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

This reverts commit 81a1355ea065924e0c6426772af7c16d90432ccd.

11 files changed, 6 insertions, 229 deletions

diff --git a/dev-python/pyBigWig/Manifest b/dev-python/pyBigWig/Manifest
deleted file mode 100644
index 3bb2f4b10..000000000
--- a/dev-python/pyBigWig/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pyBigWig-0.3.4.tar.gz 59804 SHA256 9c1b3ed26c7d35e5acb62d1653781b47a7b6e57b74361a9a59f3f3191532887a SHA512 9d7c174aa9d8242a5fb88a9a696201c7b5637ac66ae1aef730a5c4cc695f150094d830e0d575614f3f4a5cdf177bbc37a9fe06ced7ccc866906420288e24f319 WHIRLPOOL fa27a423f3c3d940fd9754aae98e80ca2140cf595599627e16e6a5de0ca10c2c064f310fcc43ec4e0c267411263722ac2e7a2b52f2e1abc65a0c7709bd063059
diff --git a/dev-python/pyBigWig/metadata.xml b/dev-python/pyBigWig/metadata.xml
deleted file mode 100644
index f68a1b6fa..000000000
--- a/dev-python/pyBigWig/metadata.xml
+++ /dev/null
@@ -1,12 +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>
-</pkgmetadata>
diff --git a/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild
deleted file mode 100644
index 33664c388..000000000
--- a/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild
+++ /dev/null
@@ -1,16 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-DESCRIPTION="Python extension written in C for quick access to and creation of bigWig files"
-HOMEPAGE="https://github.com/dpryan79/pyBigWig"
-SRC_URI="https://github.com/dpryan79/pyBigWig/archive/0.3.4.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="sci-biology/libBigWig"
-RDEPEND="${DEPEND}"
diff --git a/dev-python/pyBigWig/pyBigWig-9999.ebuild b/dev-python/pyBigWig/pyBigWig-9999.ebuild
deleted file mode 100644
index 0e2cd40c8..000000000
--- a/dev-python/pyBigWig/pyBigWig-9999.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit git-r3
-
-DESCRIPTION="Python extension written in C for quick access to and creation of bigWig files"
-HOMEPAGE="https://github.com/dpryan79/pyBigWig"
-EGIT_REPO_URI="https://github.com/dpryan79/pyBigWig.git"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="sci-biology/libBigWig"
-RDEPEND="${DEPEND}"
diff --git a/sci-biology/deeptools/Manifest b/sci-biology/deeptools/Manifest
deleted file mode 100644
index c0a50f45e..000000000
--- a/sci-biology/deeptools/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST deeptools-2.5.0.tar.gz 59620916 SHA256 2636f96b0781a05149949bebcc3634810c030c7b83187456a275619908bf8787 SHA512 5bd10d4c58cdd7b3318028eb28f6ca9252d42899dee8eb8ad6af1b372ad26fbcc605b712c3369ec45350600f2c822a17679062b9f536f454e5bfb0381715f98f WHIRLPOOL 422bd2a3d9ca2b7f697ae127c487d472c672fcef955b761cb5b5783dbf56ed14c3d05c3f01360fe02aeef01f427ecf45370dc8f0eb1c9e93080ac9938e2cc88e
diff --git a/sci-biology/deeptools/deeptools-2.5.0.ebuild b/sci-biology/deeptools/deeptools-2.5.0.ebuild
deleted file mode 100644
index 6f9a41d54..000000000
--- a/sci-biology/deeptools/deeptools-2.5.0.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_5 )
-
-inherit distutils-r1
-
-[ "$PV" == "9999" ] && inherit git-2
-
-DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig"
-HOMEPAGE="https://github.com/fidelram/deepTools"
-if [ "$PV" == "9999" ]; then
-	EGIT_REPO_URI="https://github.com/fidelram/deepTools"
-	KEYWORDS=""
-else
-	SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND=">=dev-python/numpy-1.8.0
-		>=sci-libs/scipy-0.17.0
-		>=dev-python/py2bit-0.1.0
-		>=dev-python/pyBigWig-0.2.1
-		>=sci-biology/pysam-0.8
-		>=dev-python/matplotlib-1.4.0"
-RDEPEND="${DEPEND}"
-
diff --git a/sci-biology/deeptools/deeptools-9999.ebuild b/sci-biology/deeptools/deeptools-9999.ebuild
deleted file mode 100644
index 4d6d2fa77..000000000
--- a/sci-biology/deeptools/deeptools-9999.ebuild
+++ /dev/null
@@ -1,34 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_5 )
-
-inherit distutils-r1
-
-[ "$PV" == "9999" ] && inherit git-2
-
-DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig"
-HOMEPAGE="https://github.com/fidelram/deepTools"
-if [ "$PV" == "9999" ]; then
-	EGIT_REPO_URI="https://github.com/fidelram/deepTools"
-	KEYWORDS=""
-else
-	SRC_URI="https://github.com/fidelram/deepTools/archive/2.5.0.tar.gz -> ${P}.tar.gz"
-	KEYWORDS="~amd64"
-fi
-
-LICENSE="GPL-3"
-SLOT="0"
-IUSE=""
-
-DEPEND=">=dev-python/numpy-1.8.0
-		>=sci-libs/scipy-0.17.0
-		>=dev-python/py2bit-0.1.0
-		>=dev-python/pyBigWig-0.2.1
-		>=sci-biology/pysam-0.8
-		>=dev-python/matplotlib-1.4.0"
-RDEPEND="${DEPEND}"
-
diff --git a/sci-biology/deeptools/metadata.xml b/sci-biology/deeptools/metadata.xml
deleted file mode 100644
index f68a1b6fa..000000000
--- a/sci-biology/deeptools/metadata.xml
+++ /dev/null
@@ -1,12 +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>
-</pkgmetadata>
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"
-}
diff --git a/sci-biology/plinkseq/plinkseq-9999.ebuild b/sci-biology/plinkseq/plinkseq-9999.ebuild
index cffdaff97..461e62f84 100644
--- a/sci-biology/plinkseq/plinkseq-9999.ebuild
+++ b/sci-biology/plinkseq/plinkseq-9999.ebuild
@@ -20,6 +20,7 @@ IUSE=""
 
 DEPEND="sys-libs/zlib
 	dev-libs/protobuf
+	www-servers/mongoose
 	!sci-biology/fsl" # file collision on /usr/bin/mm
 RDEPEND="${DEPEND}"
 
@@ -28,9 +29,7 @@ src_prepare(){
 	sed -e "s/= -static/=/g" -i config_defs.Makefile || die
 	rm -rf sources/ext/protobuf-* || die
 	rm sources/ext/protobuf sources/ext/sources/include/google || die
-	# we cannot zap calls to bundled mongoose because www-servers/mongoose does not build a library at all
-	# rm -rf sources/mongoose || die
-	# sed -e "s@$(MONGOOSE_LIB_DIR) @@;s@$(MONGOOSE_INC) @@;s@$(MONGOOSE_LIB_BASE_DIR) @@" - Makefile || die
+	rm -rf sources/mongoose || die
 	sed -e 's@^all:.*@all: # skipping compilation of bundled dev-libs/protobuf@' -i sources/ext/Makefile || die
 	find . -name \*.proto | while read f; do \
 		d=`dirname $f`; \
@@ -45,13 +44,11 @@ src_prepare(){
 	sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/matrix.pb.cpp || die
 	sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/variant.pb.cpp || die
 	local myinc=`pkg-config protobuf --variable=includedir`
-	sed -e 's@$(PROTOBUF_LIB_BASE_DIR)/$(INC_DIR)/@'"${myinc}@" -i Makefile || die
+	sed -e "s@\$(PROTOBUF_LIB_BASE_DIR)/\$(INC_DIR)/@$myinc@" -i Makefile || die
 	local mylib=`pkg-config protobuf --variable=libdir`
-	sed -e 's@$(PROTOBUF_LIB_BASE_DIR)/$(BLD_LIB_DIR)/@'"-L${mylib} @" -i Makefile || die # note the trailing space as it get prepended to PROTOBUF_LIBS
-	# anyway $(PROTOBUF_LIB_FULL_PATH) is a necessary build target, just drop it
-	sed -e 's@^PROTOBUF_LIB_FULL_PATH =.*/@PROTOBUF_LIB_FULL_PATH =@' -i Makefile || die
+	sed -e "s@$(PROTOBUF_LIB_BASE_DIR)/$(BLD_LIB_DIR)/@$mylib@" -i Makefile || die
 	local mylibs=`pkg-config protobuf --libs`
-	sed -e "s@libprotobuf.a@ ${mylibs}@ " -i Makefile || die
+	sed -e "s@libprotobuf.a@$mylibs@" -i Makefile || die
 }
 
 src_install(){