* [gentoo-commits] proj/sci:master commit in: sci-biology/genseed/
@ 2011-12-13 11:51 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2011-12-13 11:51 UTC (permalink / raw
To: gentoo-commits
commit: 78b98026b04382485abbf4722874ae13c267d3ed
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Dec 13 11:50:50 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Dec 13 11:50:50 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=78b98026
A seed-driven progressive assembly program
(Portage version: 2.1.10.38/git/Linux i686, unsigned Manifest commit)
---
sci-biology/genseed/ChangeLog | 10 ++++++++++
sci-biology/genseed/genseed-1.0.22.ebuild | 24 ++++++++++++++++++++++++
sci-biology/genseed/metadata.xml | 9 +++++++++
3 files changed, 43 insertions(+), 0 deletions(-)
diff --git a/sci-biology/genseed/ChangeLog b/sci-biology/genseed/ChangeLog
new file mode 100644
index 0000000..7107e74
--- /dev/null
+++ b/sci-biology/genseed/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/genseed
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*genseed-1.0.22 (13 Dec 2011)
+
+ 13 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +genseed-1.0.22.ebuild, +metadata.xml:
+ A seed-driven progressive assembly program genseed-1.0.22.ebuild
+
diff --git a/sci-biology/genseed/genseed-1.0.22.ebuild b/sci-biology/genseed/genseed-1.0.22.ebuild
new file mode 100644
index 0000000..f52cc86
--- /dev/null
+++ b/sci-biology/genseed/genseed-1.0.22.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+DESCRIPTION="Seed-driven progressive assembly program using legacy NCBI blast, CAP3, and optionally cross_match"
+HOMEPAGE="http://www.coccidia.icb.usp.br/genseed/"
+SRC_URI="http://www.coccidia.icb.usp.br/genseed/download/${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~x86 ~amd64"
+IUSE=""
+
+# FIXME: I am not sure whether we want to introduce yet another USE variable "phrap"
+# This tools can optionally use cross_match from sci-biology/phrap but it will
+# be installed only by users having the licence
+DEPEND="sci-biology/cap3-bin
+ dev-lang/perl
+ sci-biology/ncbi-tools"
+RDEPEND=""
+
+src_install() {
+ dobin genseed.pl
+}
diff --git a/sci-biology/genseed/metadata.xml b/sci-biology/genseed/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/genseed/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] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/genseed/
@ 2011-12-13 12:04 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2011-12-13 12:04 UTC (permalink / raw
To: gentoo-commits
commit: b56459972f6507ccff7c07b66b0821d1c3364f48
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Dec 13 12:03:55 2011 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Dec 13 12:03:55 2011 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b5645997
ebuild doc cleanup
(Portage version: 2.1.10.38/git/Linux i686, unsigned Manifest commit)
---
sci-biology/genseed/ChangeLog | 4 ++++
sci-biology/genseed/genseed-1.0.22.ebuild | 6 +++---
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/sci-biology/genseed/ChangeLog b/sci-biology/genseed/ChangeLog
index 7107e74..b60e59d 100644
--- a/sci-biology/genseed/ChangeLog
+++ b/sci-biology/genseed/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 13 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ genseed-1.0.22.ebuild:
+ ebuild doc cleanup genseed-1.0.22.ebuild
+
*genseed-1.0.22 (13 Dec 2011)
13 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/genseed/genseed-1.0.22.ebuild b/sci-biology/genseed/genseed-1.0.22.ebuild
index f52cc86..d90d3fb 100644
--- a/sci-biology/genseed/genseed-1.0.22.ebuild
+++ b/sci-biology/genseed/genseed-1.0.22.ebuild
@@ -11,9 +11,9 @@ SLOT="0"
KEYWORDS="~x86 ~amd64"
IUSE=""
-# FIXME: I am not sure whether we want to introduce yet another USE variable "phrap"
-# This tools can optionally use cross_match from sci-biology/phrap but it will
-# be installed only by users having the licence
+ # I am not sure whether we want to introduce yet another USE variable "phrap"
+ # This tools optionally uses cross_match if vector masking is required
+ # (sci-biology/phrap but it will be installed only by users having that licence.
DEPEND="sci-biology/cap3-bin
dev-lang/perl
sci-biology/ncbi-tools"
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/genseed/
@ 2014-11-10 15:14 Justin Lecher
0 siblings, 0 replies; 4+ messages in thread
From: Justin Lecher @ 2014-11-10 15:14 UTC (permalink / raw
To: gentoo-commits
commit: 8084f5f52b096ed560f8889c736a10060911e0f8
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Nov 10 13:18:12 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Nov 10 13:18:12 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8084f5f5
sci-biology/genseed: Bump to EAPI=5
Package-Manager: portage-2.2.14
---
sci-biology/genseed/ChangeLog | 6 +++++-
sci-biology/genseed/genseed-1.0.22.ebuild | 19 ++++++++++++-------
sci-biology/genseed/metadata.xml | 10 +++++-----
3 files changed, 22 insertions(+), 13 deletions(-)
diff --git a/sci-biology/genseed/ChangeLog b/sci-biology/genseed/ChangeLog
index b60e59d..d52eb15 100644
--- a/sci-biology/genseed/ChangeLog
+++ b/sci-biology/genseed/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/genseed
-# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 10 Nov 2014; Justin Lecher <jlec@gentoo.org> genseed-1.0.22.ebuild,
+ metadata.xml:
+ Bump to EAPI=5
+
13 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
genseed-1.0.22.ebuild:
ebuild doc cleanup genseed-1.0.22.ebuild
diff --git a/sci-biology/genseed/genseed-1.0.22.ebuild b/sci-biology/genseed/genseed-1.0.22.ebuild
index 1bf97f9..f87e06f 100644
--- a/sci-biology/genseed/genseed-1.0.22.ebuild
+++ b/sci-biology/genseed/genseed-1.0.22.ebuild
@@ -2,6 +2,8 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
+EAPI=5
+
DESCRIPTION="Seed-driven progressive assembly program using legacy NCBI blast, CAP3, and optionally cross_match"
HOMEPAGE="http://www.coccidia.icb.usp.br/genseed/"
SRC_URI="http://www.coccidia.icb.usp.br/genseed/download/${P}.tar.gz"
@@ -11,14 +13,17 @@ SLOT="0"
KEYWORDS="~x86 ~amd64"
IUSE=""
- # I am not sure whether we want to introduce yet another USE variable "phrap"
- # This tools optionally uses cross_match if vector masking is required
- # (sci-biology/phrap but it will be installed only by users having that licence.
-DEPEND="sci-biology/cap3-bin
- dev-lang/perl
- sci-biology/ncbi-tools"
+ # I am not sure whether we want to introduce yet another USE variable "phrap"
+ # This tools optionally uses cross_match if vector masking is required
+ # (sci-biology/phrap but it will be installed only by users having that licence.
+DEPEND="
+ sci-biology/cap3-bin
+ dev-lang/perl
+ sci-biology/ncbi-tools"
RDEPEND=""
+S="${WORKDIR}"
+
src_install() {
- dobin genseed.pl
+ newbin ${PN}.pl ${PN}
}
diff --git a/sci-biology/genseed/metadata.xml b/sci-biology/genseed/metadata.xml
index 07b5255..2bc8930 100644
--- a/sci-biology/genseed/metadata.xml
+++ b/sci-biology/genseed/metadata.xml
@@ -1,9 +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>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/genseed/
@ 2015-04-17 23:56 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2015-04-17 23:56 UTC (permalink / raw
To: gentoo-commits
commit: 1da87d46903e851d0e8128d895a38d699bfebc73
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 23:01:57 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 23:01:57 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1da87d46
sci-biology/genseed: some cleanup
Package-Manager: portage-2.2.18
sci-biology/genseed/ChangeLog | 7 +++++--
sci-biology/genseed/genseed-1.0.22.ebuild | 10 ++++++----
2 files changed, 11 insertions(+), 6 deletions(-)
diff --git a/sci-biology/genseed/ChangeLog b/sci-biology/genseed/ChangeLog
index d52eb15..ce4b289 100644
--- a/sci-biology/genseed/ChangeLog
+++ b/sci-biology/genseed/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/genseed
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ genseed-1.0.22.ebuild:
+ sci-biology/genseed: some cleanup
+
10 Nov 2014; Justin Lecher <jlec@gentoo.org> genseed-1.0.22.ebuild,
metadata.xml:
Bump to EAPI=5
@@ -15,4 +19,3 @@
13 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+genseed-1.0.22.ebuild, +metadata.xml:
A seed-driven progressive assembly program genseed-1.0.22.ebuild
-
diff --git a/sci-biology/genseed/genseed-1.0.22.ebuild b/sci-biology/genseed/genseed-1.0.22.ebuild
index f87e06f..5a1f876 100644
--- a/sci-biology/genseed/genseed-1.0.22.ebuild
+++ b/sci-biology/genseed/genseed-1.0.22.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -13,9 +13,6 @@ SLOT="0"
KEYWORDS="~x86 ~amd64"
IUSE=""
- # I am not sure whether we want to introduce yet another USE variable "phrap"
- # This tools optionally uses cross_match if vector masking is required
- # (sci-biology/phrap but it will be installed only by users having that licence.
DEPEND="
sci-biology/cap3-bin
dev-lang/perl
@@ -27,3 +24,8 @@ S="${WORKDIR}"
src_install() {
newbin ${PN}.pl ${PN}
}
+
+pkg_postinst(){
+ einfo "Ideally install also sci-biology/phrap which provides cross_match"
+ einfo "It is used for vector masking"
+}
^ permalink raw reply related [flat|nested] 4+ messages in thread
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