svn commit: r548685 - in head/biology/canu: . files
Jason W. Bacon
jwb at FreeBSD.org
Mon Sep 14 22:27:38 UTC 2020
Author: jwb
Date: Mon Sep 14 22:27:37 2020
New Revision: 548685
URL: https://svnweb.freebsd.org/changeset/ports/548685
Log:
biology/canu: Upgrade to 2.1
Numerous functional improvements for ease of use and output quality
A few bug fixes
Reported by: portscout
Modified:
head/biology/canu/Makefile
head/biology/canu/distinfo
head/biology/canu/files/patch-pipelines_canu_Execution.pm
head/biology/canu/pkg-plist
Modified: head/biology/canu/Makefile
==============================================================================
--- head/biology/canu/Makefile Mon Sep 14 22:20:53 2020 (r548684)
+++ head/biology/canu/Makefile Mon Sep 14 22:27:37 2020 (r548685)
@@ -1,9 +1,10 @@
# $FreeBSD$
PORTNAME= canu
-DISTVERSIONPREFIX= v
-DISTVERSION= 2.0
+DISTVERSION= 2.1
CATEGORIES= biology java perl5
+# Github auto-generated tarballs lack submodules
+MASTER_SITES= https://github.com/marbl/canu/releases/download/v2.1/
MAINTAINER= jwb at FreeBSD.org
COMMENT= Single molecule sequence assembler
@@ -12,17 +13,17 @@ LICENSE= GPLv2
LICENSE_FILE= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL
BROKEN_powerpc64= fails to build: utgcns/libboost/boost/smart_ptr/detail/sp_counted_impl.hpp:81:5: error: 'get_deleter' declared as a 'virtual' field
+NOT_FOR_ARCHS= armv6 armv7 i386 powerpc
+NOT_FOR_ARCHS_REASON= __int128 is not supported on this target
LIB_DEPENDS= libboost_regex.so:devel/boost-libs
RUN_DEPENDS= gnuplot:math/gnuplot
USES= compiler:openmp gmake perl5
USE_JAVA= yes
-USE_GITHUB= yes
JAVA_RUN= yes
JAVA_VERSION= 1.8+
-GH_ACCOUNT= marbl
WRKSRC_SUBDIR= src
# Upstream Makefile compiles directly into ${DESTDIR}${PREFIX} rather than
@@ -43,24 +44,22 @@ pre-configure:
-e 's|-fexpensive-optimizations||g' \
${WRKSRC}/Makefile
@${REINPLACE_CMD} \
- -e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}/canu|g' \
+ -e 's|RealBin/../lib/site_perl|RealBin/../${SITE_PERL_REL}/canu|g' \
${WRKSRC}/pipelines/canu.pl
# Upstream does not want to use lib/perl5/site_perl
post-build:
- @${MKDIR} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5
- ${MV} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/site_perl \
- ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5
+ @${MKDIR} ${WRKSRC}/build/lib/perl5
+ ${MV} ${WRKSRC}/build/lib/site_perl ${WRKSRC}/build/lib/perl5
do-install:
@${MKDIR} ${STAGEDIR}${PREFIX}
- (cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \
- ${COPYTREE_BIN} bin ${STAGEDIR}${PREFIX})
- # STRIP_CMD fails without this on 11.1 under poudriere
+ (cd ${WRKSRC}/build && ${COPYTREE_BIN} bin ${STAGEDIR}${PREFIX})
+ # STRIP_CMD fails without this under poudriere
@${CHMOD} u+w ${STAGEDIR}${PREFIX}/bin/*
@${STRIP_CMD} \
`file ${STAGEDIR}${PREFIX}/bin/* | ${GREP} ELF | cut -d : -f 1`
- (cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \
+ (cd ${WRKSRC}/build && \
${COPYTREE_SHARE} "lib share" ${STAGEDIR}${PREFIX})
.include <bsd.port.post.mk>
Modified: head/biology/canu/distinfo
==============================================================================
--- head/biology/canu/distinfo Mon Sep 14 22:20:53 2020 (r548684)
+++ head/biology/canu/distinfo Mon Sep 14 22:27:37 2020 (r548685)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1584624503
-SHA256 (marbl-canu-v2.0_GH0.tar.gz) = e2e6e8b5ec4dd4cfba5e372f4a64b2c01fbd544d4b5867746021f10771a6f4ef
-SIZE (marbl-canu-v2.0_GH0.tar.gz) = 3443777
+TIMESTAMP = 1599584712
+SHA256 (canu-2.1.tar.gz) = 73c70d2d6326bdaf471549f2d1eb7a1bf1e0fbf45cdc4a830bd6ce9fe3f3c231
+SIZE (canu-2.1.tar.gz) = 3313120
Modified: head/biology/canu/files/patch-pipelines_canu_Execution.pm
==============================================================================
--- head/biology/canu/files/patch-pipelines_canu_Execution.pm Mon Sep 14 22:20:53 2020 (r548684)
+++ head/biology/canu/files/patch-pipelines_canu_Execution.pm Mon Sep 14 22:27:37 2020 (r548685)
@@ -1,20 +1,9 @@
---- pipelines/canu/Execution.pm.orig 2018-10-22 16:47:31 UTC
+--- pipelines/canu/Execution.pm.orig 2020-09-07 19:08:24 UTC
+++ pipelines/canu/Execution.pm
-@@ -333,10 +333,6 @@ sub resetIteration ($) {
- sub getInstallDirectory () {
- my $installDir = $FindBin::RealBin;
+@@ -762,8 +762,8 @@ sub submitScript ($$) {
-- if ($installDir =~ m!^(.*)/\w+-\w+/bin$!) {
-- $installDir = $1;
-- }
--
- return($installDir);
- }
-@@ -784,8 +780,8 @@ sub submitScript ($$) {
-
-
-sub buildGridArray ($$$$) {
- my ($name, $bgn, $end, $opt) = @_;
+sub buildGridArray (@) {
@@ -22,7 +11,7 @@
my $off = 0;
# In some grids (SGE) this is the maximum size of an array job.
-@@ -823,8 +819,42 @@ sub buildGridArray ($$$$) {
+@@ -803,9 +803,43 @@ sub buildGridArray ($$$$) {
$off = "-F \"$off\"";
}
@@ -35,7 +24,7 @@
+ elsif( $opt =~ m/(ARRAY_JOBS)/ )
+ {
+ $opt =~ s/$1/$bgn-$end/; # Replace ARRAY_JOBS with 'bgn-end'
-+
+
+ if( lc( getGlobal( 'gridEngine' ) ) eq 'slurm' && $end > 1 )
+ {
+ if( $name =~ m/^cormhap_/i && defined getGlobal( 'slurmCormhapCoreLimit' ) )
@@ -64,10 +53,11 @@
+ }
+ }
+ }
-
++
return($opt, $off);
}
-@@ -973,7 +1003,7 @@ sub buildGridJob ($$$$$$$$$) {
+
+@@ -951,7 +985,7 @@ sub buildGridJob ($$$$$$$$$) {
my $jobNameT = makeUniqueJobName($jobType, $asm);
my ($jobName, $jobOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayName"));
Modified: head/biology/canu/pkg-plist
==============================================================================
--- head/biology/canu/pkg-plist Mon Sep 14 22:20:53 2020 (r548684)
+++ head/biology/canu/pkg-plist Mon Sep 14 22:27:37 2020 (r548685)
@@ -5,6 +5,7 @@ bin/canu
bin/canu-time
bin/canu.defaults
bin/correctOverlaps
+bin/draw-tig
bin/dumpBlob
bin/edalign
bin/errorEstimate
@@ -13,14 +14,14 @@ bin/filterCorrectionLayouts
bin/filterCorrectionOverlaps
bin/findErrors
bin/findErrors-Dump
+bin/fixErrors
bin/generateCorrectionLayouts
+bin/layoutReads
bin/loadCorrectedReads
bin/loadErates
bin/loadTrimmedReads
bin/mergeRanges
bin/meryl
-bin/meryl-import
-bin/meryl-lookup
bin/mhapConvert
bin/mmapConvert
bin/ovStoreBucketizer
@@ -37,7 +38,6 @@ bin/overlapInCore
bin/overlapInCorePartition
bin/overlapPair
bin/prefixEditDistance-matchLimitGenerate
-bin/sequence
bin/splitHaplotype
bin/splitReads
bin/sqStoreCreate
@@ -45,12 +45,10 @@ bin/sqStoreDumpFASTQ
bin/sqStoreDumpMetaData
bin/tgStoreCompress
bin/tgStoreDump
-bin/tgStoreFilter
bin/tgStoreLoad
bin/tgTigDisplay
bin/trimReads
bin/utgcns
-bin/wtdbgConvert
lib/libcanu.a
%%SITE_PERL%%/canu/Configure.pm
%%SITE_PERL%%/canu/Consensus.pm
@@ -77,6 +75,3 @@ lib/libcanu.a
%%SITE_PERL%%/canu/SequenceStore.pm
%%SITE_PERL%%/canu/Unitig.pm
%%JAVAJARDIR%%/mhap-2.1.3.jar
-share/sequence/pacbio
-share/sequence/pacbio-hifi
-share/sequence/ultra-long-nanopore
More information about the svn-ports-all
mailing list