commit: 717a929b44dd20599cfb826e521397cebda099ce Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Wed Feb 3 04:49:05 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Wed Feb 3 04:49:05 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=717a929b
sci-biology/pileup: EAPI bump Package-Manager: Portage-3.0.14, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> sci-biology/pileup/pileup-0.6.ebuild | 41 ++++++++++++++++-------------------- 1 file changed, 18 insertions(+), 23 deletions(-) diff --git a/sci-biology/pileup/pileup-0.6.ebuild b/sci-biology/pileup/pileup-0.6.ebuild index 54c16576b..ad978f70f 100644 --- a/sci-biology/pileup/pileup-0.6.ebuild +++ b/sci-biology/pileup/pileup-0.6.ebuild @@ -1,36 +1,36 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 DESCRIPTION="SSAHA2-based pipeline to align reads" -HOMEPAGE="http://www.sanger.ac.uk/resources/software/ssaha2/"; +HOMEPAGE="https://www.sanger.ac.uk/resources/software/ssaha2/"; SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/ssaha2/pileup.tgz -> ${P}.tgz" # http://samtools.sourceforge.net/pileup.shtml # LICENSE="GRL" SLOT="0" -KEYWORDS="" -IUSE="" +KEYWORDS="~amd64" -DEPEND="" -RDEPEND="${DEPEND}" - -S="${WORKDIR}"/pileup_v"${PV}" +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" + default + sed -i -e "s/^CC= gcc/#CC= gcc/" \ + -e "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" + sed -i -e "s/^CC = cc/#CC = cc/" \ + -e "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/$d/Makefile || die "sed failed to fix Makefile" + sed -i -e "s/^CC = gcc/#CC = gcc/" \ + -e "s/^CFLAGS = -Wall -O4/#CFLAGS = -Wall -O4/" \ + ssaha_pileup/other_codes/$d/Makefile || die "sed failed to fix Makefile" done } @@ -40,22 +40,17 @@ src_compile(){ 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 + emake clean default done } src_install(){ cd ssaha_pileup/ssaha_pileup || die "Cannot cd to "${S}"ssaha_pileup/ssaha_pileup" - dobin ssaha_pileup ssaha_solexa ssaha_pairs ssaha_clean ssaha_mates ssaha_cigar ssaha_indel view_pileup ssaha_reads ssaha_merge ssaha_check-cigar "dobin failed" + dobin ssaha_pileup ssaha_solexa ssaha_pairs ssaha_clean ssaha_mates ssaha_cigar ssaha_indel view_pileup ssaha_reads ssaha_merge ssaha_check-cigar - cd "${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 $f "dobin failed" - done + cd "${S}/ssaha_pileup/other_codes" || die + dobin get_seqreads/get_seqreads ssaha_split/ssaha_split ssaha_parseSNP/ssaha_parseSNP search_read/search_read # TODO: # pileup_v0.6/ssaha_pileup/tag.pl
