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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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