commit: 74c8a3dd36ff9ef2fbde4c219ee4feb07f673128 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Sat Feb 18 22:41:56 2017 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Sat Feb 18 22:41:56 2017 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=74c8a3dd
sci-biology/phusion: allmost corrected build process Package-Manager: Portage-2.3.3, Repoman-2.3.1 sci-biology/phusion/phusion-2.1c.ebuild | 22 ++++++++++++++++++++-- 1 file changed, 20 insertions(+), 2 deletions(-) diff --git a/sci-biology/phusion/phusion-2.1c.ebuild b/sci-biology/phusion/phusion-2.1c.ebuild index 83b3f546b..35bd43425 100644 --- a/sci-biology/phusion/phusion-2.1c.ebuild +++ b/sci-biology/phusion/phusion-2.1c.ebuild @@ -4,7 +4,7 @@ EAPI=5 -inherit eutils +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/"; @@ -15,7 +15,13 @@ LICENSE="all-rights-reserved" # temporarily placed value # 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="" +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" @@ -30,6 +36,18 @@ 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(){
