gentoo resync : 30.09.2020

9 files changed, 65 insertions, 121 deletions

diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index a0154d513f37..4c7f9b88e8d6 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest
index ff09184da36d..251ea4a9b645 100644
--- a/sci-biology/bwa/Manifest
+++ b/sci-biology/bwa/Manifest
@@ -1,5 +1,5 @@
-AUX bwa-0.7.15-Makefile.patch 933 BLAKE2B f62d9b7f8c55ed55f9d6b63628ddc89077e8e01bb2c99e1c215374fd05114e2007ada0867d629c0b9edf2a700299dc6ad1bc736e5b0a2ae143695c03625d5532 SHA512 d76d6aac355b2ad52d3aa1ca59defc33017cfbdcec96939db4807acf7f35d6bcd4e21728998fb0fd3633742cfd9edaa7b62ab1eaff26829296967fefdbc185b4
-AUX bwa-0.7.16a-gcc-10.patch 126 BLAKE2B 366d380329b7e4317c3145b5f3b0ed5aed00383ffd839129955a5c9c6e24473b1d655f0322eba94d5d35dd635b9bc8f739e3515f05d9e915cdf172a838429b54 SHA512 93e357c616666004c332a9cc425c5b57bd1a72accd0ce5ed111847cfa3b4f3125d65907919e3b792dd58061677a4f66b0413039b040d9e911e75b8fecf370db0
-DIST bwa-0.7.16a.tar.bz2 190773 BLAKE2B e1064381b6b1aa4c9b78d12222c7b783a55676a163b94ad8596a2af64c9b0d60bbebd8e840aaa13b25e1ca4f10466c2c39c99830f1ca58e558d724d1ad583944 SHA512 8bbe223f79efd328d66adb88baf995e894f5944aad912ac1b464dc84dc9b4e22ddf77b60dcbe468e0eedc344ee58d08dc498777f0d2794a2c1e0ddd33dad606d
-EBUILD bwa-0.7.16a.ebuild 699 BLAKE2B 3dbbd9aa120126cf4856fe2ee361e025d176545b52dfdd643f945d99146ad73ec2d1b4ea8a51fc8724c2ea441b50f0525cf9ffcde74d3a6aac26a1cbb6a5a366 SHA512 40cfd075cb3514217bcf35481e76336d13b45ebd3622c8ffe697e63bf73fab5891542bc02313a9b1114827e5e59cede785bc7c248c75b6659c1d7589b0aabd76
+AUX bwa-0.7.17-Makefile.patch 1341 BLAKE2B 21b566233ab5838174648a5316bc0c05ede4e3b6ecc1e8761556810d0c5bf5f026677fe8836ea397630f2c1d7ad45624bb6c5c26724fe1d072c9cd77889ae3c0 SHA512 0c4679d79c04ebcb8d86d7dc276cef390cd5260a08b37d7735b40d3aede634e3d98a8834154d3cf23903cf999abb00cf06661f912f6ada6d53f1242be7d1c140
+AUX bwa-0.7.17-gcc-10.patch 228 BLAKE2B c80d2fb9f1414705881178983227d762920051597edc99cca194a041b7d4dfec4d925b872448478804fbefa6881b58851e8d1a35a24b0efbc405b72f5f31cd62 SHA512 32bb9732ab9971bf26ecdaec9d512470bc970c26d1a928edb88957a4216cad1e650f0df2b69ab0214392503bbd483eade1212ed3e799393fa076b3ecdc5d5427
+DIST bwa-0.7.17.tar.gz 232593 BLAKE2B fa48aad72a47547d66c767e2e2a5aadfcfc7c77c517410812230f51a2222ee66bb04383b068036b696af0a57b04b35e97bed11e3c44793aa899a8c0807f3df5e SHA512 114e61b7cc5edcb67172d1eca7be1fa670ea33dd48b5c02c98318e254871363775c0dab327fd7ee7023200a5fedc745fa01cbe0fd9550d783f091d4df6926f48
+EBUILD bwa-0.7.17.ebuild 751 BLAKE2B b46e83d917a259affadb85c333c69821af7d54070409c5119e0d10c1a3e6136fd8fb8118f18b0e1525985b21d5d61fa00ecb3988403c42a4fd02eea5513eb5f7 SHA512 fb8c1d63bcb526c37795fa315dd4bbb8ffeb2bd6634f43ac82e1352416ffddddd44e38fcd7ec0a0608fd33143176618a418cbeb5b346f12e64172f071cf00d0d
 MISC metadata.xml 348 BLAKE2B f6e4a9e3beee19fa7b231fdf89cbed2f0bcb96eddb8e7be4d47b0f6f78253ad747e89f803edc5b929536c02993b654af5933c1d4470284484d83c6724b38656e SHA512 512439b23a870d55169998b035a6f9d8a10c0746c7e20d1f969a11a7b98eef297e71fc8fdf600a20f321e1f95a2c763d3e98ff4f089952eec38138ebf0291c6a
diff --git a/sci-biology/bwa/bwa-0.7.16a.ebuild b/sci-biology/bwa/bwa-0.7.17.ebuild
index b29bf210169a..3da06fd74f92 100644
--- a/sci-biology/bwa/bwa-0.7.16a.ebuild
+++ b/sci-biology/bwa/bwa-0.7.17.ebuild
@@ -6,18 +6,21 @@ EAPI=7
 inherit toolchain-funcs
 
 DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner"
-HOMEPAGE="https://bio-bwa.sourceforge.net/"
-SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2"
+HOMEPAGE="https://github.com/lh3/bwa/"
+SRC_URI="https://github.com/lh3/bwa/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="GPL-3"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~x64-macos"
 
-RDEPEND="dev-lang/perl"
+DEPEND="sys-libs/zlib"
+RDEPEND="
+	${DEPEND}
+	dev-lang/perl"
 
 PATCHES=(
-	"${FILESDIR}"/${PN}-0.7.15-Makefile.patch
-	"${FILESDIR}"/${PN}-0.7.16a-gcc-10.patch
+	"${FILESDIR}"/${PN}-0.7.17-Makefile.patch
+	"${FILESDIR}"/${PN}-0.7.17-gcc-10.patch
 )
 DOCS=( NEWS.md README-alt.md README.md )
 
diff --git a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
deleted file mode 100644
index 39b437a02897..000000000000
--- a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- bwa-0.7.13/Makefile
-+++ bwa-0.7.13/Makefile
-@@ -1,8 +1,8 @@
--CC=			gcc
-+CC?=			gcc
- #CC=			clang --analyze
--CFLAGS=		-g -Wall -Wno-unused-function -O2
-+CFLAGS?=		-g -Wall -Wno-unused-function -O2
- WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
--AR=			ar
-+AR?=			ar
- DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
- LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o
- AOBJS=		QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
-@@ -26,10 +26,10 @@
- all:$(PROG)
- 
- bwa:libbwa.a $(AOBJS) main.o
--		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
-+		$(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
- 
- bwamem-lite:libbwa.a example.o
--		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
-+		$(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
- 
- libbwa.a:$(LOBJS)
- 		$(AR) -csru $@ $(LOBJS)
diff --git a/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch b/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch
deleted file mode 100644
index 40056ffeaaa9..000000000000
--- a/sci-biology/bwa/files/bwa-0.7.16a-gcc-10.patch
+++ /dev/null
@@ -1,7 +0,0 @@
---- a/rle.h
-+++ b/rle.h
-@@ -32,3 +32,3 @@ extern "C" {
- 
--const uint8_t rle_auxtab[8];
-+extern const uint8_t rle_auxtab[8];
- 
diff --git a/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch
new file mode 100644
index 000000000000..944369cb75e2
--- /dev/null
+++ b/sci-biology/bwa/files/bwa-0.7.17-Makefile.patch
@@ -0,0 +1,42 @@
+--- a/Makefile
++++ b/Makefile
+@@ -1,9 +1,7 @@
+-CC=			gcc
+ #CC=			clang --analyze
+-CFLAGS=		-g -Wall -Wno-unused-function -O2
++CFLAGS+=		-Wall -Wno-unused-function
+ WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
+-AR=			ar
+-DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
++CPPFLAGS+=		-DHAVE_PTHREAD $(WRAP_MALLOC)
+ LOBJS=		utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o \
+ 			QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
+ AOBJS=		bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
+@@ -21,16 +19,13 @@
+ 
+ .SUFFIXES:.c .o .cc
+ 
+-.c.o:
+-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+-
+ all:$(PROG)
+ 
+ bwa:libbwa.a $(AOBJS) main.o
+-		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
++		$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
+ 
+ bwamem-lite:libbwa.a example.o
+-		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
++		$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) example.o -o $@ -L. -lbwa $(LIBS)
+ 
+ libbwa.a:$(LOBJS)
+ 		$(AR) -csru $@ $(LOBJS)
+@@ -39,7 +34,7 @@
+ 		rm -f gmon.out *.o a.out $(PROG) *~ *.a
+ 
+ depend:
+-	( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) -- *.c )
++	( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(CPPFLAGS) -- *.c )
+ 
+ # DO NOT DELETE THIS LINE -- make depend depends on it.
+ 
diff --git a/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch b/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch
new file mode 100644
index 000000000000..1babb8356c4a
--- /dev/null
+++ b/sci-biology/bwa/files/bwa-0.7.17-gcc-10.patch
@@ -0,0 +1,11 @@
+--- a/rle.h
++++ b/rle.h
+@@ -30,7 +30,7 @@
+  *** 43+3 codec ***
+  ******************/
+ 
+-const uint8_t rle_auxtab[8];
++extern const uint8_t rle_auxtab[8];
+ 
+ #define RLE_MIN_SPACE 18
+ #define rle_nptr(block) ((uint16_t*)(block))
diff --git a/sci-biology/seaview/Manifest b/sci-biology/seaview/Manifest
index 97b3063f1c7c..370ccb30d448 100644
--- a/sci-biology/seaview/Manifest
+++ b/sci-biology/seaview/Manifest
@@ -1,7 +1,5 @@
-DIST seaview_4.3.5.tar.gz 309530 BLAKE2B a4210b179bba5ab40215603738fe844d48b4f953e7b79749786afcedce0625f17c343a2d4ed2a45d4a7cfc2d4c9abbb7ab856e98405694160ecfac186f86fadd SHA512 b20c018da9a29d79fe0393fed5d29117729492ea8f36e72d4aeb98044a3de4a13331bd29e76ca552a08f6da764e57e69f9fb0325fc031551514d7a54b56c849a
 DIST seaview_4.5.4.tar.gz 420608 BLAKE2B 14b044706440da88987cd6b546595497f2de61e8d03615bfce4634104914a56544a464b0abedc83e6c96329697dccb2087c2b1af5a1fdbf0d9bdc26418a49a75 SHA512 a8a2e49a13f87ae4279311068147169b1e17874e9ce5787003b854c7271efc7a128db6916bb883a9b7b0b90f855fe40d83c77e9fd9f5751464e04346b9923301
 DIST seaview_4.6.tar.gz 424258 BLAKE2B e958ff4b1f6bb283a2122d65917a352914f33e5c9593c34c449800fbcac74b0dd4fa98bb1f47c45e11f24e07dfebb3ced54fbd8440b2bcd2b1df32dc398d5892 SHA512 e005d9dcc9e03c5636404e94f0059f7d4a9289fe77ecdab765e3ca2b59d826b8711a344f3824d079383a7ede0fe17b3b06694dfb7b709bb6a0a1e38cef6ee1d6
-EBUILD seaview-4.3.5.ebuild 2013 BLAKE2B 91c192d7cb22411f7af4366088c1e47c657fc75855cab2a289d4a1d7cec206302b2670612117334d6c6b79d25c578daf3da5cbd053dc98602ead9033c3b90f35 SHA512 41eeabeb570a22219f7ad649a4eb127b94a253f914ea6637fcce518da3607e3fb42b528d3aa436f6b86e54b695d31900b29558ec0696c1e4bf3264c42cdfc945
 EBUILD seaview-4.5.4.ebuild 2013 BLAKE2B 91c192d7cb22411f7af4366088c1e47c657fc75855cab2a289d4a1d7cec206302b2670612117334d6c6b79d25c578daf3da5cbd053dc98602ead9033c3b90f35 SHA512 41eeabeb570a22219f7ad649a4eb127b94a253f914ea6637fcce518da3607e3fb42b528d3aa436f6b86e54b695d31900b29558ec0696c1e4bf3264c42cdfc945
 EBUILD seaview-4.6.ebuild 1997 BLAKE2B 1c7c01e0a52f943b9506954d84519c8ff09b15d307476aa659f7bb49af9de1ea02076bb74bcebaac49a571d18624455879c321faa7458f8ac2660773eb4b8706 SHA512 5768df52c205ccfaa4d2d52ec753125dd77eb91a7b0be959dbc67aca00c0a66dc3f13b125d073450a81a06eea29880503981942042c77a0c6e1bb8f19f070cb8
 MISC metadata.xml 621 BLAKE2B 9c56cc2099ed696942e2958926ee8c9f24be26fd273e74a7f789d368c3a222f084363ec3a4eada5e1197c4a81f533074f4b05c43d1e9c951e66261d55bc4d9e8 SHA512 7c49694ef56359e58b76b0dd7715d28615a541655c6ccaa2d7d64041c7340082bd5026fa2baa5a15e51e3aa27309d5a72ab836a5ee554366eb324406a50a09c4
diff --git a/sci-biology/seaview/seaview-4.3.5.ebuild b/sci-biology/seaview/seaview-4.3.5.ebuild
deleted file mode 100644
index 33ee6f65ccbd..000000000000
--- a/sci-biology/seaview/seaview-4.3.5.ebuild
+++ /dev/null
@@ -1,76 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils multilib toolchain-funcs
-
-DESCRIPTION="A graphical multiple sequence alignment editor"
-HOMEPAGE="http://pbil.univ-lyon1.fr/software/seaview.html"
-SRC_URI="ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/${PN}_${PV}.tar.gz"
-
-LICENSE="public-domain"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE="+xft"
-
-CDEPEND="
-	sys-libs/zlib
-	x11-libs/fltk:1
-	x11-libs/libX11
-	xft? (
-		x11-libs/libXft
-		x11-libs/fltk:1[xft] )"
-RDEPEND="${CDEPEND}
-	sci-biology/clustalw
-	|| ( sci-libs/libmuscle sci-biology/muscle )
-	sci-biology/phyml"
-DEPEND="${CDEPEND}
-	virtual/pkgconfig"
-
-S="${WORKDIR}/${PN}"
-
-src_prepare() {
-	# respect CXXFLAGS (package uses them as CFLAGS)
-	sed \
-		-e "s:^CC.*:CC = $(tc-getCC):" \
-		-e "s:^CXX.*:CXX = $(tc-getCXX):" \
-		-e "s:\$(OPT):${CXXFLAGS}:" \
-		-e "s:^OPT:#OPT:" \
-		-e "s:^FLTK = .*$:FLTK = ${EPREFIX}/usr/include/fltk-1:" \
-		-e "s:^#IFLTK .*:IFLTK = $(fltk-config --use-images --cflags):" \
-		-e "s:^#LFLTK .*:LFLTK = $(fltk-config --use-images --ldflags):" \
-		-e "s:^USE_XFT:#USE_XFT:" \
-		-e "s:^#HELPFILE:HELPFILE:" \
-		-e "s:/usr/share/doc/seaview/seaview.htm:${EPREFIX}/usr/share/seaview/seaview.htm:" \
-		-e "s:^#PHYMLNAME:PHYMLNAME:" \
-		-e 's:-lXinerama::g' \
-		-e 's:-lpng::g' \
-		-e 's:-ljpeg::g' \
-		-e 's:-lfontconfig::g' \
-		-i Makefile || die "sed failed while editing Makefile"
-
-	if use xft; then
-		sed \
-			-e "s:^#USE_XFT .*:USE_XFT = -DUSE_XFT $($(tc-getPKG_CONFIG) --cflags xft):" \
-			-e "s:-lXft:$($(tc-getPKG_CONFIG) --libs xft):" \
-			-i Makefile || die "sed failed while editing Makefile to enable xft"
-	else
-		sed -i -e "s:-lXft::" Makefile || die
-	fi
-}
-
-src_install() {
-	dobin seaview
-
-	# /usr/share/seaview/seaview.html is hardcoded in the binary, see Makefile
-	insinto /usr/share/seaview
-	doins example.nxs seaview.html
-
-	insinto /usr/share/seaview/images
-	doins seaview.xpm
-
-	make_desktop_entry seaview Seaview
-
-	doman seaview.1
-}