[gentoo-commits] proj/sci:master commit in: sci-biology/phusion/, profiles/updates/

[gentoo-commits] proj/sci:master commit in: sci-biology/phusion/, profiles/updates/

[Andrew Ammerlaan]

commit:     287342602b6146c42fac21e85322cd69d8b4af59
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Feb  3 04:26:43 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Wed Feb  3 04:28:32 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=28734260

sci-biology/fusion: remove, duplicate of fusion2

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 profiles/updates/1Q-2021                |  1 +
 sci-biology/phusion/metadata.xml        | 12 -------
 sci-biology/phusion/phusion-2.1c.ebuild | 59 ---------------------------------
 3 files changed, 1 insertion(+), 71 deletions(-)

diff --git a/profiles/updates/1Q-2021 b/profiles/updates/1Q-2021
index 562e445bc..a314a6bef 100644
--- a/profiles/updates/1Q-2021
+++ b/profiles/updates/1Q-2021
@@ -6,3 +6,4 @@ move sci-misc/elmer-front sci-misc/elmer-fem
 move sci-misc/elmer-meshgend2d sci-misc/elmer-fem
 move sci-misc/elmer-post sci-misc/elmer-fem
 move sci-misc/elmer-meta sci-misc/elmer-fem
+move sci-biology/fusion  sci-biology/fusion2

diff --git a/sci-biology/phusion/metadata.xml b/sci-biology/phusion/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/phusion/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/phusion/phusion-2.1c.ebuild b/sci-biology/phusion/phusion-2.1c.ebuild
deleted file mode 100644
index 7c72e31fd..000000000
--- a/sci-biology/phusion/phusion-2.1c.ebuild
+++ /dev/null
@@ -1,59 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils flag-o-matic toolchain-funcs
-
-DESCRIPTION="Whole genome shotgun assembler using phrap (for Sanger-based reads)"
-HOMEPAGE="http://www.sanger.ac.uk/resources/software/phusion/"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/phusion/phusion_pipeline_v2.1c.tar.gz"
-
-LICENSE="all-rights-reserved" # temporarily placed value
-# from http://genome.cshlp.org/content/13/1/81.full
-# Availability
-# Phusion is undergoing a rewrite of the code to make this a portable package. It will be made available free of charge to academic sites, but requires licensing for commercial use. For more information please contact the authors.
-SLOT="0"
-KEYWORDS="" # compile process does not exit upon errors
-# one file does not compile
-# x86_64-pc-linux-gnu-gcc  -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native  -o contigoverlap  contigoverlap.o  -lm
-# contigoverlap.o: In function `HashFasta':
-# contigoverlap.c:(.text+0xbb1): relocation truncated to fit: R_X86_64_PC32 against symbol `n_Entry' defined in COMMON section in contigoverlap.o
-# contigoverlap.o: In function `Reads_Overlap':
-# contigoverlap.c:(.text+0x2637): relocation truncated to fit: R_X86_64_32S against symbol `qinfo' defined in COMMON section in contigoverlap.o
-IUSE=""
-
-DEPEND="app-shells/tcsh"
-RDEPEND="${DEPEND}
-	sci-biology/phrap
-	dev-lang/perl"
-
-# contains bundled ssaha
-# file collision with sci-biology/shrimp on /usr/bin/fasta2fastq
-
-S="${WORKDIR}"/"phusion_pipeline_v2.1c"
-
-src_prepare(){
-	cp -pf "${EPREFIX}"/usr/bin/phrap src/phrap/phrap.manylong || die
-	# prevent file collision with sci-biology/shrimp-2.2.3 and sci-biology/phusion2-3.0
-	sed -e "s#fasta2fastq#fasta2fastq_"${PN}"#" -i src/fasta2fastq/fasta2fastq.c \
-		src/fasta2fastq/Makefile || die
-	sed -e "s#ctgreads.pl#ctgreads_"${PN}".pl#" -i src/Tcsh_scripts/*.csh || die
-	mv src/fasta2fastq/fasta2fastq.c src/fasta2fastq/fasta2fastq_"${PN}".c || die
-	mv src/Perl_scripts/ctgreads.pl src/Perl_scripts/ctgreads_"${PN}".pl || die
-	find . -name Makefile | while read f; do
-		sed -e "s/^CC =/CC = $(tc-getCC) #/" -i "$f" || die
-		sed -e "s/^ CFLAGS2 =/ CFLAGS2 = ${CFLAGS} #/" -i "$f" || die
-		sed -e "s/^CFLAGS =/CFLAGS = ${CFLAGS} #/" -i "$f" || die
-		sed -e "s/^ CFLAGS =/ CFLAGS = ${CFLAGS} #/" -i "$f" || die
-	done
-}
-
-src_compile(){
-	tcsh install.csh || csh install.csh || die
-}
-
-src_install(){
-	dobin bin/*
-	dodoc README.1st releaseNote_v2.1c doc/*
-}