* [gentoo-commits] proj/sci:master commit in: sci-biology/quorum/
@ 2015-04-30 20:52 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2015-04-30 20:52 UTC (permalink / raw
To: gentoo-commits
commit: 867286135a316edde90c74b2ee0832b6d6db7a45
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 30 20:51:52 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 30 20:51:52 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=86728613
sci-biology/quorum: new package
Package-Manager: portage-2.2.18
sci-biology/quorum/ChangeLog | 10 ++++++++++
sci-biology/quorum/metadata.xml | 9 +++++++++
sci-biology/quorum/quorum-0.2.1.ebuild | 17 +++++++++++++++++
sci-biology/quorum/quorum-1.0.0.ebuild | 17 +++++++++++++++++
4 files changed, 53 insertions(+)
diff --git a/sci-biology/quorum/ChangeLog b/sci-biology/quorum/ChangeLog
new file mode 100644
index 0000000..3ab4833
--- /dev/null
+++ b/sci-biology/quorum/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/quorum
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*quorum-0.2.1 (30 Apr 2015)
+*quorum-1.0.0 (30 Apr 2015)
+
+ 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+ +quorum-0.2.1.ebuild, +quorum-1.0.0.ebuild:
+ sci-biology/quorum: new package
diff --git a/sci-biology/quorum/metadata.xml b/sci-biology/quorum/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/quorum/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>
diff --git a/sci-biology/quorum/quorum-0.2.1.ebuild b/sci-biology/quorum/quorum-0.2.1.ebuild
new file mode 100644
index 0000000..b6cdfb1
--- /dev/null
+++ b/sci-biology/quorum/quorum-0.2.1.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Illumina reads error corrector"
+HOMEPAGE="http://www.genome.umd.edu/quorum.html"
+SRC_URI="ftp://ftp.genome.umd.edu/pub/QuorUM/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="=sci-biology/jellyfish-1.1*"
+RDEPEND="${DEPEND}"
diff --git a/sci-biology/quorum/quorum-1.0.0.ebuild b/sci-biology/quorum/quorum-1.0.0.ebuild
new file mode 100644
index 0000000..53a773a
--- /dev/null
+++ b/sci-biology/quorum/quorum-1.0.0.ebuild
@@ -0,0 +1,17 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Illumina reads error corrector"
+HOMEPAGE="http://www.genome.umd.edu/quorum.html"
+SRC_URI="ftp://ftp.genome.umd.edu/pub/QuorUM/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="=sci-biology/jellyfish-2.1.4"
+RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/quorum/
@ 2015-04-30 21:15 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2015-04-30 21:15 UTC (permalink / raw
To: gentoo-commits
commit: 1b983d16797ad73d9994367f8bbaf2314cf20db8
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 30 21:14:51 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 30 21:14:51 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1b983d16
sci-biology/quorum: avoid full path on linker commandline /usr/lib64/libjellyfish-2.0.so
Package-Manager: portage-2.2.18
sci-biology/quorum/ChangeLog | 5 +++++
sci-biology/quorum/quorum-0.2.1.ebuild | 6 +++++-
sci-biology/quorum/quorum-1.0.0.ebuild | 4 ++++
3 files changed, 14 insertions(+), 1 deletion(-)
diff --git a/sci-biology/quorum/ChangeLog b/sci-biology/quorum/ChangeLog
index 3ab4833..e7b52a9 100644
--- a/sci-biology/quorum/ChangeLog
+++ b/sci-biology/quorum/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 30 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> quorum-0.2.1.ebuild,
+ quorum-1.0.0.ebuild:
+ sci-biology/quorum: avoid full path on linker commandline
+ /usr/lib64/libjellyfish-2.0.so
+
*quorum-0.2.1 (30 Apr 2015)
*quorum-1.0.0 (30 Apr 2015)
diff --git a/sci-biology/quorum/quorum-0.2.1.ebuild b/sci-biology/quorum/quorum-0.2.1.ebuild
index b6cdfb1..d2a540a 100644
--- a/sci-biology/quorum/quorum-0.2.1.ebuild
+++ b/sci-biology/quorum/quorum-0.2.1.ebuild
@@ -13,5 +13,9 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-DEPEND="=sci-biology/jellyfish-1.1*"
+DEPEND="=sci-biology/jellyfish-1.1.11"
RDEPEND="${DEPEND}"
+
+src_configure(){
+ econf --enable-relative-paths --with-relative-jf-path
+}
diff --git a/sci-biology/quorum/quorum-1.0.0.ebuild b/sci-biology/quorum/quorum-1.0.0.ebuild
index 53a773a..6870eed 100644
--- a/sci-biology/quorum/quorum-1.0.0.ebuild
+++ b/sci-biology/quorum/quorum-1.0.0.ebuild
@@ -15,3 +15,7 @@ IUSE=""
DEPEND="=sci-biology/jellyfish-2.1.4"
RDEPEND="${DEPEND}"
+
+src_configure(){
+ econf --enable-relative-paths --with-relative-jf-path
+}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/quorum/
@ 2017-01-10 1:03 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2017-01-10 1:03 UTC (permalink / raw
To: gentoo-commits
commit: c9b497cf9c7652a6144938a083d9d3bdd6fa99b5
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 10 01:03:05 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 10 01:03:05 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c9b497cf
sci-biology/quorum: lightly relax required versions
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/quorum/quorum-0.2.1.ebuild | 5 +++--
sci-biology/quorum/quorum-1.0.0.ebuild | 6 +++---
2 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/sci-biology/quorum/quorum-0.2.1.ebuild b/sci-biology/quorum/quorum-0.2.1.ebuild
index cd1d8c3..7eb97a6 100644
--- a/sci-biology/quorum/quorum-0.2.1.ebuild
+++ b/sci-biology/quorum/quorum-0.2.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -13,7 +13,8 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-DEPEND="=sci-biology/jellyfish-1.1.11"
+DEPEND=">=sci-biology/jellyfish-1.1.11
+ <=sci-biology/jellyfish-2.0.0"
RDEPEND="${DEPEND}"
src_configure(){
diff --git a/sci-biology/quorum/quorum-1.0.0.ebuild b/sci-biology/quorum/quorum-1.0.0.ebuild
index a3c108f..fa46b63 100644
--- a/sci-biology/quorum/quorum-1.0.0.ebuild
+++ b/sci-biology/quorum/quorum-1.0.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -10,10 +10,10 @@ SRC_URI="ftp://ftp.genome.umd.edu/pub/QuorUM/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
IUSE=""
-DEPEND="=sci-biology/jellyfish-2.1.4"
+DEPEND=">=sci-biology/jellyfish-2.1.4"
RDEPEND="${DEPEND}"
src_configure(){
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/quorum/
@ 2017-05-15 13:39 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2017-05-15 13:39 UTC (permalink / raw
To: gentoo-commits
commit: edaf9d6441ded1afa54328f6e78775e487ffe5fc
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 15 13:39:20 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 15 13:39:20 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=edaf9d64
sci-biology/quorum: version bump
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/quorum/{quorum-1.0.0.ebuild => quorum-1.1.1.ebuild} | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/sci-biology/quorum/quorum-1.0.0.ebuild b/sci-biology/quorum/quorum-1.1.1.ebuild
similarity index 65%
rename from sci-biology/quorum/quorum-1.0.0.ebuild
rename to sci-biology/quorum/quorum-1.1.1.ebuild
index 2b4acfc09..1c5f29e2b 100644
--- a/sci-biology/quorum/quorum-1.0.0.ebuild
+++ b/sci-biology/quorum/quorum-1.1.1.ebuild
@@ -1,11 +1,12 @@
# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
DESCRIPTION="Illumina reads error corrector"
-HOMEPAGE="http://www.genome.umd.edu/quorum.html"
-SRC_URI="ftp://ftp.genome.umd.edu/pub/QuorUM/${P}.tar.gz"
+HOMEPAGE="http://www.genome.umd.edu/quorum.html
+ https://github.com/gmarcais/Quorum"
+SRC_URI="https://github.com/gmarcais/Quorum/releases/download/v1.1.1/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
@@ -17,4 +18,5 @@ RDEPEND="${DEPEND}"
src_configure(){
econf --enable-relative-paths --with-relative-jf-path
+ default
}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/quorum/
@ 2017-05-15 16:13 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2017-05-15 16:13 UTC (permalink / raw
To: gentoo-commits
commit: 2c533f390f2eb2ff45a2f8f31834ca5a45b2b85d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon May 15 16:12:58 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon May 15 16:12:58 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2c533f39
sci-biology/quorum: improve DESCRIPTION text
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/quorum/quorum-0.2.1.ebuild | 2 +-
sci-biology/quorum/quorum-1.1.1.ebuild | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/quorum/quorum-0.2.1.ebuild b/sci-biology/quorum/quorum-0.2.1.ebuild
index 6771b40e0..58c4ae79e 100644
--- a/sci-biology/quorum/quorum-0.2.1.ebuild
+++ b/sci-biology/quorum/quorum-0.2.1.ebuild
@@ -3,7 +3,7 @@
EAPI=5
-DESCRIPTION="Illumina reads error corrector"
+DESCRIPTION="Correct substitution errors in Illumina reads"
HOMEPAGE="http://www.genome.umd.edu/quorum.html"
SRC_URI="ftp://ftp.genome.umd.edu/pub/QuorUM/${P}.tar.gz"
diff --git a/sci-biology/quorum/quorum-1.1.1.ebuild b/sci-biology/quorum/quorum-1.1.1.ebuild
index 1c5f29e2b..8a3ced37f 100644
--- a/sci-biology/quorum/quorum-1.1.1.ebuild
+++ b/sci-biology/quorum/quorum-1.1.1.ebuild
@@ -3,10 +3,10 @@
EAPI=6
-DESCRIPTION="Illumina reads error corrector"
+DESCRIPTION="Correct substitution errors in Illumina reads"
HOMEPAGE="http://www.genome.umd.edu/quorum.html
https://github.com/gmarcais/Quorum"
-SRC_URI="https://github.com/gmarcais/Quorum/releases/download/v1.1.1/${P}.tar.gz"
+SRC_URI="https://github.com/gmarcais/Quorum/releases/download/v${PV}/${P}.tar.gz"
LICENSE="GPL-3"
SLOT="0"
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/quorum/
@ 2018-05-01 22:38 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2018-05-01 22:38 UTC (permalink / raw
To: gentoo-commits
commit: 8ca2d5383f188ff26ee9714b431dfed95c8b9b7a
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May 1 22:37:57 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May 1 22:37:57 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8ca2d538
sci-biology/quorum: drop old
Anyway it doe snot compile with gcc-7.3.0, see
https://github.com/gmarcais/Jellyfish/issues/122
Package-Manager: Portage-2.3.31, Repoman-2.3.9
sci-biology/quorum/quorum-0.2.1-r1.ebuild | 28 ----------------------------
1 file changed, 28 deletions(-)
diff --git a/sci-biology/quorum/quorum-0.2.1-r1.ebuild b/sci-biology/quorum/quorum-0.2.1-r1.ebuild
deleted file mode 100644
index d7bb7675a..000000000
--- a/sci-biology/quorum/quorum-0.2.1-r1.ebuild
+++ /dev/null
@@ -1,28 +0,0 @@
-# Copyright 1999-2018 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit eutils autotools
-
-DESCRIPTION="Correct substitution errors in Illumina reads"
-HOMEPAGE="http://www.genome.umd.edu/quorum.html"
-SRC_URI="ftp://ftp.genome.umd.edu/pub/QuorUM/${P}.tar.gz"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-IUSE=""
-
-DEPEND="sci-biology/jellyfish:1"
-RDEPEND="${DEPEND}"
-
-src_prepare(){
- default
- epatch "${FILESDIR}"/"${P}"-use-jellyfish1.patch
- eautoreconf
-}
-
-src_configure(){
- econf --enable-relative-paths --with-relative-jf-path
-}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/quorum/
@ 2021-03-06 13:35 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2021-03-06 13:35 UTC (permalink / raw
To: gentoo-commits
commit: ab0138b5b38bb3d6b7ef839f590325bb4acb2d6b
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 6 13:35:27 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 6 13:35:27 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ab0138b5
sci-biology/quorum: EAPI bump, fix build
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/quorum/quorum-1.1.1.ebuild | 12 +++++++++---
1 file changed, 9 insertions(+), 3 deletions(-)
diff --git a/sci-biology/quorum/quorum-1.1.1.ebuild b/sci-biology/quorum/quorum-1.1.1.ebuild
index 6fa222ff7..4af286fcb 100644
--- a/sci-biology/quorum/quorum-1.1.1.ebuild
+++ b/sci-biology/quorum/quorum-1.1.1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
DESCRIPTION="Correct substitution errors in Illumina reads"
HOMEPAGE="http://www.genome.umd.edu/quorum.html
@@ -11,11 +11,17 @@ SRC_URI="https://github.com/gmarcais/Quorum/releases/download/v${PV}/${P}.tar.gz
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
DEPEND=">=sci-biology/jellyfish-2.1.4:2"
RDEPEND="${DEPEND}"
+src_prepare() {
+ default
+ # fix jellyfish include path
+ find -type f -name "*.cc" -exec sed -i -e 's/<jellyfish\//<jellyfish2\//g' {} + || die
+ find -type f -name "*.hpp" -exec sed -i -e 's/<jellyfish\//<jellyfish2\//g' {} + || die
+}
+
src_configure(){
econf --enable-relative-paths --with-relative-jf-path
default
^ permalink raw reply related [flat|nested] 7+ messages in thread
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