[gentoo-commits] repo/gentoo:master commit in: sci-biology/emboss/

[Manuel Rüger]

commit:     0db67f06dd6358a4c5294cc79450616900e9160a
Author:     Manuel Rüger <mrueg <AT> gentoo <DOT> org>
AuthorDate: Wed Aug 26 17:21:50 2015 +0000
Commit:     Manuel Rüger <mrueg <AT> gentoo <DOT> org>
CommitDate: Wed Aug 26 17:21:50 2015 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0db67f06

sci-biology/emboss: Restore old version.

This commit reverts 0d040c84fbb38ead35451769d2b65a33af2fbf2a.

Package-Manager: portage-2.2.20.1
RepoMan-Options: --force

 sci-biology/emboss/Manifest            |   1 +
 sci-biology/emboss/emboss-6.0.1.ebuild | 112 +++++++++++++++++++++++++++++++++
 2 files changed, 113 insertions(+)

diff --git a/sci-biology/emboss/Manifest b/sci-biology/emboss/Manifest
index 6eae2dd..c364f2c 100644
--- a/sci-biology/emboss/Manifest
+++ b/sci-biology/emboss/Manifest
@@ -1,3 +1,4 @@
+DIST EMBOSS-6.0.1.tar.gz 20204153 SHA256 3e352902aa9dab88bf486457ff23794f19398dfc6b550c4bf175dfcad34c233d
 DIST EMBOSS-6.3.1.tar.gz 23572243 SHA256 4f3290600a970c2a23a7e47f884d1fc8156ec40538f7191a6e83e23680d27a8d
 DIST EMBOSS-6.6.0.tar.gz 117962028 SHA256 7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e SHA512 2d28a03381f7dc98d205aa50202fbbac02ad218fc775d86579d310296be124403623484b1907154d915f15cd32a9f8cf16ecfaa6c4a28b362e24dc8e6380b75a WHIRLPOOL 25241e865b1ad4e5459f84a2b0def7cd00a6e2904db714838dfe0533e01f8373cfdd4c78df225f9d2a77ead4cb9998791bd19f46b32e220810ad950fa288b9fe
 DIST emboss-6.3.1_p4.patch.gz 4070 SHA256 61d1b62e3148541d496103711db6526ba76488a0899af2c98264b03bf8d6e24c

diff --git a/sci-biology/emboss/emboss-6.0.1.ebuild b/sci-biology/emboss/emboss-6.0.1.ebuild
new file mode 100644
index 0000000..0edfd7a
--- /dev/null
+++ b/sci-biology/emboss/emboss-6.0.1.ebuild
@@ -0,0 +1,112 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=1
+
+inherit eutils
+
+DESCRIPTION="The European Molecular Biology Open Software Suite - A sequence analysis package"
+HOMEPAGE="http://emboss.sourceforge.net/"
+SRC_URI="ftp://${PN}.open-bio.org/pub/EMBOSS/old/${PV}/EMBOSS-${PV}.tar.gz"
+LICENSE="GPL-2 LGPL-2"
+
+SLOT="0"
+KEYWORDS="amd64 ppc x86"
+IUSE="X png minimal"
+
+DEPEND="
+	X? ( x11-libs/libXt )
+	png? (
+		sys-libs/zlib
+		media-libs/libpng
+		media-libs/gd
+		)
+	!minimal? (
+		sci-biology/primer3
+		sci-biology/clustalw
+		)"
+
+RDEPEND="${DEPEND}
+	!sys-devel/cons"
+
+PDEPEND="
+	!minimal? (
+		sci-biology/aaindex
+		sci-biology/cutg
+		sci-biology/prints
+		sci-biology/prosite
+		sci-biology/rebase
+		sci-biology/transfac
+	)"
+
+S="${WORKDIR}/EMBOSS-${PV}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}"/${PN}-5.0.0-as-needed.patch
+
+	local link_string="$(pkg-config --libs x11)"
+	if use png; then
+		link_string="${link_string} -lgd $(pkg-config --libs libpng)"
+	fi
+	sed -e "s:PATCH_PLPLOT:${link_string}:" -i plplot/Makefile.in \
+		|| die "Failed to patch ajax Makefile"
+}
+
+src_compile() {
+	local myconf
+	myconf="--includedir=${D}/usr/include/emboss"
+	use X || myconf="${EXTRA_CONF} --without-x"
+	use png || myconf="${EXTRA_CONF} --without-pngdriver"
+
+	econf ${myconf}
+	# Do not install the JEMBOSS component (the --without-java configure option
+	# does not work). JEMBOSS will eventually be available as a separate package.
+	sed -i -e "s/SUBDIRS = plplot ajax nucleus emboss test doc jemboss/SUBDIRS = plplot ajax nucleus emboss test doc/" \
+			Makefile || die
+	emake || die
+}
+
+src_install() {
+	einstall || die "Failed to install program files."
+
+	dodoc AUTHORS ChangeLog FAQ NEWS README THANKS \
+			|| die "Failed to install documentation."
+	newdoc "${FILESDIR}"/${PN}-README.Gentoo-1 README.Gentoo \
+			|| die "Failed to install Gentoo readme file."
+
+	# Install env file for setting libplplot and acd files path.
+	cat <<- EOF > 22emboss
+		# plplot libs dir
+		PLPLOT_LIB="/usr/share/EMBOSS/"
+		# ACD files location
+		EMBOSS_ACDROOT="/usr/share/EMBOSS/acd"
+	EOF
+	doenvd 22emboss || die "Failed to install environment file."
+
+	# Symlink preinstalled docs to "/usr/share/doc".
+	dosym /usr/share/EMBOSS/doc/manuals /usr/share/doc/${PF}/manuals || die
+	dosym /usr/share/EMBOSS/doc/programs /usr/share/doc/${PF}/programs || die
+	dosym /usr/share/EMBOSS/doc/tutorials /usr/share/doc/${PF}/tutorials || die
+	dosym /usr/share/EMBOSS/doc/html /usr/share/doc/${PF}/html || die
+
+	# Clashes #330507
+	mv "${D}"/usr/bin/{digest,pepdigest} || die
+
+	# Remove useless dummy files from the image.
+	find emboss/data -name dummyfile -delete || die "Failed to remove dummy files."
+
+	# Move the provided codon files to a different directory. This will avoid
+	# user confusion and file collisions on case-insensitive file systems (see
+	# bug #115446). This change is documented in "README.Gentoo".
+	mv "${D}"/usr/share/EMBOSS/data/CODONS{,.orig} || \
+			die "Failed to move CODON directory."
+
+	# Move the provided restriction enzyme prototypes file to a different name.
+	# This avoids file collisions with versions of rebase that install their
+	# own enzyme prototypes file (see bug #118832).
+	mv "${D}"/usr/share/EMBOSS/data/embossre.equ{,.orig} || \
+			die "Failed to move enzyme equivalence file."
+}