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[pkgsrc/trunk]: pkgsrc/biology/canu biology/canu: import canu-1.8
details: https://anonhg.NetBSD.org/pkgsrc/rev/1a35146c61ed
branches: trunk
changeset: 389705:1a35146c61ed
user: bacon <bacon%pkgsrc.org@localhost>
date: Mon Jan 07 02:33:17 2019 +0000
description:
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
diffstat:
biology/canu/DESCR | 12 ++
biology/canu/Makefile | 80 +++++++++++++++++
biology/canu/PLIST | 80 +++++++++++++++++
biology/canu/distinfo | 10 ++
biology/canu/patches/patch-Makefile | 48 ++++++++++
biology/canu/patches/patch-pipelines_canu_Defaults.pm | 24 +++++
biology/canu/patches/patch-pipelines_canu_Execution.pm | 83 ++++++++++++++++++
biology/canu/patches/patch-utility_objectStore.C | 19 ++++
8 files changed, 356 insertions(+), 0 deletions(-)
diffs (truncated from 388 to 300 lines):
diff -r df1b86add850 -r 1a35146c61ed biology/canu/DESCR
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/canu/DESCR Mon Jan 07 02:33:17 2019 +0000
@@ -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
diff -r df1b86add850 -r 1a35146c61ed biology/canu/Makefile
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/canu/Makefile Mon Jan 07 02:33:17 2019 +0000
@@ -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"
diff -r df1b86add850 -r 1a35146c61ed biology/canu/PLIST
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/canu/PLIST Mon Jan 07 02:33:17 2019 +0000
@@ -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
diff -r df1b86add850 -r 1a35146c61ed biology/canu/distinfo
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/canu/distinfo Mon Jan 07 02:33:17 2019 +0000
@@ -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
diff -r df1b86add850 -r 1a35146c61ed biology/canu/patches/patch-Makefile
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/canu/patches/patch-Makefile Mon Jan 07 02:33:17 2019 +0000
@@ -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++
diff -r df1b86add850 -r 1a35146c61ed biology/canu/patches/patch-pipelines_canu_Defaults.pm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/canu/patches/patch-pipelines_canu_Defaults.pm Mon Jan 07 02:33:17 2019 +0000
@@ -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'");
diff -r df1b86add850 -r 1a35146c61ed biology/canu/patches/patch-pipelines_canu_Execution.pm
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/canu/patches/patch-pipelines_canu_Execution.pm Mon Jan 07 02:33:17 2019 +0000
@@ -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);
+ }
+
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