diff options
Diffstat (limited to 'sci-biology/phusion/phusion-2.1c.ebuild')
| -rw-r--r-- | sci-biology/phusion/phusion-2.1c.ebuild | 59 |
1 files changed, 0 insertions, 59 deletions
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/* -} |