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CVS commit: pkgsrc/biology/canu
Module Name: pkgsrc
Committed By: bacon
Date: Mon Jan 7 02:33:17 UTC 2019
Added Files:
pkgsrc/biology/canu: DESCR Makefile PLIST distinfo
pkgsrc/biology/canu/patches: patch-Makefile
patch-pipelines_canu_Defaults.pm patch-pipelines_canu_Execution.pm
patch-utility_objectStore.C
Log Message:
biology/canu: import canu-1.8
Canu is a fork of the Celera Assembler, designed for high-noise single-molecule
sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
Canu is a hierarchical assembly pipeline which runs in four steps:
Detect overlaps in high-noise sequences using MHAP
Generate corrected sequence consensus
Trim corrected sequences
Assemble trimmed corrected sequences
To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/canu/DESCR pkgsrc/biology/canu/Makefile \
pkgsrc/biology/canu/PLIST pkgsrc/biology/canu/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/canu/patches/patch-Makefile \
pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm \
pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm \
pkgsrc/biology/canu/patches/patch-utility_objectStore.C
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
Added files:
Index: pkgsrc/biology/canu/DESCR
diff -u /dev/null pkgsrc/biology/canu/DESCR:1.1
--- /dev/null Mon Jan 7 02:33:17 2019
+++ pkgsrc/biology/canu/DESCR Mon Jan 7 02:33:17 2019
@@ -0,0 +1,12 @@
+Canu is a fork of the Celera Assembler, designed for high-noise single-molecule
+sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
+
+Canu is a hierarchical assembly pipeline which runs in four steps:
+
+ Detect overlaps in high-noise sequences using MHAP
+
+ Generate corrected sequence consensus
+
+ Trim corrected sequences
+
+ Assemble trimmed corrected sequences
Index: pkgsrc/biology/canu/Makefile
diff -u /dev/null pkgsrc/biology/canu/Makefile:1.1
--- /dev/null Mon Jan 7 02:33:17 2019
+++ pkgsrc/biology/canu/Makefile Mon Jan 7 02:33:17 2019
@@ -0,0 +1,80 @@
+# $NetBSD: Makefile,v 1.1 2019/01/07 02:33:17 bacon Exp $
+
+DISTNAME= canu-1.8
+CATEGORIES= biology java
+MASTER_SITES= ${MASTER_SITE_GITHUB:=marbl/}
+GITHUB_TAG= v${PKGVERSION_NOREV}
+
+MAINTAINER= bacon%NetBSD.org@localhost
+HOMEPAGE= http://canu.readthedocs.io/
+COMMENT= Single molecule sequence assembler for genomes large and small
+LICENSE= gnu-gpl-v2
+
+DEPENDS+= gnuplot>0:../../graphics/gnuplot
+
+# Makefile compiles directly into ${DESTDIR}${PREFIX}
+SUBST_CLASSES+= optimize
+SUBST_STAGE.optimize= pre-configure
+SUBST_SED.optimize+= -e 's|-g3||g'
+SUBST_SED.optimize+= -e 's|-O3||g'
+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_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_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
+
+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
+
+# May work on other 64-bit processors, but untested
+ONLY_FOR_PLATFORM= *-*-x86_64
+
+USE_LANGUAGES= c c++
+USE_JAVA= run
+USE_JAVA2= 8
+USE_TOOLS+= gmake pax perl
+GCC_REQD+= 4.8
+
+WRKSRC= ${WRKDIR}/canu-${PKGVERSION_NOREV}/src
+MAKE_ENV+= DESTDIR=${WRKSRC}
+
+TMP_INST= ${WRKSRC}${PREFIX}/${OPSYS}-${MACHINE_ARCH:S/x86_64/amd64/}
+SITE_PERL_REL= lib/perl5/site_perl
+JAVAJARDIR= share/java/classes
+INSTALLATION_DIRS= bin ${JAVAJARDIR}
+
+post-extract:
+ ${CHMOD} -R g-w ${WRKDIR}
+
+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
+ cd ${TMP_INST}/lib/perl5 && ${PAX} -wr * ${DESTDIR}${PREFIX}/lib/perl5
+ cd ${TMP_INST}/share && ${PAX} -wr * ${DESTDIR}${PREFIX}/share
+
+.include "../../devel/boost-libs/buildlink3.mk"
+.include "../../lang/perl5/module.mk"
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/canu/PLIST
diff -u /dev/null pkgsrc/biology/canu/PLIST:1.1
--- /dev/null Mon Jan 7 02:33:17 2019
+++ pkgsrc/biology/canu/PLIST Mon Jan 7 02:33:17 2019
@@ -0,0 +1,80 @@
+@comment $NetBSD: PLIST,v 1.1 2019/01/07 02:33:17 bacon Exp $
+bin/alignGFA
+bin/bogart
+bin/bogus
+bin/canu
+bin/correctOverlaps
+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/generateCorrectionLayouts
+bin/loadCorrectedReads
+bin/loadErates
+bin/loadTrimmedReads
+bin/meryl
+bin/mhapConvert
+bin/mmapConvert
+bin/ovStoreBucketizer
+bin/ovStoreBuild
+bin/ovStoreConfig
+bin/ovStoreDump
+bin/ovStoreIndexer
+bin/ovStoreSorter
+bin/ovStoreStats
+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
+lib/perl5/site_perl/canu/Defaults.pm
+lib/perl5/site_perl/canu/Execution.pm
+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_PBSTorque.pm
+lib/perl5/site_perl/canu/Grid_SGE.pm
+lib/perl5/site_perl/canu/Grid_Slurm.pm
+lib/perl5/site_perl/canu/HaplotypeReads.pm
+lib/perl5/site_perl/canu/Meryl.pm
+lib/perl5/site_perl/canu/Output.pm
+lib/perl5/site_perl/canu/OverlapBasedTrimming.pm
+lib/perl5/site_perl/canu/OverlapErrorAdjustment.pm
+lib/perl5/site_perl/canu/OverlapInCore.pm
+lib/perl5/site_perl/canu/OverlapMMap.pm
+lib/perl5/site_perl/canu/OverlapMhap.pm
+lib/perl5/site_perl/canu/OverlapStore.pm
+lib/perl5/site_perl/canu/Report.pm
+lib/perl5/site_perl/canu/SequenceStore.pm
+lib/perl5/site_perl/canu/Unitig.pm
+share/java/classes/mhap-2.1.3.jar
Index: pkgsrc/biology/canu/distinfo
diff -u /dev/null pkgsrc/biology/canu/distinfo:1.1
--- /dev/null Mon Jan 7 02:33:17 2019
+++ pkgsrc/biology/canu/distinfo Mon Jan 7 02:33:17 2019
@@ -0,0 +1,10 @@
+$NetBSD: distinfo,v 1.1 2019/01/07 02:33:17 bacon Exp $
+
+SHA1 (canu-1.8.tar.gz) = 7dd79415aa5ecb95f05109f0d8d58f7cbfc336e9
+RMD160 (canu-1.8.tar.gz) = 78d4872b4034f526037ce225c699debd910bd586
+SHA512 (canu-1.8.tar.gz) = 650bc96675f371596f8e7748d4ab2d229f0262bf84cee8fed59af43d534d76095a72e4ba0b4a5ce9f561992268c317964cda2f6c89ee514f4920e2ba47fbc86c
+Size (canu-1.8.tar.gz) = 2465314 bytes
+SHA1 (patch-Makefile) = aa83003677cbb12558e438c776402ec48df0598d
+SHA1 (patch-pipelines_canu_Defaults.pm) = 55a4631d86abb1881b0cc997514d44c536209ea6
+SHA1 (patch-pipelines_canu_Execution.pm) = fbb080c06ea5d2393d1835a61771715d2aef0274
+SHA1 (patch-utility_objectStore.C) = c8407de79abbaf296f027f704080cc7e878b85f4
Index: pkgsrc/biology/canu/patches/patch-Makefile
diff -u /dev/null pkgsrc/biology/canu/patches/patch-Makefile:1.1
--- /dev/null Mon Jan 7 02:33:17 2019
+++ pkgsrc/biology/canu/patches/patch-Makefile Mon Jan 7 02:33:17 2019
@@ -0,0 +1,48 @@
+$NetBSD: patch-Makefile,v 1.1 2019/01/07 02:33:17 bacon Exp $
+
+# Template Makefile requires platform-specific defaults for each OS
+# To be sent upstream following commit
+
+--- Makefile.orig 2018-10-22 16:47:31.000000000 +0000
++++ Makefile
+@@ -545,6 +545,40 @@ endif
+ endif
+
+
++ifeq (${OSTYPE}, NetBSD)
++ CC ?= gcc
++ CXX ?= g++
++
++ # GCC
++ CXXFLAGS += -pthread -fopenmp -fPIC
++ LDFLAGS += -pthread -fopenmp -lm -lexecinfo
++
++ #CXXFLAGS += -Wall -Wextra -Wformat -Wno-unused -Wno-parentheses
++ CXXFLAGS += -Wall -Wextra -Wformat -Wno-unused-function -Wno-unused-parameter -Wno-unused-variable -Wno-char-subscripts -Wno-write-strings -Wno-sign-compare -Wno-format-truncation
++
++ # Google Performance Tools malloc and heapchecker (HEAPCHECK=normal)
++ #CXXFLAGS +=
++ #LDFLAGS += -ltcmalloc
++
++ # Google Performance Tools cpu profiler (CPUPROFILE=/path)
++ #CXXFLAGS +=
++ #LDFLAGS += -lprofiler
++
++ # callgrind
++ #CXXFLAGS += -g3 -Wa,--gstabs -save-temps
++
++ ifeq ($(BUILDOPTIMIZED), 1)
++ else
++ CXXFLAGS += -g3
++ endif
++
++ ifeq ($(BUILDDEBUG), 1)
++ else
++ CXXFLAGS += -O3 -finline-functions -fomit-frame-pointer
++ endif
++endif
++
++
+ ifneq (,$(findstring CYGWIN, ${OSTYPE}))
+ CC ?= gcc
+ CXX ?= g++
Index: pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm
diff -u /dev/null pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.1
--- /dev/null Mon Jan 7 02:33:17 2019
+++ pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm Mon Jan 7 02:33:17 2019
@@ -0,0 +1,24 @@
+$NetBSD: patch-pipelines_canu_Defaults.pm,v 1.1 2019/01/07 02:33:17 bacon Exp $
+
+# Add resource limits for SLURM
+# Upstream is considering a scheduler-independent approach to this feature
+
+--- pipelines/canu/Defaults.pm.orig 2018-06-22 08:20:52.000000000 +0000
++++ pipelines/canu/Defaults.pm
+@@ -812,6 +812,16 @@ sub setDefaults () {
+ setDefault("gridEngineArraySubmitID", undef, "Grid engine configuration, not documented");
+ setDefault("gridEngineJobID", undef, "Grid engine configuration, not documented");
+
++ ##### Slurm-specific parameters for controlling the number of
++ ##### cores / tasks dispatched per step or globally (WIP)
++
++ setDefault( 'slurmCormhapCoreLimit', undef, 'Maximum number of cores allocated for MHAP pre-computing and alignment within the correction phase' );
++ setDefault( 'slurmOvbCoreLimit', undef, 'Maximum number of single-core tasks dispatched for the ovlStore bucketizing step within the trimming phase' );
++ setDefault( 'slurmOvsCoreLimit', undef, 'Maximum number of single-core tasks dispatched for the ovlStore sorting step within the trimming phase' );
++ setDefault( 'slurmRedCoreLimit', undef, 'Maximum number of cores allocated for read error detection within the unitigging phase' );
++ setDefault( 'slurmArrayTaskLimit', undef, 'Maximum number of tasks permitted for each step throughout assembly' );
++ setDefault( 'slurmArrayCoreLimit', undef, 'Maximum number of cores allocated for each step throughout assembly' );
++
+ ##### Grid Engine Pipeline
+
+ setDefault("useGrid", 1, "If 'true', enable grid-based execution; if 'false', run all jobs on the local machine; if 'remote', create jobs for grid execution but do not submit; default 'true'");
Index: pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm
diff -u /dev/null pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.1
--- /dev/null Mon Jan 7 02:33:17 2019
+++ pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm Mon Jan 7 02:33:17 2019
@@ -0,0 +1,83 @@
+$NetBSD: patch-pipelines_canu_Execution.pm,v 1.1 2019/01/07 02:33:17 bacon Exp $
+
+# Add resource limits for SLURM
+# Upstream is considering a scheduler-independent approach to this feature
+
+--- pipelines/canu/Execution.pm.orig 2018-06-22 08:20:52.000000000 +0000
++++ pipelines/canu/Execution.pm
+@@ -303,10 +303,6 @@ sub skipStage ($$@) {
+ sub getInstallDirectory () {
+ my $installDir = $FindBin::RealBin;
+
+- if ($installDir =~ m!^(.*)/\w+-\w+/bin$!) {
+- $installDir = $1;
+- }
+-
+ return($installDir);
+ }
+
+@@ -694,8 +690,8 @@ sub submitScript ($$) {
+
+
+
+-sub buildGridArray ($$$$) {
+- my ($name, $bgn, $end, $opt) = @_;
++sub buildGridArray (@) {
++ my ( $name, $bgn, $end, $opt, $thr ) = @_;
+ my $off = 0;
+
+ # In some grids (SGE) this is the maximum size of an array job.
+@@ -725,8 +721,42 @@ sub buildGridArray ($$$$) {
+ $off = "-F \"$off\"";
+ }
+
+- $opt =~ s/ARRAY_NAME/$name/g; # Replace ARRAY_NAME with 'job name'
+- $opt =~ s/ARRAY_JOBS/$bgn-$end/g; # Replace ARRAY_JOBS with 'bgn-end'
++ if( $opt =~ m/(ARRAY_NAME)/ )
++ {
++ $opt =~ s/$1/$name/; # Replace ARRAY_NAME with 'job name'
++ }
++ elsif( $opt =~ m/(ARRAY_JOBS)/ )
++ {
++ $opt =~ s/$1/$bgn-$end/; # Replace ARRAY_JOBS with 'bgn-end'
++
++ if( lc( getGlobal( 'gridEngine' ) ) eq 'slurm' && $end > 1 )
++ {
++ if( $name =~ m/^cormhap_/i && defined getGlobal( 'slurmCormhapCoreLimit' ) )
++ {
++ $opt .= '%' . int( getGlobal( 'slurmCormhapCoreLimit' ) / $thr );
++ }
++ elsif( $name =~ m/^ovb_/i && defined getGlobal( 'slurmOvbCoreLimit' ) )
++ {
++ $opt .= '%' . getGlobal( 'slurmOvbCoreLimit' );
++ }
++ elsif( $name =~ m/^ovs_/i && defined getGlobal( 'slurmOvsCoreLimit' ) )
++ {
++ $opt .= '%' . getGlobal( 'slurmOvsCoreLimit' );
++ }
++ elsif( $name =~ m/^red_/i && defined getGlobal( 'slurmRedCoreLimit' ) )
++ {
++ $opt .= '%' . int( getGlobal( 'slurmRedCoreLimit' ) / $thr );
++ }
++ elsif( defined getGlobal( 'slurmArrayTaskLimit' ) )
++ {
++ $opt .= '%' . getGlobal( 'slurmArrayTaskLimit' );
++ }
++ elsif( defined getGlobal( 'slurmArrayCoreLimit' ) )
++ {
++ $opt .= '%' . int( getGlobal( 'slurmArrayCoreLimit' ) / $thr );
++ }
++ }
++ }
+
+ return($opt, $off);
+ }
+@@ -870,7 +900,7 @@ sub buildGridJob ($$$$$$$$$) {
+ 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, $script);
+
Index: pkgsrc/biology/canu/patches/patch-utility_objectStore.C
diff -u /dev/null pkgsrc/biology/canu/patches/patch-utility_objectStore.C:1.1
--- /dev/null Mon Jan 7 02:33:17 2019
+++ pkgsrc/biology/canu/patches/patch-utility_objectStore.C Mon Jan 7 02:33:17 2019
@@ -0,0 +1,19 @@
+$NetBSD: patch-utility_objectStore.C,v 1.1 2019/01/07 02:33:17 bacon Exp $
+
+# NetBSD does not provide WEXITED
+# Empty bitmask should suffice in this case
+
+--- utility/objectStore.C.orig 2018-12-23 01:57:06.000000000 +0000
++++ utility/objectStore.C
+@@ -286,6 +286,11 @@ fetchFromObjectStore(char *requested) {
+ // Otherwise, we're still the parent, so wait for the (-1 == any) child
+ // process to terminate.
+
++// NetBSD does not provide WEXITED so send empty bitmask
++#ifdef __NetBSD__
++#define WEXITED 0
++#endif
++
+ waitpid(-1, &err, WEXITED);
+
+ if ((WIFEXITED(err)) &&
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