gentoo auto-resync : 05:05:2023 - 11:30:40

4 files changed, 0 insertions, 282 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 76d2671f3099..24bc9f5dae8c 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/samtools/Manifest b/sci-biology/samtools/Manifest
index c996903e5f43..d9bbfcc05f0a 100644
--- a/sci-biology/samtools/Manifest
+++ b/sci-biology/samtools/Manifest
@@ -1,6 +1,3 @@
-AUX samtools-0.1.20-buildsystem.patch 6737 BLAKE2B 71445f57735903bccc2720a32f42b27093f670e383d2d194b5692b1ba536e3df44204711cf4574b3933e5ce00605b661b1a36d79ca7f193ce36816271a3f8214 SHA512 ecb05971fbea4570ec161a165cb581b38ed727bb7e5b769862984bf035414cd564ab809882dc3272f8b192feeb86e29247d7327afa73ff668b01c03c58bb177d
-DIST samtools-0.1.20.tar.gz 566387 BLAKE2B a62d74c408877754af50f5e5fea0e2289ec1e0c9f25013ed0d039bfe8ef61108600d917f8c9d356e98aca632795b4eb0f01ea1b54526a652577fb74a38a433c2 SHA512 15bd8cf401d14c1ab4faa591b6054f5ea9731c4e966f37f71d33d9081a270cfeb91e8a3d80c631e0725b49da81387f824c206e8c21553ad554d0cfc5c238a6e5
 DIST samtools-1.17.tar.bz2 8605080 BLAKE2B 09cb0bff7bf7113a77f57fdb879765b28b65461a574e4a1ab20ae2327af46e5616e04f03eb68706d42ba0643e887d7921974a3d78c5f87d296a4c3b691215260 SHA512 107a6df858c6bd2556ba4e86cc1922c3184df095f347039fa94bfd24e5ee21e1a4a9fba5a7cce248a06ad47f99978d9aae570efee7e30e165f33ea848a2cd3c3
-EBUILD samtools-0.1.20-r4.ebuild 2049 BLAKE2B d377712eaca931258b37645e6a6b3cc379fdb550ef83a0c272a3eb564d7753185fea53416973e4fdf2c25b79475a81ae72b646ce22c570c934e4eabce8a9ded6 SHA512 c0d387f715ebf1f746ea4e4a7eab85a86ef0bff646c9a69639b17ef02e93c39982941d7eb811a6d67b0e635c9c4e05924d2b89a6809c3bd0592db91894dab4aa
 EBUILD samtools-1.17.ebuild 926 BLAKE2B c2baac0d68599fadfc1825e2c0046c0596d50cedd15e6859bbfffbd3d735ae6dca2e873d835120da7be8a9c91ce17dd449010dfa956899de69c807da0cc60c7c SHA512 d43c9a9da338c0820f0237925895684077a2df428be3892f3433f050c3082d605a1edefdb265ded6f123eed491dc05578d4e46177eb79d7fdad3eebc710e3764
 MISC metadata.xml 409 BLAKE2B c94eab9ebda4844beb471694106e353ccbbaca53e69de680301c6cfab3f3b6224ec94fcd631c9de2811d309463e5ee6decf2e443bfc68921f3362c6a312cd3af SHA512 fb2d3686e1ee70e4e80266a26603b3e52b680b1537a4569493a3a0511b93e2acdb2be3136df7ae54905a9f86fb7e53fa054607262751ebd8f54903f1905dad24
diff --git a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch b/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
deleted file mode 100644
index eb9f6934a96f..000000000000
--- a/sci-biology/samtools/files/samtools-0.1.20-buildsystem.patch
+++ /dev/null
@@ -1,206 +0,0 @@
---- samtools-0.1.20/bcftools/Makefile
-+++ samtools-0.1.20/bcftools/Makefile
-@@ -1,6 +1,6 @@
--CC=			gcc
--CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
--DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
-+CC?=		gcc
-+CFLAGS?=	-g -Wall -O2 #-m64 #-arch ppc
-+CPPFLAGS+=	-D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
- LOBJS=		bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
- OMISC=		..
- AOBJS=		call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o
-@@ -11,14 +11,14 @@
- .SUFFIXES:.c .o
- 
- .c.o:
--		$(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@
-+		$(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(INCLUDES) $< -o $@
- 
- all-recur lib-recur clean-recur cleanlocal-recur install-recur:
- 		@target=`echo $@ | sed s/-recur//`; \
- 		wdir=`pwd`; \
- 		list='$(SUBDIRS)'; for subdir in $$list; do \
- 			cd $$subdir; \
--			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-+			$(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
- 				INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
- 			cd $$wdir; \
- 		done;
-@@ -31,7 +31,7 @@
- 		$(AR) -csru $@ $(LOBJS)
- 
- bcftools:lib $(AOBJS)
--		$(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread
- 
- bcf.o:bcf.h
- vcf.o:bcf.h
---- samtools-0.1.20/Makefile
-+++ samtools-0.1.20/Makefile
-@@ -4,10 +4,10 @@
- #   make git-stamp
- VERSION=
- 
--CC=			gcc
--CFLAGS=		-g -Wall $(VERSION) -O2
--#LDFLAGS=		-Wl,-rpath,\$$ORIGIN/../lib
--DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
-+CC?=		gcc
-+CFLAGS?=	-g -Wall $(VERSION) -O2
-+#LDFLAGS+=	-Wl,-rpath,\$$ORIGIN/../lib
-+CPPFLAGS+=	-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
- KNETFILE_O=	knetfile.o
- LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
- 			bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
-@@ -28,14 +28,14 @@
- .PHONY: all lib
- 
- .c.o:
--		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-+		$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
- 
- all-recur lib-recur clean-recur cleanlocal-recur install-recur:
- 		@target=`echo $@ | sed s/-recur//`; \
- 		wdir=`pwd`; \
- 		list='$(SUBDIRS)'; for subdir in $$list; do \
- 			cd $$subdir; \
--			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-+			$(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
- 				INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
- 			cd $$wdir; \
- 		done;
-@@ -48,22 +48,22 @@
- .PHONY:all lib clean cleanlocal
- .PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
- 
--lib:libbam.a
-+lib:libbam-0.1-legacy.a
- 
--libbam.a:$(LOBJS)
-+libbam-0.1-legacy.a:$(LOBJS)
- 		$(AR) -csru $@ $(LOBJS)
- 
- samtools:lib-recur $(AOBJS)
--		$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. -lbam-0.1-legacy -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
- 
- razip:razip.o razf.o $(KNETFILE_O)
--		$(CC) $(CFLAGS) -o $@ $^ -lz
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz
- 
- bgzip:bgzip.o bgzf.o $(KNETFILE_O)
--		$(CC) $(CFLAGS) -o $@ $^ -lz -lpthread
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz -lpthread
- 
- bgzf.o:bgzf.c bgzf.h
--		$(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
-+		$(CC) -c $(CFLAGS) $(CPPFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
- 
- razip.o:razf.h
- bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
-@@ -90,17 +90,17 @@
- faidx_main.o:faidx.h razf.h
- 
- 
--libbam.1.dylib-local:$(LOBJS)
--		libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
-+libbam-0.1-legacy.1.dylib-local:$(LOBJS)
-+		libtool -dynamic $(LOBJS) -o libbam-0.1-legacy.1.dylib -lc -lz
- 
--libbam.so.1-local:$(LOBJS)
--		$(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
-+libbam-0.1-legacy.so.1-local:$(LOBJS)
-+		$(CC) $(LDFLAGS) -shared -Wl,-soname,libbam-0.1-legacy.so -o libbam-0.1-legacy.so.1 $(LOBJS) -lc -lz -lm -lpthread
- 
- dylib:
- 		@$(MAKE) cleanlocal; \
- 		case `uname` in \
--			Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
--			Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
-+			Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.so.1-local;; \
-+			Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.1.dylib-local;; \
- 			*) echo 'Unknown OS';; \
- 		esac
- 
---- samtools-0.1.20/misc/Makefile
-+++ samtools-0.1.20/misc/Makefile
-@@ -1,8 +1,8 @@
--CC=			gcc
--CXX=		g++
--CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
--CXXFLAGS=	$(CFLAGS)
--DFLAGS=		-D_FILE_OFFSET_BITS=64
-+CC?=		gcc
-+CXX?=		g++
-+CFLAGS?=	-g -Wall -O2 #-m64 #-arch ppc
-+CXXFLAGS?=	$(CFLAGS)
-+CPPFLAGS+=	-D_FILE_OFFSET_BITS=64
- OBJS=		
- PROG=		md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck
- INCLUDES=	-I..
-@@ -11,7 +11,7 @@
- .SUFFIXES:.c .o
- 
- .c.o:
--		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
-+		$(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
- 
- all:$(PROG)
- 
-@@ -20,7 +20,7 @@
- 		wdir=`pwd`; \
- 		list='$(SUBDIRS)'; for subdir in $$list; do \
- 			cd $$subdir; \
--			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
-+			$(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
- 				INCLUDES="$(INCLUDES)" $$target || exit 1; \
- 			cd $$wdir; \
- 		done;
-@@ -28,31 +28,31 @@
- lib:
- 
- bamcheck:bamcheck.o
--		$(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam-0.1-legacy -lpthread -lz
- 
- bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
- 		$(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c
- 
- ace2sam:ace2sam.o
--		$(CC) $(CFLAGS) -o $@ ace2sam.o -lz
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ ace2sam.o -lz
- 
- wgsim:wgsim.o
--		$(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ wgsim.o -lm -lz
- 
- md5fa:md5.o md5fa.o md5.h ../kseq.h
--		$(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5.o md5fa.o -lz
- 
- md5sum-lite:md5sum-lite.o
--		$(CC) $(CFLAGS) -o $@ md5sum-lite.o
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5sum-lite.o
- 
- md5sum-lite.o:md5.c md5.h
- 		$(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
- 
- maq2sam-short:maq2sam.c
--		$(CC) $(CFLAGS) -o $@ maq2sam.c -lz
-+		$(CC) $(CFLAGS) $(LDFLAGS) -o $@ maq2sam.c -lz
- 
- maq2sam-long:maq2sam.c
--		$(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
-+		$(CC) $(CFLAGS) -DMAQ_LONGREADS $(LDFLAGS) -o $@ maq2sam.c -lz
- 
- md5fa.o:md5.h md5fa.c
- 		$(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
---- samtools-0.1.20/misc/varfilter.py
-+++ samtools-0.1.20/misc/varfilter.py
-@@ -1,4 +1,4 @@
--#!/software/bin/python
-+#!/usr/bin/env python
- 
- # Author: lh3, converted to python and modified to add -C option by Aylwyn Scally
- #
diff --git a/sci-biology/samtools/samtools-0.1.20-r4.ebuild b/sci-biology/samtools/samtools-0.1.20-r4.ebuild
deleted file mode 100644
index f4b779aa838b..000000000000
--- a/sci-biology/samtools/samtools-0.1.20-r4.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit multilib toolchain-funcs
-
-DESCRIPTION="Utilities for analysing and manipulating the SAM/BAM alignment formats"
-HOMEPAGE="http://samtools.sourceforge.net/"
-SRC_URI="https://github.com/samtools/samtools/archive/${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0.1-legacy"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x64-macos"
-
-RDEPEND="
-	sys-libs/ncurses:0=
-	dev-lang/perl"
-DEPEND="${RDEPEND}"
-BDEPEND="virtual/pkgconfig"
-
-PATCHES=( "${FILESDIR}"/${P}-buildsystem.patch )
-
-src_prepare() {
-	default
-	tc-export CC AR
-}
-
-src_compile() {
-	local _ncurses="$($(tc-getPKG_CONFIG) --libs ncurses)"
-	emake dylib LIBCURSES="${_ncurses}"
-	emake LIBCURSES="${_ncurses}"
-}
-
-src_install() {
-	# install executables and hide them away from sight
-	dobin samtools bcftools/{bcftools,vcfutils.pl} misc/{*.py,*.pl,wgsim,ace2sam} \
-		misc/{md5sum-lite,maq2sam-short,bamcheck,maq2sam-long,md5fa,plot-bamcheck}
-	mv "${ED}"/usr/{bin,${PN}-${SLOT}} || die
-	mkdir "${ED}"/usr/bin || die
-	mv "${ED}"/usr/{${PN}-${SLOT},bin/} || die
-
-	# remove py2 script, has been removed upstream anyways
-	# https://github.com/samtools/samtools/issues/1125
-	rm "${ED}"/usr/bin/${PN}-${SLOT}/varfilter.py || die
-
-	# fix perl shebangs
-	pushd "${ED}"/usr/bin/${PN}-${SLOT} >/dev/null || die
-		local i
-		for i in plot-bamcheck *.pl; do
-			sed -e '1s:.*:#!/usr/bin/env perl:' -i "${i}" || die
-		done
-	popd >/dev/null || die
-
-	dolib.so libbam-${SLOT}$(get_libname 1)
-	dosym libbam-${SLOT}$(get_libname 1) /usr/$(get_libdir)/libbam-${SLOT}$(get_libname)
-
-	insinto /usr/include/bam-${SLOT}
-	doins *.h
-
-	mv ${PN}{,-${SLOT}}.1 || die
-	doman ${PN}-${SLOT}.1
-	einstalldocs
-
-	dodoc -r examples
-	docompress -x /usr/share/doc/${PF}/examples
-}
-
-pkg_postinst() {
-	elog "This version of samtools should *not* be your first choice for working"
-	elog "with NGS data. It is installed solely for programs requiring it."
-	elog "It is recommended that you use >=sci-biology/samtools-1.10."
-}