[gentoo-commits] proj/sci:master commit in: sci-biology/Atlas2/

["Horea Christian" <horea.christ@gmail.com>]

commit:     1a7addf40ba3a1e97f3fefe12d9b71086f954c71
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 22:35:48 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 22:43:20 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a7addf4

sci-biology/Atlas2: removed discontinued package

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/Atlas2/Atlas2-1.4.3.ebuild | 40 ----------------------------------
 sci-biology/Atlas2/metadata.xml        | 21 ------------------
 2 files changed, 61 deletions(-)

diff --git a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
deleted file mode 100644
index 2305fb15d..000000000
--- a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-inherit ruby-fakegem
-
-DESCRIPTION="Variant analysis tools from whole exome capture sequencing (WECS)"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas2"
-SRC_URI="http://downloads.sourceforge.net/project/atlas2/Atlas2_v1.4.3.zip"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
-	sci-biology/samtools:0
-	sci-biology/blat
-	sci-biology/phrap
-	sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/all/"${PN}"_v"${PV}"
-
-src_compile(){
-	cd SOLiD-SNP-caller || die
-	default
-
-	cd ../vcfPrinter || die
-	# TODO: install the *.rb files
-
-	cd ../Atlas-Indel2 || die
-	# TODO: install the *.rb and files in lib/
-
-	cd ../Atlas-SNP2 || die
-	# TODO: install
-}

diff --git a/sci-biology/Atlas2/metadata.xml b/sci-biology/Atlas2/metadata.xml
deleted file mode 100644
index 7ce5225f5..000000000
--- a/sci-biology/Atlas2/metadata.xml
+++ /dev/null
@@ -1,21 +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>
-	<longdescription>
-Atlas2 is a next-generation sequencing suite of variant analysis
-tools specializing in the separation of true SNPs and insertions
-and deletions (indels) from sequencing and mapping errors in Whole
-Exome Capture Sequencing (WECS) data.
-</longdescription>
-	<upstream>
-		<remote-id type="sourceforge">downloads</remote-id>
-	</upstream>
-</pkgmetadata>