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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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