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

[Marius Brehler]

commit:     6c039b13fc211799fc9de0a6e92df997f90169ed
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Oct  3 21:22:56 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon Oct  3 21:24:00 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6c039b13

sci-biology/consed: Remove, latest version in main tree

 sci-biology/consed/consed-29.ebuild | 93 -------------------------------------
 sci-biology/consed/metadata.xml     | 12 -----
 2 files changed, 105 deletions(-)

diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild
deleted file mode 100644
index 002e007..0000000
--- a/sci-biology/consed/consed-29.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
-
-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/samtools-0.1.18
-	>=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 += /' "${S}"/misc/*/Makefile || die
-	sed \
-		-e "s!\$szPhredParameterFile = .*!\$szPhredParameterFile = \$ENV{'PHRED_PARAMETER_FILE'} || \'"${EPREFIX}"/usr/share/phred/phredpar.dat\';!" \
-		-i "${S}"/scripts/* || die
-}
-
-src_compile() {
-	einfo "consed does not compile with >=sys-devel/gcc-4.6:* but 4.4.7 works"
-	default
-	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
-	touch "${ED}"/etc/consedrc || die "Cannot create a file for system-wide settings"
-	doenvd "${S}/99consed"
-	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
-}
-
-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
deleted file mode 100644
index 1699e58..0000000
--- a/sci-biology/consed/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@×××××××××××××××.cz</email>
-    <name>Martin Mokrejs</name>
-  </maintainer>
-<maintainer type="project">
-    <email>sci-biology@g.o</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>