* [gentoo-commits] proj/sci:master commit in: sci-biology/SOAPdenovo2/
@ 2017-05-15 21:14 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2017-05-15 21:14 UTC (permalink / raw
To: gentoo-commits
commit: f667c44afb6544667c0ba8fadb3d2f70fadf08ad
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 15 21:14:04 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 15 21:14:04 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f667c44a
sci-biology/SOAPdenovo2: new package
Does not respect CFLAGS, compile fails
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild | 20 ++++++++++++++++++++
sci-biology/SOAPdenovo2/metadata.xml | 12 ++++++++++++
2 files changed, 32 insertions(+)
diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild
new file mode 100644
index 000000000..cfd5749db
--- /dev/null
+++ b/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph)"
+HOMEPAGE="https://sourceforge.net/projects/soapdenovo2
+ https://github.com/aquaskyline/SOAPdenovo2
+ http://gigascience.biomedcentral.com/articles/10.1186/2047-217X-1-18"
+SRC_URI="https://sourceforge.net/projects/soapdenovo2/files/${PN}/src/r${PV}/${PN}-src-r${PV}.tgz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/"${PN}"-src-r"${PV}"
diff --git a/sci-biology/SOAPdenovo2/metadata.xml b/sci-biology/SOAPdenovo2/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/SOAPdenovo2/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SOAPdenovo2/
@ 2017-05-15 23:05 Martin Mokrejs
0 siblings, 0 replies; 3+ messages in thread
From: Martin Mokrejs @ 2017-05-15 23:05 UTC (permalink / raw
To: gentoo-commits
commit: c782b7fd95b50208635e1f8ff47ef3e2edc98eeb
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 15 23:05:01 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 15 23:05:01 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c782b7fd
sci-biology/SOAPdenovo2: a bit cleanup of the build process
Will need to bring in Debian med patches from git://anonscm.debian.org/debian-med/soapdenovo2.git
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild | 30 ++++++++++++++++++++++++--
1 file changed, 28 insertions(+), 2 deletions(-)
diff --git a/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild b/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild
index cfd5749db..0ca68007a 100644
--- a/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild
+++ b/sci-biology/SOAPdenovo2/SOAPdenovo2-240.ebuild
@@ -3,6 +3,8 @@
EAPI=6
+inherit toolchain-funcs
+
DESCRIPTION="Whole genome shotgun assembler (sparse de Bruijn graph)"
HOMEPAGE="https://sourceforge.net/projects/soapdenovo2
https://github.com/aquaskyline/SOAPdenovo2
@@ -14,7 +16,31 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND=""
+DEPEND="dev-libs/libaio
+ sci-biology/samtools:0.1-legacy"
RDEPEND="${DEPEND}"
-S="${WORKDIR}"/"${PN}"-src-r"${PV}"
+S="${WORKDIR}"/"${PN}"-src-r"${PV}" # version is 2.04-r240
+
+src_prepare(){
+ # pass to broken Makefile's a proper C++ compiler through the CC variable
+ sed -e "s/CC = g++/CC = "$(tc-getCXX)"/;s/CFLAGS=/CFLAGS = ${CXXFLAGS} #/;s/-lbam/-lbam-0.1-legacy/" -i Makefile || die
+ sed -e 's#-I./sparsePregraph/inc#-I/usr/include/bam-0.1-legacy -I./sparsePregraph/inc#' -i Makefile || die
+ sed -e "s/CC = g++/CC = "$(tc-getCXX)"/;s/CFLAGS=/CFLAGS = ${CXXFLAGS} #/;s/-lbam/-lbam-0.1-legacy/" -i sparsePregraph/Makefile || die
+ sed -e 's#-I./sparsePregraph/inc#-I/usr/include/bam-0.1-legacy -I./sparsePregraph/inc#' -i sparsePregraph/Makefile || die
+ rm -f standardPregraph/*.a standardPregraph/inc/sam.h standardPregraph/inc/bam.h standardPregraph/inc/bgzf.h \
+ sparsePregraph/inc/sam.h sparsePregraph/inc/bam.h sparsePregraph/inc/bgzf.h standardPregraph/inc/zlib.h \
+ standardPregraph/inc/zconf.h sparsePregraph/inc/zlib.h sparsePregraph/inc/zconf.h standardPregraph/inc/*.so \
+ sparsePregraph/*.a || die
+ default
+}
+
+src_compile(){
+ cd standardPregraph && emake -j1 63mer=1
+ cd ../standardPregraph && emake -j1 127mer=1
+ cd ../sparsePregraph && emake -j1
+}
+
+src_install(){
+ doman "${FILESDIR}"/SOAPdenovo2.1
+}
^ permalink raw reply related [flat|nested] 3+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SOAPdenovo2/
@ 2021-02-01 8:12 Andrew Ammerlaan
0 siblings, 0 replies; 3+ messages in thread
From: Andrew Ammerlaan @ 2021-02-01 8:12 UTC (permalink / raw
To: gentoo-commits
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
-}
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