now fulfilled by the Cairo-based code. tikzlogo requires Ruby, ImageMagick,
+  and a full TeX Live installation (including the large dev-texlive/texlive-
+  latexextra). Compared to that, the new Cairo-based code has much reduced
+  dependencies, and is hence the preferred way to generate sequence logos.
+
 *discrover-1.3.1 (15 Dec 2014)
 
   15 Dec 2014; Jonas Maaskola <jonas@maaskola.de> +discrover-1.3.1.ebuild,
diff --git a/sci-biology/discrover/Manifest b/sci-biology/discrover/Manifest
index 1c6054220..1696d9c31 100644
--- a/sci-biology/discrover/Manifest
+++ b/sci-biology/discrover/Manifest
@@ -1 +1 @@
-DIST discrover-1.3.1.tar.gz 224397 SHA256 7badd16a885657bae091c0eea101a59c10b8889c34ba53833e1b673548d150d5 SHA512 a9108c3b5ae03bec3c2cad352efc88d66de5973e51cfe97c8bbfbe52a1a24dad9acbd4aa00fd9d33de31dba6e76031c066b62a36c55048790a2814bbffe1786b WHIRLPOOL ed70b88ee64588368ffe354ac0d33e4ee48d7be427485384e1583732e138bfe2f7338076c67f29103234d5ca70a129f888ac572464e18c9ee813b72a62208637
+DIST discrover-1.4.1.tar.gz 236507 SHA256 abe181563828fd6f73941d98c954d8b0a88317cab9789c855a01b1eeb1686dc1 SHA512 950ee3fd4c37a5f9386d9800b2f5e0bb0e144818de28d35098e5de3074a9fd2572d0244034f5e4c28cc6c850741930e7139e24677a3e57dab2ab4da4277f87bf WHIRLPOOL ea415f005aa6782dec62b1c8011921e234dd929bf75f672deecc1856dea205f2bf2afa9c48b62bdbca305b8c5fe7b9d99d16d3777bb6c14cacc0020e66ba69d4
diff --git a/sci-biology/discrover/discrover-1.3.1.ebuild b/sci-biology/discrover/discrover-1.4.1.ebuild
index c892c73cf..5ae256fa1 100644
--- a/sci-biology/discrover/discrover-1.3.1.ebuild
+++ b/sci-biology/discrover/discrover-1.4.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -12,12 +12,13 @@ SRC_URI="https://github.com/maaskola/discrover/archive/${PV}.tar.gz -> ${P}.tar.
 LICENSE="GPL-3+"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="dreme doc +logo misc_scripts +rmathlib tcmalloc"
+IUSE="+cairo dreme doc tikzlogo misc_scripts +rmathlib tcmalloc"
 
 RDEPEND="
 	dev-libs/boost
+	cairo? ( x11-libs/cairo )
 	dreme? ( sci-biology/meme )
-	logo? (
+	tikzlogo? (
 		dev-lang/ruby
 		dev-texlive/texlive-latex
 		dev-texlive/texlive-latexextra
@@ -39,9 +40,10 @@ DEPEND="${RDEPEND}
 "
 src_configure() {
 	local mycmakeargs=(
+		$(cmake-utils_use_with cairo CAIRO)
 		$(cmake-utils_use_with dreme DREME)
 		$(cmake-utils_use_with doc DOC)
-		$(cmake-utils_use_with logo LOGO)
+		$(cmake-utils_use_with tikzlogo TIKZLOGO)
 		$(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
 		$(cmake-utils_use_with rmathlib RMATHLIB)
 		$(cmake-utils_use_with tcmalloc TCMALLOC)
diff --git a/sci-biology/discrover/discrover-9999.ebuild b/sci-biology/discrover/discrover-9999.ebuild
index d01dfdce2..5d3cf6316 100644
--- a/sci-biology/discrover/discrover-9999.ebuild
+++ b/sci-biology/discrover/discrover-9999.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Header: $
 
@@ -12,12 +12,13 @@ EGIT_REPO_URI="https://github.com/maaskola/${PN}"
 LICENSE="GPL-3+"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="dreme doc +logo misc_scripts +rmathlib tcmalloc"
+IUSE="+cairo dreme doc tikzlogo misc_scripts +rmathlib tcmalloc"
 
 RDEPEND="
 	dev-libs/boost
+	cairo? ( x11-libs/cairo )
 	dreme? ( sci-biology/meme )
-	logo? (
+	tikzlogo? (
 		dev-lang/ruby
 		dev-texlive/texlive-latex
 		dev-texlive/texlive-latexextra
@@ -39,9 +40,10 @@ DEPEND="${RDEPEND}
 "
 src_configure() {
 	local mycmakeargs=(
+		$(cmake-utils_use_with cairo CAIRO)
 		$(cmake-utils_use_with dreme DREME)
 		$(cmake-utils_use_with doc DOC)
-		$(cmake-utils_use_with logo LOGO)
+		$(cmake-utils_use_with tikzlogo TIKZLOGO)
 		$(cmake-utils_use_with misc_scripts MISC_SCRIPTS)
 		$(cmake-utils_use_with rmathlib RMATHLIB)
 		$(cmake-utils_use_with tcmalloc TCMALLOC)
diff --git a/sci-biology/discrover/metadata.xml b/sci-biology/discrover/metadata.xml
index cda9ddd84..24958c9f0 100644
--- a/sci-biology/discrover/metadata.xml
+++ b/sci-biology/discrover/metadata.xml
@@ -6,10 +6,13 @@
 		<name>Jonas Maaskola</name>
 	</maintainer>
 	<use>
+		<flag name="cairo">
+			Use Cairo for sequence logo plotting capabilities
+		</flag>
 		<flag name="dreme">
 			Allow to use DREME from the MEME package for seeding
 		</flag>
-		<flag name="logo">
+		<flag name="tikzlogo">
 			Enable LaTeX/TikZ based ruby script for sequence logo drawing
 		</flag>
 		<flag name="misc_scripts">