[pkgsrc/trunk]: pkgsrc/biology/canu biology/canu: fix SUBST blocks to actuall...

[rillig <rillig%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/00e1c33d3669
branches:  trunk
changeset: 431861:00e1c33d3669
user:      rillig <rillig%pkgsrc.org@localhost>
date:      Sat May 16 19:40:59 2020 +0000

description:
biology/canu: fix SUBST blocks to actually find the Java code

diffstat:

 biology/canu/Makefile |  24 +++++++-----------------
 1 files changed, 7 insertions(+), 17 deletions(-)

diffs (48 lines):

diff -r 9d227618958e -r 00e1c33d3669 biology/canu/Makefile
--- a/biology/canu/Makefile     Sat May 16 19:38:35 2020 +0000
+++ b/biology/canu/Makefile     Sat May 16 19:40:59 2020 +0000
@@ -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|-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