git: cc5fdc14d943 - main - biology/ncbi-cxx-toolkit: Update 22.0.0 -> 25.0.0

[Yuri Victorovich]

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=cc5fdc14d94309a7dbae28f96689202781c1e299

commit cc5fdc14d94309a7dbae28f96689202781c1e299
Author:     Yuri Victorovich <yuri at FreeBSD.org>
AuthorDate: 2021-08-25 19:54:09 +0000
Commit:     Yuri Victorovich <yuri at FreeBSD.org>
CommitDate: 2021-08-25 20:28:23 +0000

    biology/ncbi-cxx-toolkit: Update 22.0.0 -> 25.0.0
---
 biology/ncbi-cxx-toolkit/Makefile | 25 ++++++++++++++++++-------
 biology/ncbi-cxx-toolkit/distinfo |  6 +++---
 2 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/biology/ncbi-cxx-toolkit/Makefile b/biology/ncbi-cxx-toolkit/Makefile
index d8ab6730f753..4148f33e2d63 100644
--- a/biology/ncbi-cxx-toolkit/Makefile
+++ b/biology/ncbi-cxx-toolkit/Makefile
@@ -1,7 +1,7 @@
 PORTNAME=	ncbi-cxx-toolkit
-DISTVERSION=	22_0_0
+DISTVERSION=	25_0_0
 CATEGORIES=	biology science devel
-MASTER_SITES=	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/2019/Mar_28_2019/
+MASTER_SITES=	ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/2021/Aug_18_2021/
 DISTNAME=	ncbi_cxx--${DISTVERSION}
 
 MAINTAINER=	yuri at FreeBSD.org
@@ -10,25 +10,36 @@ COMMENT=	NCBI C++ Toolkit
 LICENSE=	PD
 LICENSE_FILE=	${WRKSRC}/doc/public/LICENSE
 
-LIB_DEPENDS=	liblmdb.so:databases/lmdb \
+LIB_DEPENDS=	libcdd.so:math/cddlib \
+		liblmdb.so:databases/lmdb \
 		libpcre.so:devel/pcre
 RUN_DEPENDS=	bash:shells/bash
 
 USES=		compiler:c++11-lang gmake mysql perl5 python shebangfix ssl xorg
-SHEBANG_FILES=	src/app/blast/get_species_taxids.sh src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl src/app/winmasker/windowmasker_2.2.22_adapter.py
 USE_XORG=	x11 xpm
 
+SHEBANG_FILES=	src/app/blast/get_species_taxids.sh
+SHEBANG_GLOB=	*.pl *.py
+
 GNU_CONFIGURE=	yes
-CONFIGURE_ARGS=	--without-debug --with-dll --without-static
+CONFIGURE_ARGS=	--without-debug --with-dll --without-static \
+		--without-vdb
+
+WRKSRC=		${WRKDIR}/public-${DISTVERSION:S/_/./g}-2021-08-18-11-21-29
 
 post-install:
 	# strip
 	@${FIND} ${STAGEDIR}${PREFIX}/bin -type f | ${GREP} -v -E '\.(sh|py|pl)$$' | ${XARGS} ${STRIP_CMD}
 	@${FIND} ${STAGEDIR}${PREFIX}/lib -name "*.so" | ${XARGS} ${STRIP_CMD}
 	# remove an empty directory
-	@${RMDIR} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/objtools/data_loaders/genbank/psg
+	#@${RMDIR} ${STAGEDIR}${PREFIX}/include/ncbi-tools++/objtools/data_loaders/genbank/psg
+	@${RMDIR} \
+		${STAGEDIR}${PREFIX}/include/ncbi-tools++/algo/ms/formats \
+		${STAGEDIR}${PREFIX}/include/ncbi-tools++/algo/ms
 	# remove the conflicting file
-	@${RM} ${STAGEDIR}${PREFIX}/lib/liblmdb.so
+	@${RM} \
+		${STAGEDIR}${PREFIX}/lib/libcdd.so \
+		${STAGEDIR}${PREFIX}/lib/liblmdb.so
 	# autoplist: thousands of files
 	@cd ${STAGEDIR}${PREFIX} && \
 		${RMDIR} include/ncbi-tools++/algo/blast/bl2api include/ncbi-tools++/objtools/test && \
diff --git a/biology/ncbi-cxx-toolkit/distinfo b/biology/ncbi-cxx-toolkit/distinfo
index 5ded16bce9b4..d85ae212645c 100644
--- a/biology/ncbi-cxx-toolkit/distinfo
+++ b/biology/ncbi-cxx-toolkit/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1600993142
-SHA256 (ncbi_cxx--22_0_0.tar.gz) = ef39429bbc7f13c44c0d327432d9cfb430f9f20d10d825e6b2c4ddd7ccce457f
-SIZE (ncbi_cxx--22_0_0.tar.gz) = 56042079
+TIMESTAMP = 1629878632
+SHA256 (ncbi_cxx--25_0_0.tar.gz) = 0158971349839b69ea96b3b88db774ac1692befd9910c040a00186e841ef5ed5
+SIZE (ncbi_cxx--25_0_0.tar.gz) = 95801019