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

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

[Martin Mokrejs]

commit:     3503dcaaadb870f97b2719158c2fcd384f7d9660
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May  5 14:48:17 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May  5 14:48:17 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3503dcaa

sci-biology/prokka: new package

Package-Manager: portage-2.2.18

 sci-biology/prokka/ChangeLog          |  9 +++++++++
 sci-biology/prokka/metadata.xml       |  9 +++++++++
 sci-biology/prokka/prokka-1.11.ebuild | 31 +++++++++++++++++++++++++++++++
 3 files changed, 49 insertions(+)

diff --git a/sci-biology/prokka/ChangeLog b/sci-biology/prokka/ChangeLog
new file mode 100644
index 0000000..4f5235a
--- /dev/null
+++ b/sci-biology/prokka/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/prokka
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*prokka-1.11 (05 May 2015)
+
+  05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+  +prokka-1.11.ebuild:
+  sci-biology/prokka: new package

diff --git a/sci-biology/prokka/metadata.xml b/sci-biology/prokka/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/prokka/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/prokka/prokka-1.11.ebuild b/sci-biology/prokka/prokka-1.11.ebuild
new file mode 100644
index 0000000..8fc53c5
--- /dev/null
+++ b/sci-biology/prokka/prokka-1.11.ebuild
@@ -0,0 +1,31 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+DESCRIPTION="Prokaryotic whole genome annotation pipeline"
+HOMEPAGE="http://www.bioinformatics.net.au/software.prokka.shtml"
+SRC_URI="http://www.vicbioinformatics.com/prokka-"${PV}".tar.gz"
+# 360MB
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+	sys-process/parallel
+	sci-biology/bioperl
+	sci-biology/prodigal
+	sci-biology/ncbi-tools++
+	sci-biology/hmmer
+	sci-biology/infernal
+	sci-biology/exonerate
+	sci-biology/barrnap"
+# >=hmmer-3.1
+# Aragorn
+# RNAmmer
+# SignalP >= 4.0
+# sequin

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

[Martin Mokrejs]

commit:     826ad960ebdf08f8c34d5cfcf29003578fb054e5
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May  5 14:52:34 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May  5 14:52:34 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=826ad960

sci-biology/prokka: more DEPs recorded

Package-Manager: portage-2.2.18

 sci-biology/prokka/ChangeLog          | 3 +++
 sci-biology/prokka/prokka-1.11.ebuild | 9 ++++++---
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/sci-biology/prokka/ChangeLog b/sci-biology/prokka/ChangeLog
index 4f5235a..caef8ba 100644
--- a/sci-biology/prokka/ChangeLog
+++ b/sci-biology/prokka/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> prokka-1.11.ebuild:
+  sci-biology/prokka: more DEPs recorded
+
 *prokka-1.11 (05 May 2015)
 
   05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,

diff --git a/sci-biology/prokka/prokka-1.11.ebuild b/sci-biology/prokka/prokka-1.11.ebuild
index 8fc53c5..c7a9d81 100644
--- a/sci-biology/prokka/prokka-1.11.ebuild
+++ b/sci-biology/prokka/prokka-1.11.ebuild
@@ -24,8 +24,11 @@ RDEPEND="${DEPEND}
 	sci-biology/infernal
 	sci-biology/exonerate
 	sci-biology/barrnap"
-# >=hmmer-3.1
+# sci-biology/minced
+# >=sci-biolohy/hmmer-3.1
 # Aragorn
-# RNAmmer
-# SignalP >= 4.0
+# >=RNAmmer-1.2
+# >=HMMmmer-2.0 (that is not sci-biology/hmmer)
+# SignalP >= 3.0
 # sequin
+# tbl2asn >= 23.0 from wget --mirror -nH -nd ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz

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

[Martin Mokrejs]

commit:     6699341249d219c4e96a930624835ae7966d183c
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue May 26 09:47:59 2015 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue May 26 09:47:59 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=66993412

sci-biology/prokka: require either of ncbi-tools++ or ncbi-blast+

Package-Manager: portage-2.2.18

 sci-biology/prokka/ChangeLog          | 3 +++
 sci-biology/prokka/prokka-1.11.ebuild | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/sci-biology/prokka/ChangeLog b/sci-biology/prokka/ChangeLog
index caef8ba..a5e4045 100644
--- a/sci-biology/prokka/ChangeLog
+++ b/sci-biology/prokka/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  26 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> prokka-1.11.ebuild:
+  sci-biology/prokka: require either of ncbi-tools++ or ncbi-blast+
+
   05 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> prokka-1.11.ebuild:
   sci-biology/prokka: more DEPs recorded
 

diff --git a/sci-biology/prokka/prokka-1.11.ebuild b/sci-biology/prokka/prokka-1.11.ebuild
index c7a9d81..9e0e86c 100644
--- a/sci-biology/prokka/prokka-1.11.ebuild
+++ b/sci-biology/prokka/prokka-1.11.ebuild
@@ -19,7 +19,7 @@ RDEPEND="${DEPEND}
 	sys-process/parallel
 	sci-biology/bioperl
 	sci-biology/prodigal
-	sci-biology/ncbi-tools++
+	sci-biology/ncbi-tools++ || ( sci-biology/ncbi-blast+ )
 	sci-biology/hmmer
 	sci-biology/infernal
 	sci-biology/exonerate

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

[Martin Mokrejs]

commit:     678475e0a889fd123f78d23beadf8d5af4c46e32
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jun 22 14:12:50 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jun 22 14:12:50 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=678475e0

sci-biology/prokka: fix logical OR in a dependency

Package-Manager: portage-2.2.28

 sci-biology/prokka/prokka-1.11.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/prokka/prokka-1.11.ebuild b/sci-biology/prokka/prokka-1.11.ebuild
index 7b16d88..5a5baca 100644
--- a/sci-biology/prokka/prokka-1.11.ebuild
+++ b/sci-biology/prokka/prokka-1.11.ebuild
@@ -19,7 +19,7 @@ RDEPEND="${DEPEND}
 	sys-process/parallel
 	sci-biology/bioperl
 	sci-biology/prodigal
-	sci-biology/ncbi-tools++ || ( sci-biology/ncbi-blast+ )
+	|| ( sci-biology/ncbi-tools++ sci-biology/ncbi-blast+ )
 	sci-biology/hmmer
 	sci-biology/infernal
 	sci-biology/exonerate

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

[Andrew Ammerlaan]

commit:     30a7dd01d0de685f5785c33971269754801eb3b8
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May  2 12:27:17 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May  2 12:27:17 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=30a7dd01

sci-biology/prokka: treeclean

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/prokka/metadata.xml         | 15 --------------
 sci-biology/prokka/prokka-1.14.6.ebuild | 36 ---------------------------------
 2 files changed, 51 deletions(-)

diff --git a/sci-biology/prokka/metadata.xml b/sci-biology/prokka/metadata.xml
deleted file mode 100644
index 9272f0d9c..000000000
--- a/sci-biology/prokka/metadata.xml
+++ /dev/null
@@ -1,15 +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>
-	<upstream>
-		<remote-id type="github">tseemann/prokka</remote-id>
-	</upstream>
-</pkgmetadata>

diff --git a/sci-biology/prokka/prokka-1.14.6.ebuild b/sci-biology/prokka/prokka-1.14.6.ebuild
deleted file mode 100644
index b56fd143f..000000000
--- a/sci-biology/prokka/prokka-1.14.6.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="Prokaryotic whole genome annotation pipeline"
-HOMEPAGE="https://vicbioinformatics.com/software.prokka.shtml"
-SRC_URI="https://github.com/tseemann/prokka/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
-	sys-process/parallel
-	sci-biology/bioperl
-	sci-biology/prodigal
-	|| ( sci-biology/ncbi-tools++ sci-biology/ncbi-blast+ )
-	sci-biology/hmmer:*
-	sci-biology/infernal
-	sci-biology/exonerate
-	sci-biology/barrnap"
-DEPEND="${RDEPEND}"
-# sci-biology/minced
-# >=sci-biolohy/hmmer-3.1
-# Aragorn
-# >=RNAmmer-1.2
-# >=HMMmmer-2.0 (that is not sci-biology/hmmer)
-# SignalP >= 3.0
-# sequin
-# tbl2asn >= 23.0 from wget --mirror -nH -nd ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz
-
-src_install() {
-	default
-	dobin bin/prokka
-}