Revert "sci-biology/deeptools: add a new package"

This reverts commit 81a1355ea065924e0c6426772af7c16d90432ccd.

2 files changed, 1 insertions, 94 deletions

diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
index b8fec0936..a095295dd 100644
--- a/sci-biology/mira/Manifest
+++ b/sci-biology/mira/Manifest
@@ -1,2 +1,2 @@
-DIST mira-4.9.6.tar.bz2 15006355 SHA256 e910479bc5f3f205913ac81cd2a24449cc175a6d1ae1fe3ae33ea0e100435b16 SHA512 f4ede2082222ba0c69626b1fb8d4fdc78c2591738883ccf19ae1a8a35bf33b9e9d6cd8364c87ea0f4404472064e19cbf49d8ed36ced9b085de5c4d9e1aabb8bd WHIRLPOOL 0784e2e00988889b8f11aadf92247273ee4db2c4889e5a60ab016787caf2256be143c7b586ad79541ddb512dedc309e94d52cd48604812f4fbb5439699b4c014
+DIST mira-4.9.5.tar.bz2 10444005 SHA256 07160f9847edcb5109fa9085109f73a18849473fc2afdcda1118faf3c5fc3d77 SHA512 f56bd9e1c6982b501534bc8c64fed0ed81f20505546d6e79b48cfed3d82780a43691e985f5be3910af55adf12a955dbf1901cb1da1f182636d5e1357d8129cf8 WHIRLPOOL be0abe4213ecbe40534bee65dba390ac3695d3763123ad93c4a32bbcded15aa2f99ef93304b8e4cdc65728f0859e2748ad828826919bf7e4fc6b8499bccbdf9c
 DIST mira_3rdparty_06-07-2012.tar.bz2 31656 SHA256 53cbbb9d57e2fa51706b3f1d055621c0863091542b8851f3ce8a45850951d7d2 SHA512 4d4dbdf7ab5126f9d47160bee8bc127b6a225de8087f6b9914c754324a74d966333207c86a3f38cf0ea9f91408707e2a24086dbe1318fdfa2870b0c39bc5033b WHIRLPOOL c9946ddc032d6864a33e7a60a4d1a515262ca2204535c7d81dcc73144b4f471f766007082d1912fc4ca219a9cbb4ac5a485451c625a7ffcc1949fb8574a3f3d2
diff --git a/sci-biology/mira/mira-4.9.6.ebuild b/sci-biology/mira/mira-4.9.6.ebuild
deleted file mode 100644
index 22ddea015..000000000
--- a/sci-biology/mira/mira-4.9.6.ebuild
+++ /dev/null
@@ -1,93 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-MIRA_3RDPARTY_PV="06-07-2012"
-MY_PV="${PV/_}" # convert from mira-4.0_rc2 (Gentoo ebuild filename derived) to mira-4.0rc2 (upstream fromat)
-
-inherit autotools eutils multilib
-
-DESCRIPTION="Whole Genome Shotgun and EST Sequence Assembler for Sanger, 454 and Solexa / Illumina"
-HOMEPAGE="http://www.chevreux.org/projects_mira.html"
-SRC_URI="
-	http://sourceforge.net/projects/mira-assembler/files/MIRA/development/"${PN}"-"${MY_PV}".tar.bz2
-	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-# 	http://sourceforge.net/projects/mira-assembler/files/MIRA/stable/"${PN}"-"${MY_PV}".tar.bz2
-#	http://sourceforge.net/projects/mira-assembler/files/MIRA/development/${P}.tar.bz2
-#	mirror://sourceforge/mira-assembler/mira_3rdparty_${MIRA_3RDPARTY_PV}.tar.bz2"
-
-S="${WORKDIR}"/"${PN}"-"${MY_PV}"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
-IUSE="doc"
-
-CDEPEND="
-	dev-libs/boost
-	dev-util/google-perftools"
-DEPEND="${CDEPEND}
-	app-editors/vim-core
-	dev-libs/expat"
-RDEPEND="${CDEPEND}"
-
-#DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED
-#	THANKS doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf )
-DOCS=( AUTHORS GETTING_STARTED NEWS README HELP_WANTED THANKS )
-
-# mira 4.9.x requires C++14 standard compliant compiler, so >=gcc-4.9.1
-src_prepare() {
-	find -name 'configure*' -or -name 'Makefile*' | xargs sed -i 's/flex++/flex -+/' || die
-	epatch \
-		"${FILESDIR}"/${PN}-3.4.0.2-boost-1.50.patch \
-		"${FILESDIR}"/${P}-cout.patch \
-		"${FILESDIR}"/${P}-DESTDIR.patch
-
-	sed \
-		-e "s:-O[23]::g" \
-		-e "s:-funroll-loops::g" \
-		-i configure.ac || die
-
-	eautoreconf
-}
-
-src_configure() {
-	econf \
-		--with-boost="${EPREFIX}/usr/$(get_libdir)" \
-		--with-boost-libdir="${EPREFIX}/usr/$(get_libdir)" \
-		--with-boost-thread=boost_thread-mt
-}
-
-#src_compile() {
-#	base_src_compile
-#	# TODO: resolve docbook incompatibility for building docs
-#	if use doc; then emake -C doc clean docs || die; fi
-#}
-
-src_install() {
-	default
-	dodoc ${DOCS[@]}
-
-	dobin "${WORKDIR}"/3rdparty/{sff_extract,qual2ball,*.pl}
-	dodoc "${WORKDIR}"/3rdparty/{README.txt,midi_screen.fasta}
-
-	# if sci-biology/staden is installed, ideally use configprotect?
-	if [ -e "${ED}"/usr/share/staden/etc/GTAGDB ]; then
-		if [ `grep -c HAF "${ED}"/usr/share/staden/etc/GTAGDB` -eq 0 ]; then
-			cat "${ED}"/usr/share/staden/etc/GTAGDB "${S}"/src/support/GTAGDB > "${WORKDIR}"/GTAGDB || die
-			insinto /usr/share/staden/etc/
-			doins "${WORKDIR}"/GTAGDB
-		fi
-	fi
-	if [ -e "/etc/consedrc/" ]; then
-		insinto /etc/consedrc
-		doins "${S}"/src/support/consedtaglib.txt
-	fi
-}
-
-pkg_postinst() {
-	einfo "Documentation is no longer built, you can find it at:"
-	einfo "http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html"
-}