sci-biology/deeptools: add a new package

Package-Manager: Portage-2.3.5, Repoman-2.3.1

2 files changed, 94 insertions, 1 deletions

diff --git a/sci-biology/mira/Manifest b/sci-biology/mira/Manifest
index a095295dd..b8fec0936 100644
--- a/sci-biology/mira/Manifest
+++ b/sci-biology/mira/Manifest
@@ -1,2 +1,2 @@
-DIST mira-4.9.5.tar.bz2 10444005 SHA256 07160f9847edcb5109fa9085109f73a18849473fc2afdcda1118faf3c5fc3d77 SHA512 f56bd9e1c6982b501534bc8c64fed0ed81f20505546d6e79b48cfed3d82780a43691e985f5be3910af55adf12a955dbf1901cb1da1f182636d5e1357d8129cf8 WHIRLPOOL be0abe4213ecbe40534bee65dba390ac3695d3763123ad93c4a32bbcded15aa2f99ef93304b8e4cdc65728f0859e2748ad828826919bf7e4fc6b8499bccbdf9c
+DIST mira-4.9.6.tar.bz2 15006355 SHA256 e910479bc5f3f205913ac81cd2a24449cc175a6d1ae1fe3ae33ea0e100435b16 SHA512 f4ede2082222ba0c69626b1fb8d4fdc78c2591738883ccf19ae1a8a35bf33b9e9d6cd8364c87ea0f4404472064e19cbf49d8ed36ced9b085de5c4d9e1aabb8bd WHIRLPOOL 0784e2e00988889b8f11aadf92247273ee4db2c4889e5a60ab016787caf2256be143c7b586ad79541ddb512dedc309e94d52cd48604812f4fbb5439699b4c014
 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
new file mode 100644
index 000000000..22ddea015
--- /dev/null
+++ b/sci-biology/mira/mira-4.9.6.ebuild
@@ -0,0 +1,93 @@
+# 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"
+}