[gentoo-commits] proj/sci:master commit in: sci-biology/SOAPdenovo2/

[Andrew Ammerlaan]

commit:     86dd71ff4e5aaf1d07e78b746045ec800fe2bafe
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Feb  1 08:12:20 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Mon Feb  1 08:12:20 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=86dd71ff

sci-biology/SOAPdenovo2: version bump 242

no keywords yet, because it does not compile

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 ...APdenovo2-241.ebuild => SOAPdenovo2-242.ebuild} | 31 +++++++++-------------
 1 file changed, 13 insertions(+), 18 deletions(-)

diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild
similarity index 51%
rename from sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild
rename to sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild
index e3679664d..8ae80d466 100644
--- a/sci-biology/SOAPdenovo2/SOAPdenovo2-241.ebuild
+++ b/sci-biology/SOAPdenovo2/SOAPdenovo2-242.ebuild
@@ -1,19 +1,18 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=7
 
-inherit toolchain-funcs eutils
+inherit toolchain-funcs
 
 DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph) (now MEGAHIT)"
 HOMEPAGE="https://github.com/aquaskyline/SOAPdenovo2
-	http://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18"
-SRC_URI="https://github.com/aquaskyline/SOAPdenovo2/archive/r241.tar.gz -> ${P}.tar.gz"
+	https://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18"
+SRC_URI="https://github.com/aquaskyline/SOAPdenovo2/archive/r${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="" # fails to compile
 
 DEPEND="dev-libs/libaio
 	sci-biology/samtools:0.1-legacy"
@@ -22,7 +21,7 @@ RDEPEND="${DEPEND}"
 S="${WORKDIR}"/"${PN}"-r"${PV}" # version is 2.04-r241
 
 src_prepare(){
-	epatch "${FILESDIR}"/SOAPdenovo2-r241-Makefile.patch
+	#eapply "${FILESDIR}"/SOAPdenovo2-r241-Makefile.patch
 	# this will be partly covered by
 	# https://github.com/aquaskyline/SOAPdenovo2/pull/44
 	#
@@ -33,15 +32,11 @@ src_prepare(){
 		sparsePregraph/inc/sam.h sparsePregraph/inc/bam.h sparsePregraph/inc/bgzf.h standardPregraph/inc/zlib.h \
 		standardPregraph/inc/zconf.h sparsePregraph/inc/zlib.h sparsePregraph/inc/zconf.h standardPregraph/inc/*.so \
 		sparsePregraph/*.a || die
+	find -type f -name "*.h" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die
+	find -type f -name "*.h" -exec sed -i -e 's/#include "bgzf.h"/#include "bam-0.1-legacy\/bgzf.h"/g' {} + || die
+	find -type f -name "*.h" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die
+	find -type f -name "*.c*" -exec sed -i -e 's/#include "bam.h"/#include "bam-0.1-legacy\/bam.h"/g' {} + || die
+	find -type f -name "*.c*" -exec sed -i -e 's/#include "bgzf.h"/#include "bam-0.1-legacy\/bgzf.h"/g' {} + || die
+	find -type f -name "*.c*" -exec sed -i -e 's/#include "sam.h"/#include "bam-0.1-legacy\/sam.h"/g' {} + || die
 	default
 }
-
-src_compile(){
-	cd standardPregraph && emake -j1 63mer=1
-	cd ../standardPregraph && emake -j1 127mer=1
-	cd ../sparsePregraph && emake -j1
-}
-
-src_install(){
-	doman "${FILESDIR}"/SOAPdenovo2.1
-}