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canu: Clean up

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Jan 4 11:16:20 2019 -0600
Changeset:	21ca01b9e6b5b6be10838e1dba55c7bb761cefd8

Modified Files:
	canu/DESCR
	canu/Makefile
	canu/PLIST
	canu/distinfo
	canu/patches/patch-Makefile
	canu/patches/patch-pipelines_canu_Defaults.pm
	canu/patches/patch-pipelines_canu_Execution.pm
	canu/patches/patch-utility_objectStore.C

Log Message:
canu: Clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=21ca01b9e6b5b6be10838e1dba55c7bb761cefd8

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

diffstat:
 canu/DESCR                                     | 13 ++++++++++++-
 canu/Makefile                                  | 18 ++++++++----------
 canu/PLIST                                     |  2 --
 canu/distinfo                                  |  8 ++++----
 canu/patches/patch-Makefile                    |  3 ++-
 canu/patches/patch-pipelines_canu_Defaults.pm  |  1 +
 canu/patches/patch-pipelines_canu_Execution.pm |  1 +
 canu/patches/patch-utility_objectStore.C       |  4 +++-
 8 files changed, 31 insertions(+), 19 deletions(-)

diffs:
diff --git a/canu/DESCR b/canu/DESCR
index 77b960193b..719f42cf95 100644
--- a/canu/DESCR
+++ b/canu/DESCR
@@ -1 +1,12 @@
-A single molecule sequence assembler for genomes large and small.
+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 --git a/canu/Makefile b/canu/Makefile
index f5ee7eda95..8716e063ed 100644
--- a/canu/Makefile
+++ b/canu/Makefile
@@ -1,10 +1,9 @@
 # $NetBSD$
 
-DISTNAME=	canu-${PV}
+DISTNAME=	canu-1.8
 CATEGORIES=	biology java
 MASTER_SITES=	${MASTER_SITE_GITHUB:=marbl/}
-GITHUB_PROJECT=	canu
-GITHUB_TAG=	v${PV}
+GITHUB_TAG=	v${PKGVERSION_NOREV}
 
 MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	http://canu.readthedocs.io/
@@ -12,7 +11,7 @@ COMMENT=	Single molecule sequence assembler for genomes large and small
 
 LICENSE=	gnu-gpl-v2
 
-DEPENDS+=	gnuplot>0:../../graphics/gnuplot
+DEPENDS=	gnuplot>0:../../graphics/gnuplot
 
 # Makefile compiles directly into ${DESTDIR}${PREFIX}
 SUBST_CLASSES+=		optimize
@@ -32,7 +31,7 @@ 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=	bogart/*.pl
 REPLACE_PERL+=	pipelines/*.pl
 REPLACE_PERL+=	bogus/*.pl
 REPLACE_PERL+=	bogart-analysis/*.pl
@@ -50,14 +49,12 @@ ONLY_FOR_PLATFORM=	*-*-x86_64
 USE_LANGUAGES=	c c++
 USE_JAVA=	run
 USE_JAVA2=	8
-USE_TOOLS+=	gmake pax perl
+USE_TOOLS=	gmake pax perl
 GCC_REQD+=	4.8
 
-WRKSRC=		${WRKDIR}/canu-${PV}/src
+WRKSRC=		${WRKDIR}/canu-${PKGVERSION_NOREV}/src
 MAKE_ENV+=	DESTDIR=${WRKSRC}
 
-PV=		1.8
-
 TMP_INST=		${WRKSRC}${PREFIX}/${OPSYS}-${MACHINE_ARCH:S/x86_64/amd64/}
 SITE_PERL_REL=		lib/perl5/site_perl
 JAVAJARDIR=		share/java/classes
@@ -69,10 +66,11 @@ post-extract:
 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 && ${PAX} -wr * ${DESTDIR}${PREFIX}/lib
+	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"
diff --git a/canu/PLIST b/canu/PLIST
index b3e3032b3b..d8d1300709 100644
--- a/canu/PLIST
+++ b/canu/PLIST
@@ -3,7 +3,6 @@ bin/alignGFA
 bin/bogart
 bin/bogus
 bin/canu
-bin/canu.defaults
 bin/correctOverlaps
 bin/dumpBlob
 bin/edalign
@@ -54,7 +53,6 @@ bin/tgTigDisplay
 bin/trimReads
 bin/utgcns
 bin/wtdbgConvert
-lib/libcanu.a
 lib/perl5/site_perl/canu/Configure.pm
 lib/perl5/site_perl/canu/Consensus.pm
 lib/perl5/site_perl/canu/CorrectReads.pm
diff --git a/canu/distinfo b/canu/distinfo
index 3046631912..a8a69b23f7 100644
--- a/canu/distinfo
+++ b/canu/distinfo
@@ -4,7 +4,7 @@ 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) = 9b86a5697e3752c55a35fcff9dd14a11de25a5f9
-SHA1 (patch-pipelines_canu_Defaults.pm) = 987c1e370bc81381824f86001f70da66ea251524
-SHA1 (patch-pipelines_canu_Execution.pm) = 4c8ad9a3be08a8e5885e3ef35dca33e85c344547
-SHA1 (patch-utility_objectStore.C) = 9b466edcfdc608345c5f9128bdd416209e08e33a
+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 --git a/canu/patches/patch-Makefile b/canu/patches/patch-Makefile
index 4bbabddab8..b72ea568ae 100644
--- a/canu/patches/patch-Makefile
+++ b/canu/patches/patch-Makefile
@@ -1,6 +1,7 @@
 $NetBSD$
 
-# Requires platform-specific defaults
+# 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
diff --git a/canu/patches/patch-pipelines_canu_Defaults.pm b/canu/patches/patch-pipelines_canu_Defaults.pm
index 0d67834a66..668ab99f50 100644
--- a/canu/patches/patch-pipelines_canu_Defaults.pm
+++ b/canu/patches/patch-pipelines_canu_Defaults.pm
@@ -1,6 +1,7 @@
 $NetBSD$
 
 # 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
diff --git a/canu/patches/patch-pipelines_canu_Execution.pm b/canu/patches/patch-pipelines_canu_Execution.pm
index 5bd8ee1624..195f5a685b 100644
--- a/canu/patches/patch-pipelines_canu_Execution.pm
+++ b/canu/patches/patch-pipelines_canu_Execution.pm
@@ -1,6 +1,7 @@
 $NetBSD$
 
 # 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
diff --git a/canu/patches/patch-utility_objectStore.C b/canu/patches/patch-utility_objectStore.C
index b361580ece..3300c4d56f 100644
--- a/canu/patches/patch-utility_objectStore.C
+++ b/canu/patches/patch-utility_objectStore.C
@@ -1,6 +1,8 @@
 $NetBSD$
 
-# Portability
+# 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) {
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