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

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* [gentoo-commits] proj/sci:master commit in: sci-biology/consed/
@ 2011-05-18  9:27 Martin Mokrejs
  0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2011-05-18  9:27 UTC (permalink / raw
  To: gentoo-commits

commit:     715640d179860f5f6b52045dc3ef496e1bd52b95
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed May 18 09:27:40 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed May 18 09:27:40 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=715640d1

sci-biology/consed-20-r1: improve message on die()

---
 sci-biology/consed/consed-20-r1.ebuild |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/sci-biology/consed/consed-20-r1.ebuild b/sci-biology/consed/consed-20-r1.ebuild
index 6cd983f..5c65e66 100644
--- a/sci-biology/consed/consed-20-r1.ebuild
+++ b/sci-biology/consed/consed-20-r1.ebuild
@@ -48,7 +48,7 @@ src_prepare() {
 }
 
 src_compile() {
-	emake || die
+	emake || die "If you have gcc-4.5 please use <=4.4 or visit bug #351152"
 	emake -C misc/mktrace || die
 	emake -C misc/phd2fasta || die
 	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die



^ permalink raw reply related	[flat|nested] 13+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/consed/
@ 2011-06-24 17:09 Justin Lecher
  0 siblings, 0 replies; 13+ messages in thread
From: Justin Lecher @ 2011-06-24 17:09 UTC (permalink / raw
  To: gentoo-commits

commit:     9ce3b537c2600df7165d219fb15a6263f2e96b52
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 24 12:50:10 2011 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Fri Jun 24 12:50:10 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9ce3b537

Sort inherit and/or USE

(Portage version: 2.2.0_alpha41/git/Linux x86_64, signed Manifest commit with key 70EB7916)

---
 sci-biology/consed/consed-20-r1.ebuild |    2 +-
 1 files changed, 1 insertions(+), 1 deletions(-)

diff --git a/sci-biology/consed/consed-20-r1.ebuild b/sci-biology/consed/consed-20-r1.ebuild
index 5c65e66..0ddce15 100644
--- a/sci-biology/consed/consed-20-r1.ebuild
+++ b/sci-biology/consed/consed-20-r1.ebuild
@@ -4,7 +4,7 @@
 
 EAPI=3
 
-inherit toolchain-funcs eutils
+inherit eutils toolchain-funcs
 
 DESCRIPTION="A genome sequence finishing program"
 HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"



^ permalink raw reply related	[flat|nested] 13+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/consed/
@ 2012-10-31  9:48 Martin Mokrejs
  0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2012-10-31  9:48 UTC (permalink / raw
  To: gentoo-commits

commit:     ba446e1d33bb277f8fbf8f44a4fdabd04bed4c4c
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Oct 31 09:47:53 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Oct 31 09:47:53 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ba446e1d

renamed dependency from openmotif to motif

Package-Manager: portage-2.1.11.31

---
 sci-biology/consed/ChangeLog           |    8 ++++++++
 sci-biology/consed/consed-20-r1.ebuild |    4 ++--
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog
new file mode 100644
index 0000000..9221d45
--- /dev/null
+++ b/sci-biology/consed/ChangeLog
@@ -0,0 +1,8 @@
+# ChangeLog for sci-biology/consed
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  31 Oct 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  consed-20-r1.ebuild:
+  renamed dependency from openmotif to motif consed-20-r1.ebuild
+

diff --git a/sci-biology/consed/consed-20-r1.ebuild b/sci-biology/consed/consed-20-r1.ebuild
index 0ddce15..759af84 100644
--- a/sci-biology/consed/consed-20-r1.ebuild
+++ b/sci-biology/consed/consed-20-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2011 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 $
 
@@ -16,7 +16,7 @@ SLOT="0"
 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


^ permalink raw reply related	[flat|nested] 13+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/consed/
@ 2014-03-23 15:49 Martin Mokrejs
  0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2014-03-23 15:49 UTC (permalink / raw
  To: gentoo-commits

commit:     6d310e83f00757cb9568b49710d8f4eb93ee3840
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 15:47:27 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 15:47:27 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6d310e83

sci-biology/consed: added versions 21 to 27

Package-Manager: portage-2.2.7

---
 sci-biology/consed/ChangeLog        | 21 ++++++++++-
 sci-biology/consed/consed-21.ebuild | 74 +++++++++++++++++++++++++++++++++++++
 sci-biology/consed/consed-22.ebuild | 74 +++++++++++++++++++++++++++++++++++++
 sci-biology/consed/consed-23.ebuild | 74 +++++++++++++++++++++++++++++++++++++
 sci-biology/consed/consed-24.ebuild | 74 +++++++++++++++++++++++++++++++++++++
 sci-biology/consed/consed-25.ebuild | 74 +++++++++++++++++++++++++++++++++++++
 sci-biology/consed/consed-26.ebuild | 74 +++++++++++++++++++++++++++++++++++++
 sci-biology/consed/consed-27.ebuild | 74 +++++++++++++++++++++++++++++++++++++
 8 files changed, 537 insertions(+), 2 deletions(-)

diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog
index 9221d45..3ce8ee3 100644
--- a/sci-biology/consed/ChangeLog
+++ b/sci-biology/consed/ChangeLog
@@ -1,8 +1,25 @@
 # ChangeLog for sci-biology/consed
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*consed-27 (23 Mar 2014)
+*consed-26 (23 Mar 2014)
+*consed-25 (23 Mar 2014)
+*consed-24 (23 Mar 2014)
+*consed-23 (23 Mar 2014)
+*consed-22 (23 Mar 2014)
+*consed-21 (23 Mar 2014)
+
+  23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  consed-20-r1.ebuild, +consed-21.ebuild, +consed-22.ebuild,
+  files/nLine.h.patch, files/nextPhredPipeline.cpp.patch, metadata.xml:
+  Added versions 21, 22, 23, 24, 25, 26, 27. None of them need the two
+  patches anymore but all of them need samtools for BAM support.
+  Compiled with x86_64-pc-linux-gnu-4.3.6.
+
   31 Oct 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
   consed-20-r1.ebuild:
-  renamed dependency from openmotif to motif consed-20-r1.ebuild
+  renamed dependency from openmotif to motif consed-20-r1.ebuild,
+  added some extra patches files/nLine.h.patch,
+  files/nextPhredPipeline.cpp.patch
 

diff --git a/sci-biology/consed/consed-21.ebuild b/sci-biology/consed/consed-21.ebuild
new file mode 100644
index 0000000..7163d60
--- /dev/null
+++ b/sci-biology/consed/consed-21.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A genome sequence finishing program"
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
+SRC_URI="${P}-sources.tar.gz
+	${P}-linux.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=x11-libs/motif-2.3:0"
+RDEPEND="${DEPEND}
+	sci-biology/samtools
+	>=sci-biology/phred-000925
+	>=sci-biology/phrap-1.080721
+	dev-lang/perl"
+
+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 -lbam -lz/' \
+		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
+		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
+		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${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 "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152"
+	emake -C misc/mktrace || die
+	emake -C misc/phd2fasta || die
+	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
+}
+
+src_install() {
+	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
+	dobin scripts/* contributions/* || die
+	insinto /usr/lib/screenLibs
+	doins misc/*.{fa*,seq} || die
+	insinto /usr/share/${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"
+}

diff --git a/sci-biology/consed/consed-22.ebuild b/sci-biology/consed/consed-22.ebuild
new file mode 100644
index 0000000..7163d60
--- /dev/null
+++ b/sci-biology/consed/consed-22.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A genome sequence finishing program"
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
+SRC_URI="${P}-sources.tar.gz
+	${P}-linux.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=x11-libs/motif-2.3:0"
+RDEPEND="${DEPEND}
+	sci-biology/samtools
+	>=sci-biology/phred-000925
+	>=sci-biology/phrap-1.080721
+	dev-lang/perl"
+
+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 -lbam -lz/' \
+		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
+		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
+		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${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 "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152"
+	emake -C misc/mktrace || die
+	emake -C misc/phd2fasta || die
+	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
+}
+
+src_install() {
+	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
+	dobin scripts/* contributions/* || die
+	insinto /usr/lib/screenLibs
+	doins misc/*.{fa*,seq} || die
+	insinto /usr/share/${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"
+}

diff --git a/sci-biology/consed/consed-23.ebuild b/sci-biology/consed/consed-23.ebuild
new file mode 100644
index 0000000..7163d60
--- /dev/null
+++ b/sci-biology/consed/consed-23.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A genome sequence finishing program"
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
+SRC_URI="${P}-sources.tar.gz
+	${P}-linux.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=x11-libs/motif-2.3:0"
+RDEPEND="${DEPEND}
+	sci-biology/samtools
+	>=sci-biology/phred-000925
+	>=sci-biology/phrap-1.080721
+	dev-lang/perl"
+
+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 -lbam -lz/' \
+		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
+		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
+		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${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 "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152"
+	emake -C misc/mktrace || die
+	emake -C misc/phd2fasta || die
+	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
+}
+
+src_install() {
+	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
+	dobin scripts/* contributions/* || die
+	insinto /usr/lib/screenLibs
+	doins misc/*.{fa*,seq} || die
+	insinto /usr/share/${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"
+}

diff --git a/sci-biology/consed/consed-24.ebuild b/sci-biology/consed/consed-24.ebuild
new file mode 100644
index 0000000..7163d60
--- /dev/null
+++ b/sci-biology/consed/consed-24.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A genome sequence finishing program"
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
+SRC_URI="${P}-sources.tar.gz
+	${P}-linux.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=x11-libs/motif-2.3:0"
+RDEPEND="${DEPEND}
+	sci-biology/samtools
+	>=sci-biology/phred-000925
+	>=sci-biology/phrap-1.080721
+	dev-lang/perl"
+
+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 -lbam -lz/' \
+		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
+		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
+		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${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 "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152"
+	emake -C misc/mktrace || die
+	emake -C misc/phd2fasta || die
+	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
+}
+
+src_install() {
+	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
+	dobin scripts/* contributions/* || die
+	insinto /usr/lib/screenLibs
+	doins misc/*.{fa*,seq} || die
+	insinto /usr/share/${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"
+}

diff --git a/sci-biology/consed/consed-25.ebuild b/sci-biology/consed/consed-25.ebuild
new file mode 100644
index 0000000..7163d60
--- /dev/null
+++ b/sci-biology/consed/consed-25.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A genome sequence finishing program"
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
+SRC_URI="${P}-sources.tar.gz
+	${P}-linux.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=x11-libs/motif-2.3:0"
+RDEPEND="${DEPEND}
+	sci-biology/samtools
+	>=sci-biology/phred-000925
+	>=sci-biology/phrap-1.080721
+	dev-lang/perl"
+
+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 -lbam -lz/' \
+		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
+		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
+		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${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 "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152"
+	emake -C misc/mktrace || die
+	emake -C misc/phd2fasta || die
+	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
+}
+
+src_install() {
+	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
+	dobin scripts/* contributions/* || die
+	insinto /usr/lib/screenLibs
+	doins misc/*.{fa*,seq} || die
+	insinto /usr/share/${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"
+}

diff --git a/sci-biology/consed/consed-26.ebuild b/sci-biology/consed/consed-26.ebuild
new file mode 100644
index 0000000..7163d60
--- /dev/null
+++ b/sci-biology/consed/consed-26.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A genome sequence finishing program"
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
+SRC_URI="${P}-sources.tar.gz
+	${P}-linux.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=x11-libs/motif-2.3:0"
+RDEPEND="${DEPEND}
+	sci-biology/samtools
+	>=sci-biology/phred-000925
+	>=sci-biology/phrap-1.080721
+	dev-lang/perl"
+
+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 -lbam -lz/' \
+		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
+		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
+		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${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 "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152"
+	emake -C misc/mktrace || die
+	emake -C misc/phd2fasta || die
+	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
+}
+
+src_install() {
+	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
+	dobin scripts/* contributions/* || die
+	insinto /usr/lib/screenLibs
+	doins misc/*.{fa*,seq} || die
+	insinto /usr/share/${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"
+}

diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild
new file mode 100644
index 0000000..7163d60
--- /dev/null
+++ b/sci-biology/consed/consed-27.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A genome sequence finishing program"
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
+SRC_URI="${P}-sources.tar.gz
+	${P}-linux.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=x11-libs/motif-2.3:0"
+RDEPEND="${DEPEND}
+	sci-biology/samtools
+	>=sci-biology/phred-000925
+	>=sci-biology/phrap-1.080721
+	dev-lang/perl"
+
+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 -lbam -lz/' \
+		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
+		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
+		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/#' "${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 "If you have gcc >= 4.5 please use <=4.4 or visit bug #351152"
+	emake -C misc/mktrace || die
+	emake -C misc/phd2fasta || die
+	(cd misc/454; $(tc-getCC) ${CFLAGS} sff2scf.c -o sff2scf) || die
+}
+
+src_install() {
+	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf} || die "Please try gcc-4.4.4 if build with 4.5.2 failed, bug #351152"
+	dobin scripts/* contributions/* || die
+	insinto /usr/lib/screenLibs
+	doins misc/*.{fa*,seq} || die
+	insinto /usr/share/${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 related	[flat|nested] 13+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/consed/
@ 2014-04-02  9:32 Martin Mokrejs
  0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2014-04-02  9:32 UTC (permalink / raw
  To: gentoo-commits

commit:     4209a296d2ae3587c269da77976813d6f80d2b0b
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Apr  2 09:30:37 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Apr  2 09:30:37 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4209a296

sci-biology/consed: replace hardcoded CONSED_HOME path in installed perl scripts to fix situations when user has for some reason an empty CONSED_HOME

Package-Manager: portage-2.2.7

---
 sci-biology/consed/ChangeLog           | 7 ++++++-
 sci-biology/consed/consed-20-r1.ebuild | 1 +
 sci-biology/consed/consed-21.ebuild    | 1 +
 sci-biology/consed/consed-22.ebuild    | 1 +
 sci-biology/consed/consed-23.ebuild    | 1 +
 sci-biology/consed/consed-24.ebuild    | 1 +
 sci-biology/consed/consed-25.ebuild    | 1 +
 sci-biology/consed/consed-26.ebuild    | 1 +
 sci-biology/consed/consed-27.ebuild    | 1 +
 9 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog
index 3ce8ee3..0fe8c19 100644
--- a/sci-biology/consed/ChangeLog
+++ b/sci-biology/consed/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  02 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> consed-20-r1.ebuild,
+  consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild,
+  consed-25.ebuild, consed-26.ebuild, consed-27.ebuild:
+  sci-biology/consed: replace hardcoded CONSED_HOME path in installed perl
+  scripts to fix situations when user has for some reason an empty CONSED_HOME
+
 *consed-27 (23 Mar 2014)
 *consed-26 (23 Mar 2014)
 *consed-25 (23 Mar 2014)
@@ -22,4 +28,3 @@
   renamed dependency from openmotif to motif consed-20-r1.ebuild,
   added some extra patches files/nLine.h.patch,
   files/nextPhredPipeline.cpp.patch
-

diff --git a/sci-biology/consed/consed-20-r1.ebuild b/sci-biology/consed/consed-20-r1.ebuild
index 2eb8df3..cfcb66e 100644
--- a/sci-biology/consed/consed-20-r1.ebuild
+++ b/sci-biology/consed/consed-20-r1.ebuild
@@ -65,6 +65,7 @@ src_install() {
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
 	doenvd "${S}/99consed" || die
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
 	dodoc README.txt *_announcement.txt || die
 }
 

diff --git a/sci-biology/consed/consed-21.ebuild b/sci-biology/consed/consed-21.ebuild
index 7163d60..55ba90a 100644
--- a/sci-biology/consed/consed-21.ebuild
+++ b/sci-biology/consed/consed-21.ebuild
@@ -64,6 +64,7 @@ src_install() {
 		align454reads align454reads_answer solexa_example \
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
 	doenvd "${S}/99consed" || die
 	dodoc README.txt *_announcement.txt || die
 }

diff --git a/sci-biology/consed/consed-22.ebuild b/sci-biology/consed/consed-22.ebuild
index 7163d60..d0a26e8 100644
--- a/sci-biology/consed/consed-22.ebuild
+++ b/sci-biology/consed/consed-22.ebuild
@@ -65,6 +65,7 @@ src_install() {
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
 	doenvd "${S}/99consed" || die
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
 	dodoc README.txt *_announcement.txt || die
 }
 

diff --git a/sci-biology/consed/consed-23.ebuild b/sci-biology/consed/consed-23.ebuild
index 7163d60..d0a26e8 100644
--- a/sci-biology/consed/consed-23.ebuild
+++ b/sci-biology/consed/consed-23.ebuild
@@ -65,6 +65,7 @@ src_install() {
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
 	doenvd "${S}/99consed" || die
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
 	dodoc README.txt *_announcement.txt || die
 }
 

diff --git a/sci-biology/consed/consed-24.ebuild b/sci-biology/consed/consed-24.ebuild
index 7163d60..d0a26e8 100644
--- a/sci-biology/consed/consed-24.ebuild
+++ b/sci-biology/consed/consed-24.ebuild
@@ -65,6 +65,7 @@ src_install() {
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
 	doenvd "${S}/99consed" || die
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
 	dodoc README.txt *_announcement.txt || die
 }
 

diff --git a/sci-biology/consed/consed-25.ebuild b/sci-biology/consed/consed-25.ebuild
index 7163d60..d0a26e8 100644
--- a/sci-biology/consed/consed-25.ebuild
+++ b/sci-biology/consed/consed-25.ebuild
@@ -65,6 +65,7 @@ src_install() {
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
 	doenvd "${S}/99consed" || die
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
 	dodoc README.txt *_announcement.txt || die
 }
 

diff --git a/sci-biology/consed/consed-26.ebuild b/sci-biology/consed/consed-26.ebuild
index 7163d60..d0a26e8 100644
--- a/sci-biology/consed/consed-26.ebuild
+++ b/sci-biology/consed/consed-26.ebuild
@@ -65,6 +65,7 @@ src_install() {
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
 	doenvd "${S}/99consed" || die
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
 	dodoc README.txt *_announcement.txt || die
 }
 

diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild
index 7163d60..d0a26e8 100644
--- a/sci-biology/consed/consed-27.ebuild
+++ b/sci-biology/consed/consed-27.ebuild
@@ -65,6 +65,7 @@ src_install() {
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
 	doenvd "${S}/99consed" || die
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
 	dodoc README.txt *_announcement.txt || die
 }
 


^ permalink raw reply related	[flat|nested] 13+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/consed/
@ 2014-04-05 11:39 Martin Mokrejs
  0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2014-04-05 11:39 UTC (permalink / raw
  To: gentoo-commits

commit:     1efa11df584f6796903837ee2272ea628686889d
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr  5 11:38:06 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr  5 11:38:06 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1efa11df

sci-biology/consed: fix more hardcoded paths

Package-Manager: portage-2.2.7

---
 sci-biology/consed/ChangeLog           | 5 +++++
 sci-biology/consed/consed-20-r1.ebuild | 4 +++-
 sci-biology/consed/consed-21.ebuild    | 4 +++-
 sci-biology/consed/consed-22.ebuild    | 4 +++-
 sci-biology/consed/consed-23.ebuild    | 4 +++-
 sci-biology/consed/consed-24.ebuild    | 4 +++-
 sci-biology/consed/consed-25.ebuild    | 4 +++-
 sci-biology/consed/consed-26.ebuild    | 4 +++-
 sci-biology/consed/consed-27.ebuild    | 4 +++-
 9 files changed, 29 insertions(+), 8 deletions(-)

diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog
index 0fe8c19..ed7f9c8 100644
--- a/sci-biology/consed/ChangeLog
+++ b/sci-biology/consed/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> consed-20-r1.ebuild,
+  consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild,
+  consed-25.ebuild, consed-26.ebuild, consed-27.ebuild:
+  sci-biology/consed: fix more hardcoded paths
+
   02 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> consed-20-r1.ebuild,
   consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild,
   consed-25.ebuild, consed-26.ebuild, consed-27.ebuild:

diff --git a/sci-biology/consed/consed-20-r1.ebuild b/sci-biology/consed/consed-20-r1.ebuild
index cfcb66e..7f7ddc1 100644
--- a/sci-biology/consed/consed-20-r1.ebuild
+++ b/sci-biology/consed/consed-20-r1.ebuild
@@ -65,7 +65,9 @@ src_install() {
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
 	doenvd "${S}/99consed" || die
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
+	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
+	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
 	dodoc README.txt *_announcement.txt || die
 }
 

diff --git a/sci-biology/consed/consed-21.ebuild b/sci-biology/consed/consed-21.ebuild
index 55ba90a..77ec1a2 100644
--- a/sci-biology/consed/consed-21.ebuild
+++ b/sci-biology/consed/consed-21.ebuild
@@ -64,7 +64,9 @@ src_install() {
 		align454reads align454reads_answer solexa_example \
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
+	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
+	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
 	doenvd "${S}/99consed" || die
 	dodoc README.txt *_announcement.txt || die
 }

diff --git a/sci-biology/consed/consed-22.ebuild b/sci-biology/consed/consed-22.ebuild
index d0a26e8..e7c9186 100644
--- a/sci-biology/consed/consed-22.ebuild
+++ b/sci-biology/consed/consed-22.ebuild
@@ -65,7 +65,9 @@ src_install() {
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
 	doenvd "${S}/99consed" || die
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
+	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
+	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
 	dodoc README.txt *_announcement.txt || die
 }
 

diff --git a/sci-biology/consed/consed-23.ebuild b/sci-biology/consed/consed-23.ebuild
index d0a26e8..e7c9186 100644
--- a/sci-biology/consed/consed-23.ebuild
+++ b/sci-biology/consed/consed-23.ebuild
@@ -65,7 +65,9 @@ src_install() {
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
 	doenvd "${S}/99consed" || die
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
+	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
+	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
 	dodoc README.txt *_announcement.txt || die
 }
 

diff --git a/sci-biology/consed/consed-24.ebuild b/sci-biology/consed/consed-24.ebuild
index d0a26e8..e7c9186 100644
--- a/sci-biology/consed/consed-24.ebuild
+++ b/sci-biology/consed/consed-24.ebuild
@@ -65,7 +65,9 @@ src_install() {
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
 	doenvd "${S}/99consed" || die
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
+	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
+	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
 	dodoc README.txt *_announcement.txt || die
 }
 

diff --git a/sci-biology/consed/consed-25.ebuild b/sci-biology/consed/consed-25.ebuild
index d0a26e8..e7c9186 100644
--- a/sci-biology/consed/consed-25.ebuild
+++ b/sci-biology/consed/consed-25.ebuild
@@ -65,7 +65,9 @@ src_install() {
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
 	doenvd "${S}/99consed" || die
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
+	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
+	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
 	dodoc README.txt *_announcement.txt || die
 }
 

diff --git a/sci-biology/consed/consed-26.ebuild b/sci-biology/consed/consed-26.ebuild
index d0a26e8..e7c9186 100644
--- a/sci-biology/consed/consed-26.ebuild
+++ b/sci-biology/consed/consed-26.ebuild
@@ -65,7 +65,9 @@ src_install() {
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
 	doenvd "${S}/99consed" || die
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
+	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
+	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
 	dodoc README.txt *_announcement.txt || die
 }
 

diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild
index d0a26e8..e7c9186 100644
--- a/sci-biology/consed/consed-27.ebuild
+++ b/sci-biology/consed/consed-27.ebuild
@@ -65,7 +65,9 @@ src_install() {
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
 	doenvd "${S}/99consed" || die
-	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl || die
+	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
+	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
+	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die
 	dodoc README.txt *_announcement.txt || die
 }
 


^ permalink raw reply related	[flat|nested] 13+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/consed/
@ 2014-04-05 13:21 Martin Mokrejs
  0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2014-04-05 13:21 UTC (permalink / raw
  To: gentoo-commits

commit:     ae0815f92cc318782734d09b18d0cf78f564c8bb
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Apr  5 13:19:25 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Apr  5 13:19:25 2014 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ae0815f9

sci-biology/consed: add a stub file for consedrc; refer to it via CONSED_PARAMETERS

Package-Manager: portage-2.2.7

---
 sci-biology/consed/ChangeLog           | 6 ++++++
 sci-biology/consed/consed-20-r1.ebuild | 3 +++
 sci-biology/consed/consed-21.ebuild    | 3 +++
 sci-biology/consed/consed-22.ebuild    | 3 +++
 sci-biology/consed/consed-23.ebuild    | 3 +++
 sci-biology/consed/consed-24.ebuild    | 3 +++
 sci-biology/consed/consed-25.ebuild    | 3 +++
 sci-biology/consed/consed-26.ebuild    | 3 +++
 sci-biology/consed/consed-27.ebuild    | 3 +++
 9 files changed, 30 insertions(+)

diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog
index ed7f9c8..4bbf7b9 100644
--- a/sci-biology/consed/ChangeLog
+++ b/sci-biology/consed/ChangeLog
@@ -5,6 +5,12 @@
   05 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> consed-20-r1.ebuild,
   consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild,
   consed-25.ebuild, consed-26.ebuild, consed-27.ebuild:
+  sci-biology/consed: add a stub file for consedrc; refer to it via
+  CONSED_PARAMETERS
+
+  05 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> consed-20-r1.ebuild,
+  consed-21.ebuild, consed-22.ebuild, consed-23.ebuild, consed-24.ebuild,
+  consed-25.ebuild, consed-26.ebuild, consed-27.ebuild:
   sci-biology/consed: fix more hardcoded paths
 
   02 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> consed-20-r1.ebuild,

diff --git a/sci-biology/consed/consed-20-r1.ebuild b/sci-biology/consed/consed-20-r1.ebuild
index 7f7ddc1..30ba866 100644
--- a/sci-biology/consed/consed-20-r1.ebuild
+++ b/sci-biology/consed/consed-20-r1.ebuild
@@ -64,6 +64,9 @@ src_install() {
 		align454reads align454reads_answer solexa_example \
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
+	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
+	mkdir -p "${D}"/etc/consedrc
+	touch "${D}"/etc/consedrc
 	doenvd "${S}/99consed" || die
 	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
 	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die

diff --git a/sci-biology/consed/consed-21.ebuild b/sci-biology/consed/consed-21.ebuild
index 77ec1a2..b7993b7 100644
--- a/sci-biology/consed/consed-21.ebuild
+++ b/sci-biology/consed/consed-21.ebuild
@@ -64,6 +64,9 @@ src_install() {
 		align454reads align454reads_answer solexa_example \
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
+	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
+	mkdir -p "${D}"/etc/consedrc
+	touch "${D}"/etc/consedrc
 	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
 	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die
 	sed -e 's#/wt1/gordon/genome#/usr/bin#' -i "${D}"/usr/bin/fastq2Phrap.perl || die

diff --git a/sci-biology/consed/consed-22.ebuild b/sci-biology/consed/consed-22.ebuild
index e7c9186..4c8dd7f 100644
--- a/sci-biology/consed/consed-22.ebuild
+++ b/sci-biology/consed/consed-22.ebuild
@@ -64,6 +64,9 @@ src_install() {
 		align454reads align454reads_answer solexa_example \
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
+	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
+	mkdir -p "${D}"/etc/consedrc
+	touch "${D}"/etc/consedrc
 	doenvd "${S}/99consed" || die
 	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
 	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die

diff --git a/sci-biology/consed/consed-23.ebuild b/sci-biology/consed/consed-23.ebuild
index e7c9186..4c8dd7f 100644
--- a/sci-biology/consed/consed-23.ebuild
+++ b/sci-biology/consed/consed-23.ebuild
@@ -64,6 +64,9 @@ src_install() {
 		align454reads align454reads_answer solexa_example \
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
+	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
+	mkdir -p "${D}"/etc/consedrc
+	touch "${D}"/etc/consedrc
 	doenvd "${S}/99consed" || die
 	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
 	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die

diff --git a/sci-biology/consed/consed-24.ebuild b/sci-biology/consed/consed-24.ebuild
index e7c9186..4c8dd7f 100644
--- a/sci-biology/consed/consed-24.ebuild
+++ b/sci-biology/consed/consed-24.ebuild
@@ -64,6 +64,9 @@ src_install() {
 		align454reads align454reads_answer solexa_example \
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
+	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
+	mkdir -p "${D}"/etc/consedrc
+	touch "${D}"/etc/consedrc
 	doenvd "${S}/99consed" || die
 	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
 	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die

diff --git a/sci-biology/consed/consed-25.ebuild b/sci-biology/consed/consed-25.ebuild
index e7c9186..4c8dd7f 100644
--- a/sci-biology/consed/consed-25.ebuild
+++ b/sci-biology/consed/consed-25.ebuild
@@ -64,6 +64,9 @@ src_install() {
 		align454reads align454reads_answer solexa_example \
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
+	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
+	mkdir -p "${D}"/etc/consedrc
+	touch "${D}"/etc/consedrc
 	doenvd "${S}/99consed" || die
 	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
 	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die

diff --git a/sci-biology/consed/consed-26.ebuild b/sci-biology/consed/consed-26.ebuild
index e7c9186..4c8dd7f 100644
--- a/sci-biology/consed/consed-26.ebuild
+++ b/sci-biology/consed/consed-26.ebuild
@@ -64,6 +64,9 @@ src_install() {
 		align454reads align454reads_answer solexa_example \
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
+	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
+	mkdir -p "${D}"/etc/consedrc
+	touch "${D}"/etc/consedrc
 	doenvd "${S}/99consed" || die
 	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
 	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die

diff --git a/sci-biology/consed/consed-27.ebuild b/sci-biology/consed/consed-27.ebuild
index e7c9186..4c8dd7f 100644
--- a/sci-biology/consed/consed-27.ebuild
+++ b/sci-biology/consed/consed-27.ebuild
@@ -64,6 +64,9 @@ src_install() {
 		align454reads align454reads_answer solexa_example \
 		solexa_example_answer selectRegions selectRegionsAnswer || die
 	echo 'CONSED_HOME='${EPREFIX}'/usr' > "${S}/99consed"
+	echo 'CONSED_PARAMETERS='${EPREFIX}'/etc/consedrc' >> "${S}/99consed"
+	mkdir -p "${D}"/etc/consedrc
+	touch "${D}"/etc/consedrc
 	doenvd "${S}/99consed" || die
 	sed -e "s#/usr/local/genome#${EPREFIX}/usr#" -i "${D}"/usr/bin/*.perl "${D}"/usr/bin/phredPhrap "${D}"/usr/bin/phredPhrapWithPhdBalls || die
 	sed -e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' -i "${D}"/usr/bin/phredPhrap || die


^ permalink raw reply related	[flat|nested] 13+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/consed/
@ 2015-07-23  0:14 Martin Mokrejs
  0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2015-07-23  0:14 UTC (permalink / raw
  To: gentoo-commits

commit:     3d70d539efdee4713fc377c55a0585791f965179
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jul 23 00:13:48 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jul 23 00:13:48 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3d70d539

sci-biology/consed-29.0: version bump

Package-Manager: portage-2.2.18

 sci-biology/consed/ChangeLog        |  9 ++++
 sci-biology/consed/consed-29.ebuild | 93 +++++++++++++++++++++++++++++++++++++
 sci-biology/consed/metadata.xml     |  9 ++++
 3 files changed, 111 insertions(+)

diff --git a/sci-biology/consed/ChangeLog b/sci-biology/consed/ChangeLog
new file mode 100644
index 0000000..a580e1e
--- /dev/null
+++ b/sci-biology/consed/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/consed
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*consed-29 (23 Jul 2015)
+
+  23 Jul 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +consed-29.ebuild,
+  +metadata.xml:
+  sci-biology/consed-29.0: version bump

diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild
new file mode 100644
index 0000000..c6e3cf9
--- /dev/null
+++ b/sci-biology/consed/consed-29.ebuild
@@ -0,0 +1,93 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/consed/consed-27.ebuild,v 1.1 2014/10/26 16:13:23 jlec Exp $
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="A genome sequence finishing program"
+HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
+SRC_URI="
+	${P}-sources.tar.gz
+	${P}-linux.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=">=x11-libs/motif-2.3:0"
+# it needs samtools-0.18 with khash.h
+# This file was about sci-biology/samtools-1.2 time moved to sci-libs/htslib-1.2.1
+RDEPEND="${DEPEND}
+	<sci-biology/samtools-1.0
+	>=sci-biology/phred-000925
+	>=sci-biology/phrap-1.080721
+	dev-lang/perl"
+
+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 -lbam -lz/' \
+		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
+		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
+		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/ -I/usr/include/htslib/#' "${S}/makefile" || die
+	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
+	sed \
+		-e 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' \
+		-i "${S}"/scripts/* || die
+}
+
+src_compile() {
+	einfo "consed does not compile with sys-devel/gcc-4.6:* or newer (but 4.4.7 works)"
+	emake
+	emake -C misc/mktrace
+	emake -C misc/phd2fasta
+	(cd misc/454; $(tc-getCC) ${CFLAGS} ${LDFLAGS} sff2scf.c -o sff2scf) || die
+}
+
+src_install() {
+	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf}
+	dobin scripts/* contributions/*
+	insinto /usr/lib/screenLibs
+	doins misc/*.{fa*,seq}
+	insinto /usr/share/${PN}/examples
+	doins -r \
+		standard polyphred autofinish assembly_view 454_newbler \
+		align454reads align454reads_answer solexa_example \
+		solexa_example_answer selectRegions selectRegionsAnswer
+	echo 'CONSED_HOME="${EPREFIX}/usr"' > "${S}"/99consed || die
+	echo 'CONSED_PARAMETERS="${EPREFIX}/etc/consedrc"' >> "${S}"/99consed || die
+	mkdir -p "${ED}"/etc/consedrc || die
+	touch "${ED}"/etc/consedrc || die
+	doenvd "${S}/99consed" || die
+	sed \
+		-e "s#/usr/local/genome#${EPREFIX}/usr#" \
+		-i "${ED}"/usr/bin/{*.perl,phredPhrap,phredPhrapWithPhdBalls} || die
+	sed \
+		-e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' \
+		-i "${ED}"/usr/bin/phredPhrap || die
+	sed \
+		-e 's#/wt1/gordon/genome#/usr/bin#' \
+		-i "${ED}"/usr/bin/fastq2Phrap.perl || die
+	dodoc README.txt *_announcement.txt || die
+}
+
+pkg_postinst() {
+	einfo "Package documentation is available at"
+	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
+}

diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/consed/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mmokrejs@fold.natur.cuni.cz</email>
+    <name>Martin Mokrejs</name>
+  </maintainer>
+</pkgmetadata>


^ permalink raw reply related	[flat|nested] 13+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/consed/
@ 2016-03-18 16:33 Martin Mokrejs
  0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2016-03-18 16:33 UTC (permalink / raw
  To: gentoo-commits

commit:     2cf8dc31a6d127404c269bcd56d5e3ae96f823e2
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Mar 18 16:33:18 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 18 16:33:18 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2cf8dc31

sci-biology/consed: fix the autogenerated /etc/env.d/ file and make sure the EPREFIX is expanded in it (should be also fixed in consed-27 in the main gentoo repo), check yourself 'printenv | grep CONSED' and do not forger env-update && . /etc/profile before re-testing; the first part of the patch now properly edits the variable in perl-based scripts/*; however, I am still getting some issue with 'consed -ace 454Contigs.ace.1 -fixContigEnds' giving me:\nabout to run: /usr/bin/fixContigEnd.perl right_contig00004|m.2.ref_160318.171619.fasta right_contig00004|m.2.ref_160318.171619.fixConsensusEndAceFile.fof\nUse of uninitialized value [1] in string eq at /usr/bin/fixContigEnd.perl line 21.\nsh: m.2.ref_160318.171619.fasta: command not found\nsh: m.2.ref_160318.171619.fixConsensusEndAceFile.fof: command not found\n

Package-Manager: portage-2.2.26

 sci-biology/consed/consed-29.ebuild | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild
index 4614477..0a8387c 100644
--- a/sci-biology/consed/consed-29.ebuild
+++ b/sci-biology/consed/consed-29.ebuild
@@ -48,12 +48,12 @@ src_prepare() {
 		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/ -I/usr/include/htslib/#' "${S}/makefile" || die
 	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
 	sed \
-		-e 's!\($szPhredParameterFile =\).*!\1 $ENV{PHRED_PARAMETER_FILE} || "'${EPREFIX}'/usr/share/phred/phredpar.dat";!' \
+		-e "s!\$szPhredParameterFile = .*!\$szPhredParameterFile = \$ENV{'PHRED_PARAMETER_FILE'} || \'"${EPREFIX}"/usr/share/phred/phredpar.dat\';!" \
 		-i "${S}"/scripts/* || die
 }
 
 src_compile() {
-	einfo "consed does not compile with sys-devel/gcc-4.6:* or newer (but 4.4.7 works)"
+	einfo "consed does not compile with >=sys-devel/gcc-4.6:* but 4.4.7 works"
 	default
 	emake -C misc/mktrace
 	emake -C misc/phd2fasta
@@ -70,8 +70,8 @@ src_install() {
 		standard polyphred autofinish assembly_view 454_newbler \
 		align454reads align454reads_answer solexa_example \
 		solexa_example_answer selectRegions selectRegionsAnswer
-	echo 'CONSED_HOME="${EPREFIX}/usr"' > "${S}"/99consed || die
-	echo 'CONSED_PARAMETERS="${EPREFIX}/etc/consedrc"' >> "${S}"/99consed || die
+	echo CONSED_HOME="${EPREFIX}"/usr > "${S}"/99consed || die
+	echo CONSED_PARAMETERS="${EPREFIX}"/etc/consedrc >> "${S}"/99consed || die
 	mkdir -p "${ED}"/etc/consedrc || die
 	touch "${ED}"/etc/consedrc || die
 	doenvd "${S}/99consed"


^ permalink raw reply related	[flat|nested] 13+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/consed/
@ 2016-03-20 17:42 Martin Mokrejs
  0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2016-03-20 17:42 UTC (permalink / raw
  To: gentoo-commits

commit:     b6afefdbd4e30944b10f4a893179b3047905d9b0
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 20 17:41:34 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 20 17:41:34 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b6afefdb

sci-biology/consed-29: add also DEPEND on >=samtools-0.1.18

Package-Manager: portage-2.2.26

 sci-biology/consed/consed-29.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild
index 0a8387c..f729bbf 100644
--- a/sci-biology/consed/consed-29.ebuild
+++ b/sci-biology/consed/consed-29.ebuild
@@ -22,6 +22,7 @@ DEPEND=">=x11-libs/motif-2.3:0"
 # This file was about sci-biology/samtools-1.2 time moved to sci-libs/htslib-1.2.1
 RDEPEND="${DEPEND}
 	<sci-biology/samtools-1.0
+	>=sci-biology/samtools-0.1.18
 	>=sci-biology/phred-000925
 	>=sci-biology/phrap-1.080721
 	dev-lang/perl"


^ permalink raw reply related	[flat|nested] 13+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/consed/
@ 2016-03-24 21:05 Martin Mokrejs
  0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2016-03-24 21:05 UTC (permalink / raw
  To: gentoo-commits

commit:     48ab377cf4374573f3972ba7fe6e554f66200479
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 24 21:05:13 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 24 21:05:13 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=48ab377c

sci-biology/consed: fix ebuild not to create /etc/consedrc/ but  to create a file /etc/consedrc instead

Package-Manager: portage-2.2.26

 sci-biology/consed/consed-29.ebuild | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild
index f729bbf..002e007 100644
--- a/sci-biology/consed/consed-29.ebuild
+++ b/sci-biology/consed/consed-29.ebuild
@@ -73,8 +73,7 @@ src_install() {
 		solexa_example_answer selectRegions selectRegionsAnswer
 	echo CONSED_HOME="${EPREFIX}"/usr > "${S}"/99consed || die
 	echo CONSED_PARAMETERS="${EPREFIX}"/etc/consedrc >> "${S}"/99consed || die
-	mkdir -p "${ED}"/etc/consedrc || die
-	touch "${ED}"/etc/consedrc || die
+	touch "${ED}"/etc/consedrc || die "Cannot create a file for system-wide settings"
 	doenvd "${S}/99consed"
 	sed \
 		-e "s#/usr/local/genome#${EPREFIX}/usr#" \


^ permalink raw reply related	[flat|nested] 13+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/consed/
@ 2016-10-04  8:10 Martin Mokrejs
  0 siblings, 0 replies; 13+ messages in thread
From: Martin Mokrejs @ 2016-10-04  8:10 UTC (permalink / raw
  To: gentoo-commits

commit:     e1a3b476590c330602639ad79e5130c1c8864c74
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Oct  4 08:10:18 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Oct  4 08:10:18 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e1a3b476

sci-biology/consed: this version now landed main tree, removing

 sci-biology/consed/consed-29.ebuild | 93 -------------------------------------
 sci-biology/consed/metadata.xml     | 12 -----
 2 files changed, 105 deletions(-)

diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild
deleted file mode 100644
index 002e007..0000000
--- a/sci-biology/consed/consed-29.ebuild
+++ /dev/null
@@ -1,93 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="A genome sequence finishing program"
-HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
-SRC_URI="
-	${P}-sources.tar.gz
-	${P}-linux.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=x11-libs/motif-2.3:0"
-# it needs samtools-0.18 with khash.h
-# This file was about sci-biology/samtools-1.2 time moved to sci-libs/htslib-1.2.1
-RDEPEND="${DEPEND}
-	<sci-biology/samtools-1.0
-	>=sci-biology/samtools-0.1.18
-	>=sci-biology/phred-000925
-	>=sci-biology/phrap-1.080721
-	dev-lang/perl"
-
-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 -lbam -lz/' \
-		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
-		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
-		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/ -I/usr/include/htslib/#' "${S}/makefile" || die
-	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
-	sed \
-		-e "s!\$szPhredParameterFile = .*!\$szPhredParameterFile = \$ENV{'PHRED_PARAMETER_FILE'} || \'"${EPREFIX}"/usr/share/phred/phredpar.dat\';!" \
-		-i "${S}"/scripts/* || die
-}
-
-src_compile() {
-	einfo "consed does not compile with >=sys-devel/gcc-4.6:* but 4.4.7 works"
-	default
-	emake -C misc/mktrace
-	emake -C misc/phd2fasta
-	(cd misc/454; $(tc-getCC) ${CFLAGS} ${LDFLAGS} sff2scf.c -o sff2scf) || die
-}
-
-src_install() {
-	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf}
-	dobin scripts/* contributions/*
-	insinto /usr/lib/screenLibs
-	doins misc/*.{fa*,seq}
-	insinto /usr/share/${PN}/examples
-	doins -r \
-		standard polyphred autofinish assembly_view 454_newbler \
-		align454reads align454reads_answer solexa_example \
-		solexa_example_answer selectRegions selectRegionsAnswer
-	echo CONSED_HOME="${EPREFIX}"/usr > "${S}"/99consed || die
-	echo CONSED_PARAMETERS="${EPREFIX}"/etc/consedrc >> "${S}"/99consed || die
-	touch "${ED}"/etc/consedrc || die "Cannot create a file for system-wide settings"
-	doenvd "${S}/99consed"
-	sed \
-		-e "s#/usr/local/genome#${EPREFIX}/usr#" \
-		-i "${ED}"/usr/bin/{*.perl,phredPhrap,phredPhrapWithPhdBalls} || die
-	sed \
-		-e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' \
-		-i "${ED}"/usr/bin/phredPhrap || die
-	sed \
-		-e 's#/wt1/gordon/genome#/usr/bin#' \
-		-i "${ED}"/usr/bin/fastq2Phrap.perl || die
-	dodoc README.txt *_announcement.txt
-}
-
-pkg_postinst() {
-	einfo "Package documentation is available at"
-	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
-}

diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml
deleted file mode 100644
index 1699e58..0000000
--- a/sci-biology/consed/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?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] 13+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/consed/
@ 2016-10-12  6:30 Marius Brehler
  0 siblings, 0 replies; 13+ messages in thread
From: Marius Brehler @ 2016-10-12  6:30 UTC (permalink / raw
  To: gentoo-commits

commit:     6c039b13fc211799fc9de0a6e92df997f90169ed
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Oct  3 21:22:56 2016 +0000
Commit:     Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Mon Oct  3 21:24:00 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6c039b13

sci-biology/consed: Remove, latest version in main tree

 sci-biology/consed/consed-29.ebuild | 93 -------------------------------------
 sci-biology/consed/metadata.xml     | 12 -----
 2 files changed, 105 deletions(-)

diff --git a/sci-biology/consed/consed-29.ebuild b/sci-biology/consed/consed-29.ebuild
deleted file mode 100644
index 002e007..0000000
--- a/sci-biology/consed/consed-29.ebuild
+++ /dev/null
@@ -1,93 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-inherit eutils toolchain-funcs
-
-DESCRIPTION="A genome sequence finishing program"
-HOMEPAGE="http://bozeman.mbt.washington.edu/consed/consed.html"
-SRC_URI="
-	${P}-sources.tar.gz
-	${P}-linux.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=x11-libs/motif-2.3:0"
-# it needs samtools-0.18 with khash.h
-# This file was about sci-biology/samtools-1.2 time moved to sci-libs/htslib-1.2.1
-RDEPEND="${DEPEND}
-	<sci-biology/samtools-1.0
-	>=sci-biology/samtools-0.1.18
-	>=sci-biology/phred-000925
-	>=sci-biology/phrap-1.080721
-	dev-lang/perl"
-
-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 -lbam -lz/' \
-		-e 's/ARCHIVES=/ARCHIVES=\n_ARCHIVES=/' \
-		-e 's/CFLGS=/CFLGS= ${CFLAGS} /' \
-		-e 's#/me1/gordon/samtools/samtools-0.1.18#/usr/include/bam/ -I/usr/include/htslib/#' "${S}/makefile" || die
-	sed -i -e 's/CFLAGS=/CFLAGS += /' "${S}"/misc/*/Makefile || die
-	sed \
-		-e "s!\$szPhredParameterFile = .*!\$szPhredParameterFile = \$ENV{'PHRED_PARAMETER_FILE'} || \'"${EPREFIX}"/usr/share/phred/phredpar.dat\';!" \
-		-i "${S}"/scripts/* || die
-}
-
-src_compile() {
-	einfo "consed does not compile with >=sys-devel/gcc-4.6:* but 4.4.7 works"
-	default
-	emake -C misc/mktrace
-	emake -C misc/phd2fasta
-	(cd misc/454; $(tc-getCC) ${CFLAGS} ${LDFLAGS} sff2scf.c -o sff2scf) || die
-}
-
-src_install() {
-	dobin consed misc/{mktrace/mktrace,phd2fasta/phd2fasta,454/sff2scf}
-	dobin scripts/* contributions/*
-	insinto /usr/lib/screenLibs
-	doins misc/*.{fa*,seq}
-	insinto /usr/share/${PN}/examples
-	doins -r \
-		standard polyphred autofinish assembly_view 454_newbler \
-		align454reads align454reads_answer solexa_example \
-		solexa_example_answer selectRegions selectRegionsAnswer
-	echo CONSED_HOME="${EPREFIX}"/usr > "${S}"/99consed || die
-	echo CONSED_PARAMETERS="${EPREFIX}"/etc/consedrc >> "${S}"/99consed || die
-	touch "${ED}"/etc/consedrc || die "Cannot create a file for system-wide settings"
-	doenvd "${S}/99consed"
-	sed \
-		-e "s#/usr/local/genome#${EPREFIX}/usr#" \
-		-i "${ED}"/usr/bin/{*.perl,phredPhrap,phredPhrapWithPhdBalls} || die
-	sed \
-		-e 's#niceExe = "/bin/nice"#niceExe = "/usr/bin/nice"#' \
-		-i "${ED}"/usr/bin/phredPhrap || die
-	sed \
-		-e 's#/wt1/gordon/genome#/usr/bin#' \
-		-i "${ED}"/usr/bin/fastq2Phrap.perl || die
-	dodoc README.txt *_announcement.txt
-}
-
-pkg_postinst() {
-	einfo "Package documentation is available at"
-	einfo "http://www.phrap.org/consed/distributions/README.${PV}.0.txt"
-}

diff --git a/sci-biology/consed/metadata.xml b/sci-biology/consed/metadata.xml
deleted file mode 100644
index 1699e58..0000000
--- a/sci-biology/consed/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?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] 13+ messages in thread

end of thread, other threads:[~2016-10-12  6:31 UTC | newest]

Thread overview: 13+ messages (download: mbox.gz follow: Atom feed
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2016-10-12  6:30 Marius Brehler
2016-10-04  8:10 Martin Mokrejs
2016-03-24 21:05 Martin Mokrejs
2016-03-18 16:33 Martin Mokrejs
2015-07-23  0:14 Martin Mokrejs
2014-04-05 13:21 Martin Mokrejs
2014-04-05 11:39 Martin Mokrejs
2014-04-02  9:32 Martin Mokrejs
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