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>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">downloads</remote-id> - </upstream> -</pkgmetadata>
