gentoo resync : 30.09.2020

6 files changed, 65 insertions, 43 deletions

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))