[gentoo-commits] proj/sci:master commit in: sci-biology/gap2caf/

["Andrew Ammerlaan" <andrewammerlaan@riseup.net>]

commit:     4811dbace02e39fc810456ddbc683dbafbe4a521
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 13:38:21 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 13:38:21 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4811dbac

sci-biology/gap2caf: remove pack, upstream gone

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/gap2caf/gap2caf-2.1.0.ebuild | 77 --------------------------------
 sci-biology/gap2caf/metadata.xml         | 15 -------
 2 files changed, 92 deletions(-)

diff --git a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild b/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
deleted file mode 100644
index 90a117a8c..000000000
--- a/sci-biology/gap2caf/gap2caf-2.1.0.ebuild
+++ /dev/null
@@ -1,77 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit autotools eutils
-
-DESCRIPTION="GAP4 file format to CAF v2 format converter for genomic assembly data"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/caf/"
-SRC_URI="
-	ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/gap2caf-2.1.0.tar.gz
-	http://downloads.sourceforge.net/staden/staden-2.0.0b8.tar.gz"
-
-LICENSE="GRL staden"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	sci-biology/staden
-	>=dev-lang/tcl-8.5:0="
-RDEPEND="${DEPEND}"
-
-#src_prepare(){
-#	epatch "${FILESDIR}"/Makefile.in-"${PV}".patch || die
-#}
-
-src_prepare(){
-	sed -i 's:/include/tcl8.4:/include:' configure.ac || die
-	sed -i 's:libtcl8.4:libtcl:' configure.ac || die
-	sed \
-		-e 's:tcl8.4:tcl:' \
-		-e 's:pkglib_PROGRAMS:pkglibexec_PROGRAMS:g' \
-		-i src/Makefile.am || die
-	eautoreconf
-	sed -i 's:/include/tcl8.4:/include:' configure || die
-	sed -i 's:libtcl8.4:libtcl:' configure || die
-}
-
-src_configure(){
-	# STADENROOT=/usr is used to find $STADENROOT/lib/staden/staden.profile and staden_config.h
-	# STADENSRC is used to locate gap4/IO.h
-	#CPPFLAGS="$CPPFLAGS -I/home/mmokrejs/proj/staden/staden/trunk/src" \
-	#LDFLAGS="$LDFLAGS -L/usr/lib/staden -lmutlib -lprimer3 -lg -lmisc" \
-	# STADENROOT=/usr/share/staden \
-	# STADENSRC="${WORKDIR}"/staden-2.0.0b8-src \
-	econf \
-		--with-stadenroot=/usr \
-		--with-tcl=/usr \
-		--with-stadensrc="${WORKDIR}"/staden-2.0.0b8-src
-	#sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' Makefile || die
-	#sed -i 's:prefix = /usr:prefix = $(DESTDIR)/usr:' src/Makefile || die
-	sed -i 's:tcl8.4:tcl:' src/Makefile || die
-
-	# The below tricks in overall do not help, only for -ltk_utils somehow
-	sed -i 's:-ltk_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -ltk_utils -rpath-link:' src/Makefile || die
-	sed -i 's:-lgap:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -lgap:' src/Makefile || die
-	sed -i 's:-lseq_utils:-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib/staden -lseq_utils:' src/Makefile || die
-	sed -i 's:-rpath-link::' src/Makefile || die
-}
-
-# TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME
-# The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files,
-# not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help.
-src_install(){
-	# do not use upstream's install it just install shell wrapper into /usr/bin/gap2caf
-	# calling "LD_LIBRARY_PATH=/usr/lib/staden /usr/lib/gap2caf/gap2caf $@"
-	# emake install DESTDIR="${D}" || die
-	#
-	# Instead, we rely on sci-biology/staden providind /etc/env.d/99staden file providing LDPATH=/usr/lib/staden
-	dobin src/gap2caf
-	dodoc README
-}
-
-# BUG #259848
-# A working ebuild which needs some files from staden source tree. That is ugly,
-# am sorting out with upstream how to get around in a clean way.

diff --git a/sci-biology/gap2caf/metadata.xml b/sci-biology/gap2caf/metadata.xml
deleted file mode 100644
index 0f267b755..000000000
--- a/sci-biology/gap2caf/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="person">
-		<email>mmokrejs@fold.natur.cuni.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>