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-rw-r--r--profiles/package.mask1
-rw-r--r--sci-biology/phrap/Manifest1
-rw-r--r--sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch100
-rw-r--r--sci-biology/phrap/metadata.xml8
-rw-r--r--sci-biology/phrap/phrap-1.080812-r2.ebuild47
5 files changed, 0 insertions, 157 deletions
diff --git a/profiles/package.mask b/profiles/package.mask
index 6496beff8e24..d442ec3896a7 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -708,7 +708,6 @@ app-eselect/eselect-sh
# GCC and Clang (-fcommon), license prohibits distributing, EAPI 6,
# last release 8 years ago. Removal on 2023-01-25.
sci-biology/consed
-sci-biology/phrap
# Ionen Wolkens <ionen@gentoo.org> (2022-12-24)
# Upstream dropped wxGTK support in >=games-emulation/pcsx2-1.7.3773,
diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest
deleted file mode 100644
index 12d65a0b5974..000000000000
--- a/sci-biology/phrap/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST phrap-1.080812-distrib.tar.gz 317350 BLAKE2B 9cc53d05184b4a55a9a80e6112498f91a622b98a853b255daedd57c892b7c2bb8ef3091ed3d141e297864c158b7e03d02313a272448d2e0fb80e1c51a906e00a SHA512 6b125b9a99b6180eb5de16bccfe068abefdb59237fd3295924c418749f2f2d6e39cdbcecc6786e42738846975334c4d8a645eae8fd0fcbda6b0e99241deb15ca
diff --git a/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch b/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch
deleted file mode 100644
index 6d30c2ce326a..000000000000
--- a/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch
+++ /dev/null
@@ -1,100 +0,0 @@
-* Fix perl shebang to be portable
-* Make build system honour LDFLAGS
-
---- a/makefile
-+++ b/makefile
-@@ -25,9 +25,8 @@
- # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated)
- #CC= icc
- #CFLAGS= -O2 -wd266,880
--CC= cc
--CFLAGS= -O2
--LFLAGS= -lm
-+CC ?= cc
-+LIBS = -lm
-
- SWATOBJS= swat.o weibull.o
-
-@@ -96,46 +95,46 @@
- chmod a+x phrapview
-
- swat: makefile $(SWATOBJS) $(SWOBJS)
-- $(CC) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LIBS)
- chmod o-r swat
-
- alpha_swat: makefile $(ALPHOBJS) $(SWOBJS)
-- $(CC) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LIBS)
- chmod o-r alpha_swat
-
- swat_counts: makefile $(COUNOBJS) $(SWOBJS)
-- $(CC) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LIBS)
- chmod o-r swat_counts
-
- swprobs: makefile $(PROBOBJS)
-- $(CC) $(CFLAGS) -o $@ $(PROBOBJS) $(LFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(PROBOBJS) $(LIBS)
-
- phrap: makefile phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS)
-- $(CC) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LIBS)
- chmod o-r phrap
-
- gcphrap: makefile gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS)
-- $(CC) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS)
- chmod o-r gcphrap
-
- cross_match: makefile cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS)
-- $(CC) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LIBS)
- chmod o-r cross_match
-
- gccross_match: makefile gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS)
-- $(CC) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS)
- chmod o-r gccross_match
-
- cluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS)
-- $(CC) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LIBS)
- chmod o-r cluster
-
- loco: makefile $(LOCOOBJS) $(SWOBJS)
-- $(CC) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LIBS)
- chmod o-r loco
-
- erf_test: $(ERFOBJS)
-- $(CC) $(CFLAGS) -o $@ $(ERFOBJS) $(LFLAGS)
-+ $(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ERFOBJS) $(LIBS)
-
- loco.o: swat.h
-
-@@ -228,7 +227,7 @@
- anomalies.o: swat.h
-
- fast_smith_wat.s: fast_smith_wat.c
-- cc -S -machine_code -source_listing -O3 fast_smith_wat.c
-+ $(CC) $(CFLAGS) -S -machine_code -source_listing fast_smith_wat.c
- #N.B. fast_smith_wat.s MUST BE EDITTED BEFORE USE!!!
-
- tig_node.o: swat.h
---- a/phrapview
-+++ b/phrapview
-@@ -1,4 +1,4 @@
--#!/usr/local/bin/perl -w
-+#!/usr/bin/env perl
-
-
- #/*****************************************************************************
-@@ -25,6 +25,7 @@
- #
- #*****************************************************************************/
-
-+use warnings;
- use strict;
- use Tk;
- #phrapview version 0.960731
diff --git a/sci-biology/phrap/metadata.xml b/sci-biology/phrap/metadata.xml
deleted file mode 100644
index ccdff086e20b..000000000000
--- a/sci-biology/phrap/metadata.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
-</pkgmetadata>
diff --git a/sci-biology/phrap/phrap-1.080812-r2.ebuild b/sci-biology/phrap/phrap-1.080812-r2.ebuild
deleted file mode 100644
index 08ea5a1fb71f..000000000000
--- a/sci-biology/phrap/phrap-1.080812-r2.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit toolchain-funcs
-
-DESCRIPTION="Shotgun assembly and alignment utilities"
-HOMEPAGE="http://www.phrap.org/"
-SRC_URI="phrap-${PV}-distrib.tar.gz"
-
-LICENSE="phrap"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=""
-RDEPEND="
- dev-lang/perl
- dev-perl/Tk"
-
-S="${WORKDIR}"
-
-RESTRICT="fetch"
-PATCHES=( "${FILESDIR}/${PN}-1.080812-fix-build-system.patch" )
-
-pkg_nofetch() {
- einfo "Please visit http://www.phrap.org/phredphrapconsed.html and obtain the file"
- einfo "\"distrib.tar.gz\", then rename it to \"phrap-${PV}-distrib.tar.gz\""
- einfo "and put it into your DISTDIR directory."
-}
-
-src_compile() {
- emake CC="$(tc-getCC)" \
- CFLAGS="${CFLAGS}" \
- LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
- dobin cross_match loco phrap phrapview swat
- newbin cluster cluster_phrap
-
- local i
- for i in {general,phrap,swat}.doc; do
- newdoc ${i} ${i}.txt
- done
-}