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bio-mocha: Fix fetch, pkglint warnings



Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sun Sep 29 07:37:09 2024 -0500
Changeset:	c7b46fb78c98d2f08b9bfaf39ce940ff401b5a27

Modified Files:
	bio-mocha/Makefile

Log Message:
bio-mocha: Fix fetch, pkglint warnings

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=c7b46fb78c98d2f08b9bfaf39ce940ff401b5a27

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

diffstat:
 bio-mocha/Makefile | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diffs:
diff --git a/bio-mocha/Makefile b/bio-mocha/Makefile
index 1d8805af41..9ca8ee4454 100644
--- a/bio-mocha/Makefile
+++ b/bio-mocha/Makefile
@@ -2,44 +2,44 @@
 
 DISTNAME=	bio-mocha-1.20
 CATEGORIES=	biology
+# Can't get ${MASTER_SITE_GITHUB:=samtools/} to work with additional distfile
 MASTER_SITES=	https://software.broadinstitute.org/software/mocha/
-MASTER_SITES+=	${MASTER_SITE_GITHUB:=samtools/}
+MASTER_SITES+=	https://github.com/samtools/bcftools/releases/download/${GH_TAG}/
 DISTFILES+=	bio-mocha_1.20-20240505.tar.gz
 DISTFILES+=	bcftools-1.21.tar.bz2
-GITHUB_PROJECT=	bcftools
-GITHUB_TAG=	1.21
+GH_TAG=		1.21
 
 OWNER=		bacon%NetBSD.org@localhost
 HOMEPAGE=	https://software.broadinstitute.org/software/mocha/
 COMMENT=	Bcftools plugin for mosaic chromosomal alteration analysis
 LICENSE=	mit
 
-REPLACE_INTERPRETER+=   R
-REPLACE.R.old=          /usr/bin/env Rscript
-REPLACE.R.new=          ${PREFIX}/bin/Rscript
-REPLACE_FILES.R=        MoCha/*.R
+REPLACE_INTERPRETER+=	R
+REPLACE.R.old=		/usr/bin/env Rscript
+REPLACE.R.new=		${PREFIX}/bin/Rscript
+REPLACE_FILES.R=	MoCha/*.R
 
 SUBST_CLASSES+=		version
 SUBST_STAGE.version=	pre-configure
 SUBST_SED.version=	-e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|"
 SUBST_FILES.version=	configure.ac
 
-DEPENDS=	bash:../../shells/bash
+DEPENDS=	bash>=0:../../shells/bash
 DEPENDS+=	bcftools>=1.16:../../biology/bcftools
 
 USE_TOOLS+=	autoconf automake autoreconf gmake perl pax
 GNU_CONFIGURE=	yes
 REPLACE_PERL=	misc/* test/test.pl
 
-WRKSRC=		${WRKDIR}/bcftools-${GITHUB_TAG}
+WRKSRC=		${WRKDIR}/bcftools-${GH_TAG}
 
 DATADIR=		${PREFIX}/share/bio-mocha
 INSTALLATION_DIRS=	libexec/bcftools
 
 post-extract:
-	@${CP} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins
-	@${MKDIR} ${WRKSRC}/MoCha
-	@${CP} ${WRKDIR}/*.R ${WRKSRC}/MoCha
+	${CP} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins
+	${MKDIR} ${WRKSRC}/MoCha
+	${CP} ${WRKDIR}/*.R ${WRKSRC}/MoCha
 
 pre-configure:
 	cd ${WRKSRC} && autoreconf -if


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