From 6b9853cc6cc0ee6efdfb43365d2d584dd1b43068 Mon Sep 17 00:00:00 2001
From: Martin Mokrejs <mmokrejs@gmail.com>
Date: Fri, 19 Mar 2021 11:11:43 +0100
Subject: [PATCH 1/2] sci-biology/GFF3toolkit: hint for a new package

Something is still broken, please fix it on your own
and cherrypick

Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>
---
 .../GFF3toolkit/GFF3toolkit-2.0.1.ebuild        | 17 +++++++++++++++++
 sci-biology/GFF3toolkit/Manifest                |  1 +
 sci-biology/GFF3toolkit/metadata.xml            | 16 ++++++++++++++++
 3 files changed, 34 insertions(+)
 create mode 100644 sci-biology/GFF3toolkit/GFF3toolkit-2.0.1.ebuild
 create mode 100644 sci-biology/GFF3toolkit/Manifest
 create mode 100644 sci-biology/GFF3toolkit/metadata.xml

diff --git a/sci-biology/GFF3toolkit/GFF3toolkit-2.0.1.ebuild b/sci-biology/GFF3toolkit/GFF3toolkit-2.0.1.ebuild
new file mode 100644
index 00000000000..beca4c7b4d6
--- /dev/null
+++ b/sci-biology/GFF3toolkit/GFF3toolkit-2.0.1.ebuild
@@ -0,0 +1,17 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Check, fix, merge, sort and extract GFF3 files"
+HOMEPAGE="https://github.com/NAL-i5K/GFF3toolkit
+	https://gff3toolkit.readthedocs.io"
+SRC_URI="https://github.com/NAL-i5K/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND=""
diff --git a/sci-biology/GFF3toolkit/Manifest b/sci-biology/GFF3toolkit/Manifest
new file mode 100644
index 00000000000..71a5070d58b
--- /dev/null
+++ b/sci-biology/GFF3toolkit/Manifest
@@ -0,0 +1 @@
+DIST GFF3toolkit-2.0.1.tar.gz 1848746 BLAKE2B fdb237b83ad7d0bfe2ec428413ea8a600daa658b9a242fa0677c4721ce34c0e865348f042879c104b132623f31f6370192c274f64f132efd1b74927d570ea36d SHA512 133c52cf08002184d46f7dd73b94e52f95de66fb7b1c754e1e39c3a42c16f0ebbb3dd5adc8625771d68092d1dc6460c0497360acdcbb5272fcbc31ab17752e36
diff --git a/sci-biology/GFF3toolkit/metadata.xml b/sci-biology/GFF3toolkit/metadata.xml
new file mode 100644
index 00000000000..5c31198b0f4
--- /dev/null
+++ b/sci-biology/GFF3toolkit/metadata.xml
@@ -0,0 +1,16 @@
+<?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">NAL-i5K/GFF3toolkit</remote-id>
+		<remote-id type="pypi">gff3tool</remote-id>
+	</upstream>
+</pkgmetadata>

From 4c1cabefa5bf4303f4ec669b09f52d4a7bacb01c Mon Sep 17 00:00:00 2001
From: Martin Mokrejs <mmokrejs@gmail.com>
Date: Mon, 22 Mar 2021 21:45:52 +0100
Subject: [PATCH 2/2] sci-biology/GFF3toolkit: add USE=minimal

The tool uses sometimes blastn and makeblastdb

Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Martin Mokrejs <mmokrejs@gmail.com>
---
 sci-biology/GFF3toolkit/GFF3toolkit-2.0.1.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/GFF3toolkit/GFF3toolkit-2.0.1.ebuild b/sci-biology/GFF3toolkit/GFF3toolkit-2.0.1.ebuild
index beca4c7b4d6..dbfcb0b8b73 100644
--- a/sci-biology/GFF3toolkit/GFF3toolkit-2.0.1.ebuild
+++ b/sci-biology/GFF3toolkit/GFF3toolkit-2.0.1.ebuild
@@ -11,7 +11,8 @@ SRC_URI="https://github.com/NAL-i5K/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
 LICENSE="public-domain"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
+IUSE="minimal"
 
-DEPEND=""
+DEPEND="!minimal? ( sci-biology/ncbi-tools++ )"
 RDEPEND="${DEPEND}"
 BDEPEND=""