[gentoo-commits] proj/sci:master commit in: dev-python/pyBigWig/, sci-biology/deeptools/, sci-biology/plinkseq/, ...

[Martin Mokrejs]

commit:     81a1355ea065924e0c6426772af7c16d90432ccd
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 31 20:51:57 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 31 20:59:27 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=81a1355e

sci-biology/deeptools: add a new package

Package-Manager: Portage-2.3.5, Repoman-2.3.1

 dev-python/pyBigWig/metadata.xml             | 12 ++++
 dev-python/pyBigWig/pyBigWig-0.3.4.ebuild    | 16 +++++
 dev-python/pyBigWig/pyBigWig-9999.ebuild     | 18 ++++++
 sci-biology/deeptools/deeptools-2.5.0.ebuild | 33 ++++++++++
 sci-biology/deeptools/deeptools-9999.ebuild  | 34 ++++++++++
 sci-biology/deeptools/metadata.xml           | 12 ++++
 sci-biology/mira/mira-4.9.6.ebuild           | 93 ++++++++++++++++++++++++++++
 sci-biology/plinkseq/plinkseq-9999.ebuild    | 13 ++--
 8 files changed, 226 insertions(+), 5 deletions(-)

diff --git a/dev-python/pyBigWig/metadata.xml b/dev-python/pyBigWig/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/dev-python/pyBigWig/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>mmokrejs@×××××××××××××××.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-biology@g.o</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
new file mode 100644
index 000000000..33664c388
--- /dev/null
+++ b/dev-python/pyBigWig/pyBigWig-0.3.4.ebuild
@@ -0,0 +1,16 @@
+# 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
new file mode 100644
index 000000000..0e2cd40c8
--- /dev/null
+++ b/dev-python/pyBigWig/pyBigWig-9999.ebuild
@@ -0,0 +1,18 @@
+# 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/deeptools-2.5.0.ebuild b/sci-biology/deeptools/deeptools-2.5.0.ebuild
new file mode 100644
index 000000000..6f9a41d54
--- /dev/null
+++ b/sci-biology/deeptools/deeptools-2.5.0.ebuild
@@ -0,0 +1,33 @@
+# 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
new file mode 100644
index 000000000..4d6d2fa77
--- /dev/null
+++ b/sci-biology/deeptools/deeptools-9999.ebuild
@@ -0,0 +1,34 @@
+# 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
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/deeptools/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="person">
+    <email>mmokrejs@×××××××××××××××.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+  <maintainer type="project">
+    <email>sci-biology@g.o</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>

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"
+}

diff --git a/sci-biology/plinkseq/plinkseq-9999.ebuild b/sci-biology/plinkseq/plinkseq-9999.ebuild
index 461e62f84..cffdaff97 100644
--- a/sci-biology/plinkseq/plinkseq-9999.ebuild
+++ b/sci-biology/plinkseq/plinkseq-9999.ebuild
@@ -20,7 +20,6 @@ IUSE=""
 
 DEPEND="sys-libs/zlib
 	dev-libs/protobuf
-	www-servers/mongoose
 	!sci-biology/fsl" # file collision on /usr/bin/mm
 RDEPEND="${DEPEND}"
 
@@ -29,7 +28,9 @@ 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
-	rm -rf sources/mongoose || 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
 	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 $f`; \
@@ -44,11 +45,13 @@ src_prepare(){
 	sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/matrix.pb.cpp || die
 	sed -e 's/google::protobuf::internal::kEmptyString/google::protobuf::internal::GetEmptyStringAlreadyInited()/g' -i sources/plinkseq/sources/lib/variant.pb.cpp || die
 	local myinc=`pkg-config protobuf --variable=includedir`
-	sed -e "s@\$(PROTOBUF_LIB_BASE_DIR)/\$(INC_DIR)/@$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)/$(BLD_LIB_DIR)/@$mylib@" -i Makefile || die
+	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 $(PROTOBUF_LIB_FULL_PATH) is a necessary build target, just drop it
+	sed -e 's@^PROTOBUF_LIB_FULL_PATH =.*/@PROTOBUF_LIB_FULL_PATH =@' -i Makefile || die
 	local mylibs=`pkg-config protobuf --libs`
-	sed -e "s@libprotobuf.a@$mylibs@" -i Makefile || die
+	sed -e "s@libprotobuf.a@ ${mylibs}@ " -i Makefile || die
 }
 
 src_install(){