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# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=5
DESCRIPTION="SSAHA2-based pipeline to align reads"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2/"
SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/pileup.tgz"
# http://samtools.sourceforge.net/pileup.shtml
#
LICENSE="GRL"
SLOT="0"
KEYWORDS=""
IUSE=""
DEPEND=""
RDEPEND="${DEPEND}"
S="${WORKDIR}"/pileup_v"${PV}"
src_prepare(){
sed -i "s/^CC= gcc/#CC= gcc/" ssaha_pileup/ssaha_pileup/makefile || die "sed failed to fix makefile"
sed -i "s/^CFLAGS= -O2/#CFLAGS= -O2/" ssaha_pileup/ssaha_pileup/makefile || die "sed failed to fix makefile"
for d in get_seqreads ssaha_split; do
sed -i "s/^CC = cc/#CC = cc/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
sed -i "s/^CFLAGS = -O4/#CFLAGS = -O4/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
done
for d in search_read ssaha_parseSNP; do
sed -i "s/^CC = gcc/#CC = gcc/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
sed -i "s/^CFLAGS = -Wall -O4/#CFLAGS = -Wall -O4/" ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile"
done
}
src_compile(){
cd ssaha_pileup/ssaha_pileup || die "Cannot cd to "${S}"ssaha_pileup/ssaha_pileup"
default
for d in get_seqreads ssaha_split ssaha_parseSNP search_read; do
cd "${S}"/ssaha_pileup/other_codes/$d || die "Cannot cd to "${S}"ssaha_pileup/other_codes/"$d
make clean
default
done
}
src_install(){
cd ssaha_pileup/ssaha_pileup || die "Cannot cd to "${S}"ssaha_pileup/ssaha_pileup"
dobin ssaha_pileup ssaha_solexa ssaha_pairs ssaha_clean ssaha_mates ssaha_cigar ssaha_indel view_pileup ssaha_reads ssaha_merge ssaha_check-cigar "dobin failed"
cd "${S}" || die
for f in ssaha_pileup/other_codes/get_seqreads/get_seqreads \
ssaha_pileup/other_codes/ssaha_split/ssaha_split \
ssaha_pileup/other_codes/ssaha_parseSNP/ssaha_parseSNP \
ssaha_pileup/other_codes/search_read/search_read; do
dobin $f "dobin failed"
done
# TODO:
# pileup_v0.6/ssaha_pileup/tag.pl
# Finally, a tcsh shell script has to be created with full paths to ssaha2 binaries
# convert the awk line from install.csh to a proper shellscript based on pileup.csh_src
}
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