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Date: Sat, 29 May 2021 17:35:18 +0000
From: "Brook Milligan" <brook@netbsd.org>
Subject: CVS commit: pkgsrc/biology/minimap2
To: pkgsrc-changes@NetBSD.org
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Module Name:	pkgsrc
Committed By:	brook
Date:		Sat May 29 17:35:18 UTC 2021

Modified Files:
	pkgsrc/biology/minimap2: Makefile PLIST

Log Message:
biology/minimap2: install minimap2 program instead of python binding

The distfile for minimap2 includes two different components: (i) the
minimap2 sequence mapping program itself, and (ii) a python binding
generally referred to as mappy.  The initial version of this package
included only the python binding.  However, it is more appropriate
that the minimap2 package should contain the program of the same name,
and a new package be created with the name mappy for the python
binding.  Splitting these into two packages makes sense, because this
allows users to install the minimap2 package without python
dependencies.


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/minimap2/Makefile \
    pkgsrc/biology/minimap2/PLIST

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.


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Modified files:

Index: pkgsrc/biology/minimap2/Makefile
diff -u pkgsrc/biology/minimap2/Makefile:1.1 pkgsrc/biology/minimap2/Makefile:1.2
--- pkgsrc/biology/minimap2/Makefile:1.1	Wed May 26 18:49:20 2021
+++ pkgsrc/biology/minimap2/Makefile	Sat May 29 17:35:18 2021
@@ -1,29 +1,27 @@
-# $NetBSD: Makefile,v 1.1 2021/05/26 18:49:20 brook Exp $
+# $NetBSD: Makefile,v 1.2 2021/05/29 17:35:18 brook Exp $
 
 GITHUB_PROJECT=	minimap2
 GITHUB_TAG=	refs/tags/v2.18
 DISTNAME=	v2.18
 PKGNAME=	${GITHUB_PROJECT}-${DISTNAME:S,^v,,}
+PKGREVISION=	1
 CATEGORIES=	biology python
 MASTER_SITES=	${MASTER_SITE_GITHUB:=lh3/}
 DIST_SUBDIR=	${GITHUB_PROJECT}
 
 MAINTAINER=	pkgsrc-users@NetBSD.org
 HOMEPAGE=	https://github.com/lh3/minimap2
-COMMENT=	Minimap2 python binding
+COMMENT=	Sequence alignment program for noisy, long reads
 LICENSE=	mit
 
 WRKSRC=		${WRKDIR}/minimap2-2.18
 USE_TOOLS+=	gmake
 
-INSTALLATION_DIRS+=	share/examples/minimap2
+INSTALLATION_DIRS+=	bin ${PKGMANDIR}/man1
 
-post-install:
-	${INSTALL_DATA} ${WRKSRC}/README.md ${DESTDIR}${PREFIX}/share/examples/minimap2
-	${INSTALL_DATA} ${WRKSRC}/cookbook.md ${DESTDIR}${PREFIX}/share/examples/minimap2
-
-BUILDLINK_DEPENDS.py-cython+=	build
-BUILDLINK_API_DEPENDS.py-cython+=	${PYPKGPREFIX}-cython>=0.29.23
-.include "../../devel/py-cython/buildlink3.mk"
-.include "../../lang/python/egg.mk"
+do-install:
+	${INSTALL} ${WRKSRC}/minimap2 ${DESTDIR}${PREFIX}/bin
+	${INSTALL_DATA} ${WRKSRC}/minimap2.1 ${DESTDIR}${PREFIX}/${PKGMANDIR}/man1
+
+.include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/minimap2/PLIST
diff -u pkgsrc/biology/minimap2/PLIST:1.1 pkgsrc/biology/minimap2/PLIST:1.2
--- pkgsrc/biology/minimap2/PLIST:1.1	Wed May 26 18:49:20 2021
+++ pkgsrc/biology/minimap2/PLIST	Sat May 29 17:35:18 2021
@@ -1,9 +1,3 @@
-@comment $NetBSD: PLIST,v 1.1 2021/05/26 18:49:20 brook Exp $
-bin/minimap2.py
-${PYSITELIB}/mappy-${PKGVERSION}-py${PYVERSSUFFIX}.egg-info/PKG-INFO
-${PYSITELIB}/mappy-${PKGVERSION}-py${PYVERSSUFFIX}.egg-info/SOURCES.txt
-${PYSITELIB}/mappy-${PKGVERSION}-py${PYVERSSUFFIX}.egg-info/dependency_links.txt
-${PYSITELIB}/mappy-${PKGVERSION}-py${PYVERSSUFFIX}.egg-info/top_level.txt
-${PYSITELIB}/mappy.so
-share/examples/minimap2/README.md
-share/examples/minimap2/cookbook.md
+@comment $NetBSD: PLIST,v 1.2 2021/05/29 17:35:18 brook Exp $
+bin/minimap2
+man/man1/minimap2.1


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