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canu: Update to 2.2
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Thu May 18 10:54:17 2023 -0500
Changeset: 152eeb58928353a3153e981a3912b6266b3f3e60
Modified Files:
canu/Makefile
canu/PLIST
canu/distinfo
canu/patches/patch-pipelines_canu_Defaults.pm
Added Files:
canu/patches/patch-pipelines_canu_Execution.pm
canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp
canu/patches/patch-utility_src_parasail_internal__sse.h
canu/patches/patch-utility_src_utility_align-ssw.H
canu/patches/patch-utility_src_utility_files.H
canu/patches/patch-utility_src_utility_logging.H
canu/patches/patch-utility_src_utility_system.H
canu/patches/patch-utility_src_utility_types.H
Log Message:
canu: Update to 2.2
Import patches from FreeBSD port
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=152eeb58928353a3153e981a3912b6266b3f3e60
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
canu/Makefile | 13 ++--
canu/PLIST | 20 +++---
canu/distinfo | 16 +++--
canu/patches/patch-pipelines_canu_Defaults.pm | 7 +--
canu/patches/patch-pipelines_canu_Execution.pm | 72 ++++++++++++++++++++++
...boost_boost_smart__ptr_detail_shared__count.hpp | 14 +++++
.../patch-utility_src_parasail_internal__sse.h | 16 +++++
canu/patches/patch-utility_src_utility_align-ssw.H | 16 +++++
canu/patches/patch-utility_src_utility_files.H | 15 +++++
canu/patches/patch-utility_src_utility_logging.H | 15 +++++
canu/patches/patch-utility_src_utility_system.H | 15 +++++
canu/patches/patch-utility_src_utility_types.H | 15 +++++
12 files changed, 209 insertions(+), 25 deletions(-)
diffs:
diff --git a/canu/Makefile b/canu/Makefile
index 09cb2bda65..b54a897aff 100644
--- a/canu/Makefile
+++ b/canu/Makefile
@@ -2,8 +2,9 @@
DISTNAME= canu-2.2
CATEGORIES= biology java
-MASTER_SITES= ${MASTER_SITE_GITHUB:=marbl/}
-GITHUB_TAG= v${PKGVERSION_NOREV}
+# Github-generaged files are incomplete
+MASTER_SITES= https://github.com/marbl/canu/releases/download/v${PKGVERSION_NOREV}/
+EXTRACT_SUFX= .tar.xz
MAINTAINER= bacon%NetBSD.org@localhost
HOMEPAGE= https://canu.readthedocs.io/
@@ -21,12 +22,12 @@ 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+= 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
@@ -51,7 +52,7 @@ USE_TOOLS+= gmake pax perl
WRKSRC= ${WRKDIR}/canu-${PKGVERSION_NOREV}/src
MAKE_ENV+= DESTDIR=${WRKSRC}
-TMP_INST= ${WRKSRC}${PREFIX}/${OPSYS}-${MACHINE_ARCH:S/x86_64/amd64/}
+TMP_INST= ${WRKSRC}/build
SITE_PERL_REL= lib/perl5/site_perl
JAVAJARDIR= share/java/classes
INSTALLATION_DIRS= bin ${JAVAJARDIR}
@@ -59,10 +60,10 @@ INSTALLATION_DIRS= bin ${JAVAJARDIR}
post-extract:
${CHMOD} -R g-w ${WRKDIR}
+# Upstream does not want to use lib/perl5/site_perl
post-build:
${MKDIR} ${TMP_INST}/lib/perl5
${MV} ${TMP_INST}/lib/site_perl ${TMP_INST}/lib/perl5
- ${RM} -f ${TMP_INST}/bin/canu.defaults
do-install:
cd ${TMP_INST}/bin && ${PAX} -wr * ${DESTDIR}${PREFIX}/bin
diff --git a/canu/PLIST b/canu/PLIST
index d8d1300709..0669bf87be 100644
--- a/canu/PLIST
+++ b/canu/PLIST
@@ -1,25 +1,26 @@
@comment $NetBSD$
bin/alignGFA
bin/bogart
-bin/bogus
bin/canu
+bin/canu-time
+bin/canu.defaults
bin/correctOverlaps
+bin/draw-tig
bin/dumpBlob
bin/edalign
bin/errorEstimate
bin/falconsense
-bin/fastqAnalyze
-bin/fastqSample
-bin/fastqSimulate
-bin/fastqSimulate-sort
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/mhapConvert
bin/mmapConvert
@@ -30,29 +31,25 @@ bin/ovStoreDump
bin/ovStoreIndexer
bin/ovStoreSorter
bin/ovStoreStats
+bin/overlapAlign
+bin/overlapCheck
bin/overlapConvert
bin/overlapImport
bin/overlapInCore
bin/overlapInCorePartition
bin/overlapPair
bin/prefixEditDistance-matchLimitGenerate
-bin/readConsensus
-bin/sequence
bin/splitHaplotype
bin/splitReads
bin/sqStoreCreate
-bin/sqStoreCreatePartition
bin/sqStoreDumpFASTQ
bin/sqStoreDumpMetaData
bin/tgStoreCompress
-bin/tgStoreCoverageStat
bin/tgStoreDump
-bin/tgStoreFilter
bin/tgStoreLoad
bin/tgTigDisplay
bin/trimReads
bin/utgcns
-bin/wtdbgConvert
lib/perl5/site_perl/canu/Configure.pm
lib/perl5/site_perl/canu/Consensus.pm
lib/perl5/site_perl/canu/CorrectReads.pm
@@ -62,6 +59,7 @@ lib/perl5/site_perl/canu/Grid.pm
lib/perl5/site_perl/canu/Grid_Cloud.pm
lib/perl5/site_perl/canu/Grid_DNANexus.pm
lib/perl5/site_perl/canu/Grid_LSF.pm
+lib/perl5/site_perl/canu/Grid_Local.pm
lib/perl5/site_perl/canu/Grid_PBSTorque.pm
lib/perl5/site_perl/canu/Grid_SGE.pm
lib/perl5/site_perl/canu/Grid_Slurm.pm
diff --git a/canu/distinfo b/canu/distinfo
index d277a05c0c..81bd3672ca 100644
--- a/canu/distinfo
+++ b/canu/distinfo
@@ -1,7 +1,15 @@
$NetBSD$
-BLAKE2s (canu-2.2.tar.gz) = ecb7c025c7cd24d90403844ac9d62bc4245fe1b63efb8bc18354542f1920a679
-SHA512 (canu-2.2.tar.gz) = 9c4389994857bdd8c75d6e1b6e9f5bba765d89716b3cc037ae8066b62fddd0c7028ce10ecdaacc762c641ea96831b95dcef07e0a27e09afe758377e1900b2694
-Size (canu-2.2.tar.gz) = 2068564 bytes
+BLAKE2s (canu-2.2.tar.xz) = 5b585a2e0a31c2181817798b5f267dd4cf43c3ffeba4b0a04ffc8021a4603aed
+SHA512 (canu-2.2.tar.xz) = af08874a319dd5fd6bbe666c8a5d0a43b7c0caaaca3a3cbf4d3fe022d6d6b8c14cd967c2e26f4fbf571129be240dcb65e92fe61fad1e51d554f15254d0b6ce8f
+Size (canu-2.2.tar.xz) = 2400192 bytes
SHA1 (patch-Makefile) = aa83003677cbb12558e438c776402ec48df0598d
-SHA1 (patch-pipelines_canu_Defaults.pm) = 55a4631d86abb1881b0cc997514d44c536209ea6
+SHA1 (patch-pipelines_canu_Defaults.pm) = 5ecea8ebac667499916b0243f34dc25838992444
+SHA1 (patch-pipelines_canu_Execution.pm) = 75c019a93f5b6a4491191b4f32931ac0b8435421
+SHA1 (patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp) = fd219645141ebe9d6f23153a2a2b0f56abc103af
+SHA1 (patch-utility_src_parasail_internal__sse.h) = 3eca097b64273ada2df6f9be895823980ea79902
+SHA1 (patch-utility_src_utility_align-ssw.H) = 146e1959207dfe1deaae7f8f9809ed72be116841
+SHA1 (patch-utility_src_utility_files.H) = bc28dfd6957a2e2928b5df6a0e1d08c8ba5b2c27
+SHA1 (patch-utility_src_utility_logging.H) = 13e9ced966710cef4a2d38fd2b752f8a726ba07b
+SHA1 (patch-utility_src_utility_system.H) = e0bab7ed20431948845fac907584215c0b891406
+SHA1 (patch-utility_src_utility_types.H) = 2d7f94b774c0d557b5f4ea89294fd82b1341f9d3
diff --git a/canu/patches/patch-pipelines_canu_Defaults.pm b/canu/patches/patch-pipelines_canu_Defaults.pm
index 668ab99f50..01da751843 100644
--- a/canu/patches/patch-pipelines_canu_Defaults.pm
+++ b/canu/patches/patch-pipelines_canu_Defaults.pm
@@ -1,11 +1,10 @@
$NetBSD$
-# Add resource limits for SLURM
-# Upstream is considering a scheduler-independent approach to this feature
+# Better task limit control under slurm
---- pipelines/canu/Defaults.pm.orig 2018-06-22 08:20:52.000000000 +0000
+--- pipelines/canu/Defaults.pm.orig 2018-10-22 16:47:31 UTC
+++ pipelines/canu/Defaults.pm
-@@ -812,6 +812,16 @@ sub setDefaults () {
+@@ -917,6 +917,16 @@ sub setDefaults () {
setDefault("gridEngineArraySubmitID", undef, "Grid engine configuration, not documented");
setDefault("gridEngineJobID", undef, "Grid engine configuration, not documented");
diff --git a/canu/patches/patch-pipelines_canu_Execution.pm b/canu/patches/patch-pipelines_canu_Execution.pm
new file mode 100644
index 0000000000..e145cf3402
--- /dev/null
+++ b/canu/patches/patch-pipelines_canu_Execution.pm
@@ -0,0 +1,72 @@
+$NetBSD$
+
+# Better task limit control under slurm
+
+--- pipelines/canu/Execution.pm.orig 2020-09-07 19:08:24 UTC
++++ pipelines/canu/Execution.pm
+@@ -762,8 +762,8 @@ sub submitScript ($$) {
+
+
+
+-sub buildGridArray ($$$$) {
+- my ($name, $bgn, $end, $opt) = @_;
++sub buildGridArray (@) {
++ my ( $name, $bgn, $end, $opt, $thr ) = @_;
+ my $off = 0;
+
+ # In some grids (SGE) this is the maximum size of an array job.
+@@ -803,9 +803,43 @@ sub buildGridArray ($$$$) {
+ $off = "-F \"$off\"";
+ }
+
+- $opt =~ s/ARRAY_NAME/$name/g; # Replace ARRAY_NAME with 'job name'
+- $opt =~ s/ARRAY_JOBS/$bgn-$end/g; # Replace ARRAY_JOBS with 'bgn-end'
++ if( $opt =~ m/(ARRAY_NAME)/ )
++ {
++ $opt =~ s/$1/$name/; # Replace ARRAY_NAME with 'job name'
++ }
++ elsif( $opt =~ m/(ARRAY_JOBS)/ )
++ {
++ $opt =~ s/$1/$bgn-$end/; # Replace ARRAY_JOBS with 'bgn-end'
+
++ if( lc( getGlobal( 'gridEngine' ) ) eq 'slurm' && $end > 1 )
++ {
++ if( $name =~ m/^cormhap_/i && defined getGlobal( 'slurmCormhapCoreLimit' ) )
++ {
++ $opt .= '%' . int( getGlobal( 'slurmCormhapCoreLimit' ) / $thr );
++ }
++ elsif( $name =~ m/^ovb_/i && defined getGlobal( 'slurmOvbCoreLimit' ) )
++ {
++ $opt .= '%' . getGlobal( 'slurmOvbCoreLimit' );
++ }
++ elsif( $name =~ m/^ovs_/i && defined getGlobal( 'slurmOvsCoreLimit' ) )
++ {
++ $opt .= '%' . getGlobal( 'slurmOvsCoreLimit' );
++ }
++ elsif( $name =~ m/^red_/i && defined getGlobal( 'slurmRedCoreLimit' ) )
++ {
++ $opt .= '%' . int( getGlobal( 'slurmRedCoreLimit' ) / $thr );
++ }
++ elsif( defined getGlobal( 'slurmArrayTaskLimit' ) )
++ {
++ $opt .= '%' . getGlobal( 'slurmArrayTaskLimit' );
++ }
++ elsif( defined getGlobal( 'slurmArrayCoreLimit' ) )
++ {
++ $opt .= '%' . int( getGlobal( 'slurmArrayCoreLimit' ) / $thr );
++ }
++ }
++ }
++
+ return($opt, $off);
+ }
+
+@@ -951,7 +985,7 @@ sub buildGridJob ($$$$$$$$$) {
+ my $jobNameT = makeUniqueJobName($jobType, $asm);
+
+ my ($jobName, $jobOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayName"));
+- my ($arrayOpt, $arrayOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayOption"));
++ my ( $arrayOpt, $arrayOff ) = buildGridArray( $jobNameT, $bgnJob, $endJob, getGlobal( "gridEngineArrayOption" ), $thr );
+
+ my $outputOption = buildOutputOption($path, $script);
+
diff --git a/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp b/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp
new file mode 100644
index 0000000000..c52437fa59
--- /dev/null
+++ b/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Portability
+
+--- utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp.orig 2021-12-18 13:01:24 UTC
++++ utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp
+@@ -25,6 +25,7 @@
+ #include <boost/config.hpp>
+ #include <boost/checked_delete.hpp>
+ #include <boost/throw_exception.hpp>
++#include <boost/detail/sp_typeinfo.hpp>
+ #include <boost/smart_ptr/bad_weak_ptr.hpp>
+ #include <boost/smart_ptr/detail/sp_counted_base.hpp>
+ #include <boost/smart_ptr/detail/sp_counted_impl.hpp>
diff --git a/canu/patches/patch-utility_src_parasail_internal__sse.h b/canu/patches/patch-utility_src_parasail_internal__sse.h
new file mode 100644
index 0000000000..28e550e08a
--- /dev/null
+++ b/canu/patches/patch-utility_src_parasail_internal__sse.h
@@ -0,0 +1,16 @@
+$NetBSD$
+
+# Portability
+
+--- utility/src/parasail/internal_sse.h.orig 2021-12-17 22:10:09 UTC
++++ utility/src/parasail/internal_sse.h
+@@ -10,7 +10,8 @@
+
+ #include <stdint.h>
+
+-#include <emmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde.h>
+
+ #include "parasail.h"
+
diff --git a/canu/patches/patch-utility_src_utility_align-ssw.H b/canu/patches/patch-utility_src_utility_align-ssw.H
new file mode 100644
index 0000000000..e0cf210ade
--- /dev/null
+++ b/canu/patches/patch-utility_src_utility_align-ssw.H
@@ -0,0 +1,16 @@
+$NetBSD$
+
+# Portability
+
+--- utility/src/utility/align-ssw.H.orig 2021-12-17 22:12:23 UTC
++++ utility/src/utility/align-ssw.H
+@@ -33,7 +33,8 @@
+ #include <stdio.h>
+ #include <stdint.h>
+ #include <string.h>
+-#include <emmintrin.h>
++#define SIMDE_ENABLE_NATIVE_ALIASES
++#include <simde.h.h>
+
+
+ #define MAPSTR "MIDNSHP=X"
diff --git a/canu/patches/patch-utility_src_utility_files.H b/canu/patches/patch-utility_src_utility_files.H
new file mode 100644
index 0000000000..fda94da303
--- /dev/null
+++ b/canu/patches/patch-utility_src_utility_files.H
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Portability
+
+--- utility/src/utility/files.H.orig 2021-12-17 20:57:15 UTC
++++ utility/src/utility/files.H
+@@ -22,7 +22,7 @@
+
+ #include "types.H"
+ #include <vector>
+-
++#include <cmath>
+
+ // Provides a safe and reliable mechanism for reading / writing
+ // binary data.
diff --git a/canu/patches/patch-utility_src_utility_logging.H b/canu/patches/patch-utility_src_utility_logging.H
new file mode 100644
index 0000000000..c687a302d8
--- /dev/null
+++ b/canu/patches/patch-utility_src_utility_logging.H
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Portability
+
+--- utility/src/utility/logging.H.orig 2023-05-18 15:39:08.832210910 +0000
++++ utility/src/utility/logging.H
+@@ -20,6 +20,8 @@
+ #ifndef LOGGING_H
+ #define LOGGING_H
+
++#include <stdarg.h>
++
+ #include "types.H"
+ #include "files.H"
+
diff --git a/canu/patches/patch-utility_src_utility_system.H b/canu/patches/patch-utility_src_utility_system.H
new file mode 100644
index 0000000000..97bb2c2211
--- /dev/null
+++ b/canu/patches/patch-utility_src_utility_system.H
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Portability
+
+--- utility/src/utility/system.H.orig 2021-12-17 20:57:47 UTC
++++ utility/src/utility/system.H
+@@ -23,7 +23,7 @@
+ #include "types.H"
+
+ #include <signal.h>
+-
++#include <cmath>
+
+
+ double getTime(void);
diff --git a/canu/patches/patch-utility_src_utility_types.H b/canu/patches/patch-utility_src_utility_types.H
new file mode 100644
index 0000000000..53f199c90a
--- /dev/null
+++ b/canu/patches/patch-utility_src_utility_types.H
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Portability
+
+--- utility/src/utility/types.H.orig 2021-12-17 20:58:13 UTC
++++ utility/src/utility/types.H
+@@ -55,7 +55,7 @@
+ #include <ctype.h>
+
+ #include <float.h>
+-#include <math.h>
++#include <cmath>
+
+ #include <assert.h>
+ #include <errno.h>
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