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>mmokr...@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biol...@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/* -}
