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

[David Seifert]

commit:     982e9dfdf15d8bc9da0c795d93278de2bae027d2
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Tue Sep 27 16:51:12 2016 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Tue Sep 27 16:51:12 2016 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=982e9dfd

sci-biology/tophat: Remove old and ancient 1.0 ebuilds

Package-Manager: portage-2.3.1

 sci-biology/tophat/Manifest             |  1 -
 sci-biology/tophat/tophat-1.0.12.ebuild | 38 ---------------------------------
 2 files changed, 39 deletions(-)

diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest
index 2bf8121..a0a9b79 100644
--- a/sci-biology/tophat/Manifest
+++ b/sci-biology/tophat/Manifest
@@ -1,2 +1 @@
-DIST tophat-1.0.12.tar.gz 468781 SHA256 f67b3f89aa79c7e14b40bcdba87f5aba6d322f869ca4260503e64ffcd2b621b2 SHA512 275e14cb6fb5f7a0874adcf843aabfda6c6868f835faa2d03e6561646ca1fc80804fe1887c51a375125f2f5ed6242e304f97ff12774a7d676b4964614d4a5bf1 WHIRLPOOL ea62ce14aae28dc0cc2b18fde870a0d3c021d9fb0c2ffb728b02b008b5f5bd416f29176fe81ed2ad8b1a41014f8a7114e2b8032426e2767effe9cc6933417cee
 DIST tophat-2.1.1.tar.gz 2259554 SHA256 37840b96f3219630082b15642c47f5ef95d14f6ee99c06a369b08b3d05684da5 SHA512 e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc WHIRLPOOL 1e0d2bc4031eaa56a3b77ca5966c2ed439a85c9b05f028f69f4477d517e51371156bbe73d499536148eb42d60641af7f294641ee79bc855fcc4df74d70dae26c

diff --git a/sci-biology/tophat/tophat-1.0.12.ebuild b/sci-biology/tophat/tophat-1.0.12.ebuild
deleted file mode 100644
index 88870c9..00000000
--- a/sci-biology/tophat/tophat-1.0.12.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="2"
-
-inherit autotools
-
-DESCRIPTION="A fast splice junction mapper for RNA-Seq reads"
-HOMEPAGE="http://tophat.cbcb.umd.edu/"
-SRC_URI="http://tophat.cbcb.umd.edu/downloads/${P}.tar.gz"
-
-LICENSE="Artistic"
-SLOT="0"
-IUSE=""
-KEYWORDS="amd64 x86"
-
-DEPEND=""
-RDEPEND="sci-biology/bowtie"
-
-src_prepare() {
-	# fix missing includes
-	sed -i '/#include <string>/ a #include <stdio.h>' "${S}/src/gff_juncs.cpp" || die
-	sed -i \
-		-e '/#include <stdio.h>/ a #include <unistd.h>' \
-		"${S}/src/prep_reads.cpp" \
-		"${S}/src/extract_reads.cpp" || die
-	# fix parallel make race
-	sed -i -e 's/\$(top_builddir)\/src\///g' src/Makefile.am || die
-	# remove broken arch-dependent CFLAGS setting
-	perl -i -ne 'print unless /case "\${host_cpu}-\${host_os}" in/../^esac/' configure.ac || die
-	eautoreconf
-}
-
-src_install() {
-	einstall || die
-	dodoc AUTHORS NEWS THANKS
-}