From 7a7bbd341b0f104d19176967a7020aa38de06dc4 Mon Sep 17 00:00:00 2001
From: Michał Górny <mgorny@gentoo.org>
Date: Fri, 9 Oct 2020 09:32:54 +0200
Subject: sci-biology/shrimp: Remove last-rited pkg
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Closes: https://bugs.gentoo.org/735440
Signed-off-by: Michał Górny <mgorny@gentoo.org>
---
 sci-biology/shrimp/Manifest            |  1 -
 sci-biology/shrimp/metadata.xml        |  8 ----
 sci-biology/shrimp/shrimp-2.2.3.ebuild | 82 ----------------------------------
 3 files changed, 91 deletions(-)
 delete mode 100644 sci-biology/shrimp/Manifest
 delete mode 100644 sci-biology/shrimp/metadata.xml
 delete mode 100644 sci-biology/shrimp/shrimp-2.2.3.ebuild

(limited to 'sci-biology')

diff --git a/sci-biology/shrimp/Manifest b/sci-biology/shrimp/Manifest
deleted file mode 100644
index 5be68cd79e21..000000000000
--- a/sci-biology/shrimp/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST SHRiMP_2_2_3.src.tar.gz 4596867 BLAKE2B 64e485b8e2524062c11c581bbcac426800c9f42f61da467378dbfd3add63f721a9da9c04df61bde3704e654a20395e799e89fc5e47129b1d3f5bc93f960470fa SHA512 029179aeeb317194b998c29aa91d1d2ce5ccbc6f9ad4a1043d1e5fc75d3344c2f39500ab07e8389c09fa179f0c9b59afee22691bc4eb5d396777f4e0fe25f2d5
diff --git a/sci-biology/shrimp/metadata.xml b/sci-biology/shrimp/metadata.xml
deleted file mode 100644
index 959160fe46b1..000000000000
--- a/sci-biology/shrimp/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-  <maintainer type="project">
-    <email>sci-biology@gentoo.org</email>
-    <name>Gentoo Biology Project</name>
-  </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/shrimp/shrimp-2.2.3.ebuild b/sci-biology/shrimp/shrimp-2.2.3.ebuild
deleted file mode 100644
index 2b57b032a1b2..000000000000
--- a/sci-biology/shrimp/shrimp-2.2.3.ebuild
+++ /dev/null
@@ -1,82 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit flag-o-matic python-single-r1 toolchain-funcs
-
-MY_PV=${PV//./_}
-
-DESCRIPTION="SHort Read Mapping Package"
-HOMEPAGE="http://compbio.cs.toronto.edu/shrimp/"
-SRC_URI="http://compbio.cs.toronto.edu/shrimp/releases/SHRiMP_${MY_PV}.src.tar.gz"
-
-LICENSE="shrimp"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="custom-cflags +cpu_flags_x86_sse2"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-# file collision on /usr/bin/utils #453044
-DEPEND="!sci-mathematics/cado-nfs"
-RDEPEND="${DEPEND}
-	${PYTHON_DEPS}"
-
-S=${WORKDIR}/SHRiMP_${MY_PV}
-
-pkg_pretend() {
-	use cpu_flags_x86_sse2 || die "This package needs sse2 support in your CPU"
-}
-
-pkg_setup() {
-	if [[ ${CC} == *gcc* ]] &&	! tc-has-openmp; then
-		elog "Please set CC to an OPENMP capable compiler (e.g. gcc[openmp] or icc"
-		die "C compiler lacks OPENMP support"
-	fi
-	python-single-r1_pkg_setup
-}
-
-src_prepare() {
-	sed \
-		-e '1 a #include <stdint.h>' \
-		-i common/dag_glue.cpp || die
-	# respect LDFLAGS wrt 331823
-	sed \
-		-e "s/LDFLAGS/LIBS/" \
-		-e "s/\$(LD)/& \$(LDFLAGS)/" \
-		-e 's/-static//' \
-		-i Makefile || die
-
-	append-flags -fopenmp
-	if ! use custom-cflags; then
-		append-flags -O3
-		replace-flags -O* -O3
-	fi
-	tc-export CXX
-
-	cd utils || die
-	sed -e '/^#!/d' -i *py || die
-	sed -e '1i#!/usr/bin/python' -i *py || die
-}
-
-src_compile() {
-	emake CXXFLAGS="${CXXFLAGS}" LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	local i
-	newdoc bin/README README.bin && rm bin/README
-	dobin bin/* utils/split-contigs utils/temp-sink
-	dodoc HISTORY README TODO SPLITTING_AND_MERGING SCORES_AND_PROBABILITES
-
-	pushd utils > /dev/null
-
-	python_doscript *py
-
-	rm *.py *.o *.c split-contigs temp-sink || die
-	insinto /usr/share/${PN}
-	doins -r *
-}
-- 
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