* [gentoo-commits] gentoo-x86 commit in sci-biology/consed: ChangeLog consed-19-r2.ebuild consed-19-r1.ebuild
@ 2010-05-22 8:53 Justin Lecher (jlec)
0 siblings, 0 replies; 3+ messages in thread
From: Justin Lecher (jlec) @ 2010-05-22 8:53 UTC (permalink / raw
To: gentoo-commits
jlec 10/05/22 08:53:38
Modified: ChangeLog consed-19-r1.ebuild
Added: consed-19-r2.ebuild
Log:
removed PHRED_PARAMETER_FILE env, #253451
(Portage version: 2.2_rc67/cvs/Linux x86_64)
Revision Changes Path
1.3 sci-biology/consed/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/ChangeLog?rev=1.3&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/ChangeLog?rev=1.3&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/ChangeLog?r1=1.2&r2=1.3
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- ChangeLog 15 Mar 2009 16:58:21 -0000 1.2
+++ ChangeLog 22 May 2010 08:53:37 -0000 1.3
@@ -1,6 +1,12 @@
# ChangeLog for sci-biology/consed
-# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.2 2009/03/15 16:58:21 weaver Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.3 2010/05/22 08:53:37 jlec Exp $
+
+*consed-19-r2 (22 May 2010)
+
+ 22 May 2010; Justin Lecher <jlec@gentoo.org> consed-19-r1.ebuild,
+ +consed-19-r2.ebuild:
+ removed PHRED_PARAMETER_FILE env, #253451, some QA
*consed-19-r1 (15 Mar 2009)
1.2 sci-biology/consed/consed-19-r1.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild?r1=1.1&r2=1.2
Index: consed-19-r1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- consed-19-r1.ebuild 15 Mar 2009 16:58:21 -0000 1.1
+++ consed-19-r1.ebuild 22 May 2010 08:53:37 -0000 1.2
@@ -1,6 +1,6 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild,v 1.1 2009/03/15 16:58:21 weaver Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild,v 1.2 2010/05/22 08:53:37 jlec Exp $
inherit toolchain-funcs
@@ -59,7 +59,6 @@
align454reads align454reads_answer solexa_example \
solexa_example_answer selectRegions selectRegionsAnswer || die
echo 'CONSED_HOME=/usr' > "${S}/99consed"
- echo 'PHRED_PARAMETER_FILE=/usr/share/phred/phredpar.dat' >> "${S}/99consed"
doenvd "${S}/99consed" || die
dodoc README.txt *_announcement.txt
}
1.1 sci-biology/consed/consed-19-r2.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild?rev=1.1&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild?rev=1.1&content-type=text/plain
Index: consed-19-r2.ebuild
===================================================================
# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild,v 1.1 2010/05/22 08:53:37 jlec Exp $
EAPI=3
inherit toolchain-funcs
DESCRIPTION="A genome sequence finishing program"
HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
SRC_URI="${P}-sources.tar.gz
${P}-linux.tar.gz"
LICENSE="phrap"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND="x11-libs/openmotif"
RDEPEND="${DEPEND}
>=sci-biology/phred-000925
>=sci-biology/phrap-1.080721"
S="${WORKDIR}"
RESTRICT="fetch"
pkg_nofetch() {
einfo "Please visit ${HOMEPAGE} and obtain the file"
einfo "\"sources.tar.gz\", then rename it to \"${P}-sources.tar.gz\""
einfo "and place it in ${DISTDIR},"
einfo "obtain the file"
einfo "\"consed_linux.tar.gz\", then rename it to \"${P}-linux.tar.gz\""
einfo "and place it in ${DISTDIR}"
}
src_prepare() {
sed -i '/#include/ s/<new.h>/<new>/' "${S}/main.cpp" || die
sed -i \
-e '/CLIBS=/ s/$/ -lXm -lXt -lSM -lICE -lXext -lXmu -lXp -lm/' \
-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
-e 's/CFLGS=/CFLGS= ${CFLAGS} /' "${S}/makefile" || die
sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
sed -i 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "${EPREFIX}/usr/share/phred/phredpar.dat";!' "${S}/scripts/"* || die
}
src_compile() {
emake || die
emake -C misc/mktrace || die
emake -C misc/phd2fasta || die
(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
}
src_install() {
dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die
dobin scripts/* contributions/* || die
insinto /usr/lib/screenLibs
doins misc/*.{fa*,seq} || die
insinto /usr/share/${PN}/examples
doins -r standard polyphred autofinish assembly_view 454_newbler \
align454reads align454reads_answer solexa_example \
solexa_example_answer selectRegions selectRegionsAnswer || die
echo 'CONSED_HOME=${EPREFIX}/usr' > "${S}/99consed"
doenvd "${S}/99consed" || die
dodoc README.txt *_announcement.txt || die
}
pkg_postinst() {
einfo "Package documentation is available at"
einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
}
^ permalink raw reply [flat|nested] 3+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/consed: ChangeLog consed-19-r2.ebuild consed-19-r1.ebuild
@ 2010-10-10 21:20 Ulrich Mueller (ulm)
0 siblings, 0 replies; 3+ messages in thread
From: Ulrich Mueller (ulm) @ 2010-10-10 21:20 UTC (permalink / raw
To: gentoo-commits
ulm 10/10/10 21:20:04
Modified: ChangeLog consed-19-r2.ebuild consed-19-r1.ebuild
Log:
Fix openmotif dependency.
(Portage version: 2.1.9.14/cvs/Linux x86_64)
Revision Changes Path
1.4 sci-biology/consed/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/ChangeLog?rev=1.4&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/ChangeLog?rev=1.4&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/ChangeLog?r1=1.3&r2=1.4
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- ChangeLog 22 May 2010 08:53:37 -0000 1.3
+++ ChangeLog 10 Oct 2010 21:20:04 -0000 1.4
@@ -1,6 +1,10 @@
# ChangeLog for sci-biology/consed
# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.3 2010/05/22 08:53:37 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.4 2010/10/10 21:20:04 ulm Exp $
+
+ 10 Oct 2010; Ulrich Mueller <ulm@gentoo.org> consed-19-r1.ebuild,
+ consed-19-r2.ebuild:
+ Fix openmotif dependency.
*consed-19-r2 (22 May 2010)
1.2 sci-biology/consed/consed-19-r2.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild?rev=1.2&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild?rev=1.2&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild?r1=1.1&r2=1.2
Index: consed-19-r2.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- consed-19-r2.ebuild 22 May 2010 08:53:37 -0000 1.1
+++ consed-19-r2.ebuild 10 Oct 2010 21:20:04 -0000 1.2
@@ -1,6 +1,6 @@
# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild,v 1.1 2010/05/22 08:53:37 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild,v 1.2 2010/10/10 21:20:04 ulm Exp $
EAPI=3
@@ -16,7 +16,7 @@
KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND="x11-libs/openmotif"
+DEPEND=">=x11-libs/openmotif-2.3:0"
RDEPEND="${DEPEND}
>=sci-biology/phred-000925
>=sci-biology/phrap-1.080721"
1.3 sci-biology/consed/consed-19-r1.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild?rev=1.3&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild?rev=1.3&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild?r1=1.2&r2=1.3
Index: consed-19-r1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- consed-19-r1.ebuild 22 May 2010 08:53:37 -0000 1.2
+++ consed-19-r1.ebuild 10 Oct 2010 21:20:04 -0000 1.3
@@ -1,6 +1,8 @@
# Copyright 1999-2010 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild,v 1.2 2010/05/22 08:53:37 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild,v 1.3 2010/10/10 21:20:04 ulm Exp $
+
+EAPI=1
inherit toolchain-funcs
@@ -14,7 +16,7 @@
KEYWORDS="~x86 ~amd64"
IUSE=""
-DEPEND="x11-libs/openmotif"
+DEPEND=">=x11-libs/openmotif-2.3:0"
RDEPEND="${DEPEND}
>=sci-biology/phred-000925
>=sci-biology/phrap-1.080721"
^ permalink raw reply [flat|nested] 3+ messages in thread
* [gentoo-commits] gentoo-x86 commit in sci-biology/consed: ChangeLog consed-19-r2.ebuild consed-19-r1.ebuild
@ 2012-10-24 19:30 Ulrich Mueller (ulm)
0 siblings, 0 replies; 3+ messages in thread
From: Ulrich Mueller (ulm) @ 2012-10-24 19:30 UTC (permalink / raw
To: gentoo-commits
ulm 12/10/24 19:30:07
Modified: ChangeLog consed-19-r2.ebuild consed-19-r1.ebuild
Log:
Update dependency after package move from x11-libs/openmotif to x11-libs/motif.
(Portage version: 2.1.11.30/cvs/Linux x86_64, signed Manifest commit with key E7BE08CA7DC6EA25)
Revision Changes Path
1.5 sci-biology/consed/ChangeLog
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/ChangeLog?rev=1.5&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/ChangeLog?rev=1.5&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/ChangeLog?r1=1.4&r2=1.5
Index: ChangeLog
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- ChangeLog 10 Oct 2010 21:20:04 -0000 1.4
+++ ChangeLog 24 Oct 2012 19:30:07 -0000 1.5
@@ -1,6 +1,11 @@
# ChangeLog for sci-biology/consed
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.4 2010/10/10 21:20:04 ulm Exp $
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/ChangeLog,v 1.5 2012/10/24 19:30:07 ulm Exp $
+
+ 24 Oct 2012; Ulrich Müller <ulm@gentoo.org> consed-19-r1.ebuild,
+ consed-19-r2.ebuild:
+ Update dependency after package move from x11-libs/openmotif to
+ x11-libs/motif.
10 Oct 2010; Ulrich Mueller <ulm@gentoo.org> consed-19-r1.ebuild,
consed-19-r2.ebuild:
1.3 sci-biology/consed/consed-19-r2.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild?rev=1.3&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild?rev=1.3&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild?r1=1.2&r2=1.3
Index: consed-19-r2.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- consed-19-r2.ebuild 10 Oct 2010 21:20:04 -0000 1.2
+++ consed-19-r2.ebuild 24 Oct 2012 19:30:07 -0000 1.3
@@ -1,6 +1,6 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild,v 1.2 2010/10/10 21:20:04 ulm Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r2.ebuild,v 1.3 2012/10/24 19:30:07 ulm Exp $
EAPI=3
@@ -16,7 +16,7 @@
KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND=">=x11-libs/openmotif-2.3:0"
+DEPEND=">=x11-libs/motif-2.3:0"
RDEPEND="${DEPEND}
>=sci-biology/phred-000925
>=sci-biology/phrap-1.080721"
1.4 sci-biology/consed/consed-19-r1.ebuild
file : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild?rev=1.4&view=markup
plain: http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild?rev=1.4&content-type=text/plain
diff : http://sources.gentoo.org/viewvc.cgi/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild?r1=1.3&r2=1.4
Index: consed-19-r1.ebuild
===================================================================
RCS file: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- consed-19-r1.ebuild 10 Oct 2010 21:20:04 -0000 1.3
+++ consed-19-r1.ebuild 24 Oct 2012 19:30:07 -0000 1.4
@@ -1,6 +1,6 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2012 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild,v 1.3 2010/10/10 21:20:04 ulm Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-19-r1.ebuild,v 1.4 2012/10/24 19:30:07 ulm Exp $
EAPI=1
@@ -16,7 +16,7 @@
KEYWORDS="~x86 ~amd64"
IUSE=""
-DEPEND=">=x11-libs/openmotif-2.3:0"
+DEPEND=">=x11-libs/motif-2.3:0"
RDEPEND="${DEPEND}
>=sci-biology/phred-000925
>=sci-biology/phrap-1.080721"
^ permalink raw reply [flat|nested] 3+ messages in thread
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2010-10-10 21:20 [gentoo-commits] gentoo-x86 commit in sci-biology/consed: ChangeLog consed-19-r2.ebuild consed-19-r1.ebuild Ulrich Mueller (ulm)
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2012-10-24 19:30 Ulrich Mueller (ulm)
2010-05-22 8:53 Justin Lecher (jlec)
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