[gentoo-commits] proj/sci:master commit in: sci-biology/consed/

[Martin Mokrejs]

commit:     3d70d539efdee4713fc377c55a0585791f965179
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jul 23 00:13:48 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jul 23 00:13:48 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3d70d539

sci-biology/consed-29.0: version bump

Package-Manager: portage-2.2.18

 sci-biology/consed/ChangeLog        |  9 ++++
 sci-biology/consed/consed-29.ebuild | 93 +++++++++++++++++++++++++++++++++++++
 sci-biology/consed/metadata.xml     |  9 ++++
 3 files changed, 111 insertions(+)

diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog
new file mode 100644
index 0000000..a580e1e
--- /dev/null
+++ b/sci-biology/consed/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/consed
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*consed-29 (23 Jul 2015)
+
+  23 Jul 2015; Martin Mokrejs <mmokrejs@×××××××××××××××.cz> +consed-29.ebuild,
+  +metadata.xml:
+  sci-biology/consed-29.0: version bump

diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild
new file mode 100644
index 0000000..c6e3cf9
--- /dev/null
+++ b/sci-biology/consed/consed-29.ebuild
@@ -0,0 +1,93 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-27.ebuild,v 1.1 2014/10/26 16:13:23 jlec Exp $
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A genome sequence finishing program"
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
+SRC_URI="
+	${P}-sources.tar.gz
+	${P}-linux.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=x11-libs/motif-2.3:0"
+# it needs samtools-0.18 with khash.h
+# This file was about sci-biology/samtools-1.2 time moved to sci-libs/htslib-1.2.1
+RDEPEND="${DEPEND}
+	<sci-biology/samtools-1.0
+	>=sci-biology/phred-000925
+	>=sci-biology/phrap-1.080721
+	dev-lang/perl"
+
+S="${WORKDIR}"
+
+RESTRICT="fetch"
+
+pkg_nofetch() {
+	einfo "Please visit ${HOMEPAGE} and obtain the file"
+	einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
+	einfo "and place it in ${DISTDIR},"
+	einfo "obtain the file"
+	einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
+	einfo "and place it in ${DISTDIR}"
+}
+
+src_prepare() {
+	sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
+	sed -i \
+		-e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm -lbam -lz/' \
+		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
+		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
+		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/ -I/usr/include/htslib/#' "${S}/makefile" || die
+	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
+	sed \
+		-e 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' \
+		-i "${S}"/scripts/* || die
+}
+
+src_compile() {
+	einfo "consed does not compile with sys-devel/gcc-4.6:* or newer (but 4.4.7 works)"
+	emake
+	emake -C misc/mktrace
+	emake -C misc/phd2fasta
+	(cd misc/454; $(tc-getCC) ${CFLAGS} ${LDFLAGS} sff2scf.c -o sff2scf) || die
+}
+
+src_install() {
+	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf}
+	dobin scripts/* contributions/*
+	insinto /usr/lib/screenLibs
+	doins misc/*.{fa*,seq}
+	insinto /usr/share/${PN}/examples
+	doins -r \
+		standard polyphred autofinish assembly_view 454_newbler \
+		align454reads align454reads_answer solexa_example \
+		solexa_example_answer selectRegions selectRegionsAnswer
+	echo 'CONSED_HOME="${EPREFIX}/usr"' > "${S}"/99consed || die
+	echo 'CONSED_PARAMETERS="${EPREFIX}/etc/consedrc"' >> "${S}"/99consed || die
+	mkdir -p "${ED}"/etc/consedrc || die
+	touch "${ED}"/etc/consedrc || die
+	doenvd "${S}/99consed" || die
+	sed \
+		-e "s#/usr/local/genome#${EPREFIX}/usr#" \
+		-i "${ED}"/usr/bin/{*.perl,phredPhrap,phredPhrapWithPhdBalls} || die
+	sed \
+		-e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' \
+		-i "${ED}"/usr/bin/phredPhrap || die
+	sed \
+		-e 's#/wt1/gordon/genome#/usr/bin#' \
+		-i "${ED}"/usr/bin/fastq2Phrap.perl || die
+	dodoc README.txt *_announcement.txt || die
+}
+
+pkg_postinst() {
+	einfo "Package documentation is available at"
+	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
+}

diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/consed/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@×××××××××××××××.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>