Add canu: Single molecule sequence assembler for genomes large and small

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: Add canu: Single molecule sequence assembler for genomes large and small
From: Jason Bacon <bacon4000%gmail.com@localhost>
Date: Thu, 24 May 2018 17:31:28 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Thu May 24 12:31:28 2018 -0500
Changeset:	d669ea0c88571ef7bf760fac33b68edcb9673888

Modified Files:
	Makefile
Added Files:
	canu/DESCR
	canu/Makefile
	canu/PLIST
	canu/TODO
	canu/distinfo
	canu/patches/patch-pipelines_canu_Execution.pm

Log Message:
Add canu: 	Single molecule sequence assembler for genomes large and small

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=d669ea0c88571ef7bf760fac33b68edcb9673888

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                                       |  1 +
 canu/DESCR                                     |  1 +
 canu/Makefile                                  | 85 +++++++++++++++++++++++
 canu/PLIST                                     | 93 ++++++++++++++++++++++++++
 canu/TODO                                      |  1 +
 canu/distinfo                                  |  7 ++
 canu/patches/patch-pipelines_canu_Execution.pm | 16 +++++
 7 files changed, 204 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index b64ed3b526..3abefddfe8 100644
--- a/Makefile
+++ b/Makefile
@@ -320,6 +320,7 @@ SUBDIR+=	canna-lib
 SUBDIR+=	canna-server
 SUBDIR+=	canto-curses
 SUBDIR+=	canto-daemon
+SUBDIR+=	canu
 SUBDIR+=	capicxx-core-runtime
 SUBDIR+=	cardpeek
 SUBDIR+=	cargo
diff --git a/canu/DESCR b/canu/DESCR
new file mode 100644
index 0000000000..77b960193b
--- /dev/null
+++ b/canu/DESCR
@@ -0,0 +1 @@
+A single molecule sequence assembler for genomes large and small.
diff --git a/canu/Makefile b/canu/Makefile
new file mode 100644
index 0000000000..868031a68b
--- /dev/null
+++ b/canu/Makefile
@@ -0,0 +1,85 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Thu Jul 20 18:34:44 CDT 2017               #
+###########################################################
+
+DISTNAME=	canu-${PV}
+CATEGORIES=	biology java
+MASTER_SITES=	${MASTER_SITE_GITHUB:=marbl/}
+GITHUB_PROJECT=	canu
+GITHUB_TAG=	v${PV}
+
+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
+
+# Screwy Makefile compiles directly into ${DESTDIR}${PREFIX}
+SUBST_CLASSES+=		optimize
+SUBST_STAGE.optimize=	post-patch
+SUBST_SED.optimize+=	-e 's|-O4|-O2|g'
+SUBST_SED.optimize+=	-e 's|-funroll-loops||g'
+SUBST_SED.optimize+=	-e 's|-fexpensive-optimizations||g'
+SUBST_FILES.optimize+=	${WRKSRC}/Makefile
+
+SUBST_CLASSES+=		jar
+SUBST_STAGE.jar=	post-patch
+SUBST_SED.jar=		-e 's|\\$$bin/mhap-|${PREFIX}/${JAVAJARDIR}/mhap-|g'
+SUBST_FILES.jar=	${WRKSRC}/pipelines/canu/OverlapMhap.pm
+
+SUBST_CLASSES+=		perl
+SUBST_STAGE.perl=	post-patch
+SUBST_SED.perl=		-e 's|RealBin/lib|RealBin/../${SITE_PERL_REL}|g'
+SUBST_FILES.perl=	${WRKSRC}/pipelines/canu.pl
+
+REPLACE_PERL+=	bogart/*.pl \
+		pipelines/*.pl \
+		bogus/*.pl \
+		bogart-analysis/*.pl \
+		overlapBasedTrimming/*.pl \
+		overlapInCore-analysis/*.pl \
+		merTrim/*.pl \
+		erateEstimate/*.pl \
+		meryl/.pl \
+		fastq-utilities/*.pl \
+		*.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=		${WRKDIR}/canu-${PV}/src
+MAKE_ENV+=	DESTDIR=${WRKSRC}
+
+PV=		1.7
+
+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
+
+do-install:
+	cd ${TMP_INST}/bin && ${PAX} -wr * ${DESTDIR}${PREFIX}/bin
+	cd ${TMP_INST}/lib && ${PAX} -wr * ${DESTDIR}${PREFIX}/lib
+	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 --git a/canu/PLIST b/canu/PLIST
new file mode 100644
index 0000000000..438a2378f3
--- /dev/null
+++ b/canu/PLIST
@@ -0,0 +1,93 @@
+@comment $NetBSD$
+bin/alignGFA
+bin/bogart
+bin/bogus
+bin/canu
+bin/canu.defaults
+bin/correctOverlaps
+bin/createFalconSenseInputs
+bin/dumpBlob
+bin/edalign
+bin/erateEstimate
+bin/errorEstimate
+bin/estimate-mer-threshold
+bin/existDB
+bin/falcon_sense
+bin/falconsense
+bin/fastqAnalyze
+bin/fastqSample
+bin/fastqSimulate
+bin/fastqSimulate-sort
+bin/filterCorrectionLayouts
+bin/filterCorrectionOverlaps
+bin/findErrors
+bin/findErrors-Dump
+bin/gatekeeperCreate
+bin/gatekeeperDumpFASTQ
+bin/gatekeeperDumpMetaData
+bin/gatekeeperPartition
+bin/generateCorrectionLayouts
+bin/leaff
+bin/loadCorrectedReads
+bin/loadTrimmedReads
+bin/maskMers
+bin/merTrim
+bin/meryl
+bin/mhapConvert
+bin/mmapConvert
+bin/ovStoreBucketizer
+bin/ovStoreBuild
+bin/ovStoreDump
+bin/ovStoreIndexer
+bin/ovStoreSorter
+bin/ovStoreStats
+bin/overlapConvert
+bin/overlapImport
+bin/overlapInCore
+bin/overlapInCorePartition
+bin/overlapPair
+bin/positionDB
+bin/prefixEditDistance-matchLimitGenerate
+bin/readConsensus
+bin/sequence
+bin/simple
+bin/simple-dump
+bin/splitHaplotype
+bin/splitReads
+bin/tgStoreCompress
+bin/tgStoreCoverageStat
+bin/tgStoreDump
+bin/tgStoreFilter
+bin/tgStoreLoad
+bin/tgTigDisplay
+bin/trimReads
+bin/trioCanu
+bin/utgcns
+lib/libcanu.a
+lib/libleaff.a
+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/ErrorEstimate.pm
+lib/perl5/site_perl/canu/Execution.pm
+lib/perl5/site_perl/canu/Gatekeeper.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/Unitig.pm
+share/java/classes/mhap-2.1.3.jar
diff --git a/canu/TODO b/canu/TODO
new file mode 100644
index 0000000000..b687356e6b
--- /dev/null
+++ b/canu/TODO
@@ -0,0 +1 @@
+Clean up and test
diff --git a/canu/distinfo b/canu/distinfo
new file mode 100644
index 0000000000..8bf866d7f9
--- /dev/null
+++ b/canu/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (canu-1.7.tar.gz) = aaaafd8516be5e4d725af407bc84b3c6f178b2ac
+RMD160 (canu-1.7.tar.gz) = bd394bb6dcebd43d2793ca1aa9bd60ec6be75beb
+SHA512 (canu-1.7.tar.gz) = dbc1dca4df4117521143843bb781227f4dfde5ba7068e47b51ccf9e9dba45eb2629b5773531e4f362f1df05eab3f1a62088c5fa231d3624af23f11d97e7a4edf
+Size (canu-1.7.tar.gz) = 2533016 bytes
+SHA1 (patch-pipelines_canu_Execution.pm) = 4f9d343e03cc802b90616844cb331b78793bd368
diff --git a/canu/patches/patch-pipelines_canu_Execution.pm b/canu/patches/patch-pipelines_canu_Execution.pm
new file mode 100644
index 0000000000..c6859316fb
--- /dev/null
+++ b/canu/patches/patch-pipelines_canu_Execution.pm
@@ -0,0 +1,16 @@
+$NetBSD$
+
+# Eliminate assumptions about install dir name
+--- pipelines/canu/Execution.pm.orig	2017-04-17 19:32:38.000000000 +0000
++++ pipelines/canu/Execution.pm
+@@ -293,10 +293,6 @@ sub skipStage ($$@) {
+ sub getInstallDirectory () {
+     my $installDir = $FindBin::RealBin;
+ 
+-    if ($installDir =~ m!^(.*)/\w+-\w+/bin$!) {
+-        $installDir = $1;
+-    }
+-
+     return($installDir);
+ }
+
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