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| author | rillig <rillig@pkgsrc.org> | 2020-05-16 19:40:59 +0000 |
|---|---|---|
| committer | rillig <rillig@pkgsrc.org> | 2020-05-16 19:40:59 +0000 |
| commit | eb95ae6ceb19887e7e51f5dd0ffcabb552862cff (patch) | |
| tree | 29f55730c0fdb1a225b4636cd8bec2568430cde0 /biology | |
| parent | 311dc39e3a0370ea03f3d9b4e9784f58ecc8a70b (diff) | |
| download | pkgsrc-eb95ae6ceb19887e7e51f5dd0ffcabb552862cff.tar.gz | |
biology/canu: fix SUBST blocks to actually find the Java code
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/canu/Makefile | 24 |
1 files changed, 7 insertions, 17 deletions
diff --git a/biology/canu/Makefile b/biology/canu/Makefile index 9067823efe6..ab94f268bcf 100644 --- a/biology/canu/Makefile +++ b/biology/canu/Makefile @@ -1,7 +1,7 @@ -# $NetBSD: Makefile,v 1.8 2020/05/14 18:30:05 rillig Exp $ +# $NetBSD: Makefile,v 1.9 2020/05/16 19:40:59 rillig Exp $ DISTNAME= canu-1.8 -PKGREVISION= 5 +PKGREVISION= 6 CATEGORIES= biology java MASTER_SITES= ${MASTER_SITE_GITHUB:=marbl/} GITHUB_TAG= v${PKGVERSION_NOREV} @@ -22,29 +22,19 @@ SUBST_SED.optimize+= -e 's|-O4||g' SUBST_SED.optimize+= -e 's|-funroll-loops||g' SUBST_SED.optimize+= -e 's|-fexpensive-optimizations||g' SUBST_SED.optimize+= -e 's|-finline-functions||g' -SUBST_FILES.optimize+= ${WRKSRC}/Makefile +SUBST_FILES.optimize+= Makefile SUBST_CLASSES+= jar SUBST_STAGE.jar= pre-configure -SUBST_SED.jar+= -e 's|\\$$bin/mhap-|${PREFIX}/${JAVAJARDIR}/mhap-|g' -SUBST_FILES.jar+= ${WRKSRC}/pipelines/canu/OverlapMhap.pm +SUBST_SED.jar+= -e 's|\\$$bin/\.\./share/java/classes/mhap-|${PREFIX}/${JAVAJARDIR}/mhap-|g' +SUBST_FILES.jar+= pipelines/canu/OverlapMhap.pm SUBST_CLASSES+= perl SUBST_STAGE.perl= pre-configure SUBST_SED.perl+= -e 's|$$FindBin::RealBin/../lib/site_perl|${PREFIX}/${SITE_PERL_REL}|g' -SUBST_FILES.perl+= ${WRKSRC}/pipelines/canu.pl +SUBST_FILES.perl+= pipelines/canu.pl -REPLACE_PERL+= bogart/*.pl -REPLACE_PERL+= pipelines/*.pl -REPLACE_PERL+= bogus/*.pl -REPLACE_PERL+= bogart-analysis/*.pl -REPLACE_PERL+= overlapBasedTrimming/*.pl -REPLACE_PERL+= overlapInCore-analysis/*.pl -REPLACE_PERL+= merTrim/*.pl -REPLACE_PERL+= erateEstimate/*.pl -REPLACE_PERL+= meryl/.pl -REPLACE_PERL+= fastq-utilities/*.pl -REPLACE_PERL+= *.pl +REPLACE_PERL+= *.pl */*.pl # May work on other 64-bit processors, but untested ONLY_FOR_PLATFORM= *-*-x86_64 |