canu: Clean up
This commit is contained in:
Jason Bacon
parent
d9ac0d381d
commit
21ca01b9e6
13
canu/DESCR
13
canu/DESCR
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A single molecule sequence assembler for genomes large and small.
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Canu is a fork of the Celera Assembler, designed for high-noise single-molecule
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sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
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Canu is a hierarchical assembly pipeline which runs in four steps:
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Detect overlaps in high-noise sequences using MHAP
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Generate corrected sequence consensus
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Trim corrected sequences
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Assemble trimmed corrected sequences
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@ -1,10 +1,9 @@
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# $NetBSD$
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DISTNAME= canu-${PV}
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DISTNAME= canu-1.8
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CATEGORIES= biology java
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MASTER_SITES= ${MASTER_SITE_GITHUB:=marbl/}
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GITHUB_PROJECT= canu
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GITHUB_TAG= v${PV}
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GITHUB_TAG= v${PKGVERSION_NOREV}
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MAINTAINER= bacon@NetBSD.org
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HOMEPAGE= http://canu.readthedocs.io/
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@ -12,7 +11,7 @@ COMMENT= Single molecule sequence assembler for genomes large and small
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LICENSE= gnu-gpl-v2
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DEPENDS+= gnuplot>0:../../graphics/gnuplot
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DEPENDS= gnuplot>0:../../graphics/gnuplot
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# Makefile compiles directly into ${DESTDIR}${PREFIX}
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SUBST_CLASSES+= optimize
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@ -32,7 +31,7 @@ SUBST_STAGE.perl= pre-configure
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SUBST_SED.perl= -e 's|$$FindBin::RealBin/../lib/site_perl|${PREFIX}/${SITE_PERL_REL}|g'
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SUBST_FILES.perl= ${WRKSRC}/pipelines/canu.pl
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REPLACE_PERL+= bogart/*.pl
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REPLACE_PERL= bogart/*.pl
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REPLACE_PERL+= pipelines/*.pl
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REPLACE_PERL+= bogus/*.pl
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REPLACE_PERL+= bogart-analysis/*.pl
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@ -50,14 +49,12 @@ ONLY_FOR_PLATFORM= *-*-x86_64
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USE_LANGUAGES= c c++
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USE_JAVA= run
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USE_JAVA2= 8
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USE_TOOLS+= gmake pax perl
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USE_TOOLS= gmake pax perl
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GCC_REQD+= 4.8
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WRKSRC= ${WRKDIR}/canu-${PV}/src
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WRKSRC= ${WRKDIR}/canu-${PKGVERSION_NOREV}/src
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MAKE_ENV+= DESTDIR=${WRKSRC}
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PV= 1.8
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TMP_INST= ${WRKSRC}${PREFIX}/${OPSYS}-${MACHINE_ARCH:S/x86_64/amd64/}
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SITE_PERL_REL= lib/perl5/site_perl
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JAVAJARDIR= share/java/classes
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@ -69,10 +66,11 @@ post-extract:
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post-build:
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${MKDIR} ${TMP_INST}/lib/perl5
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${MV} ${TMP_INST}/lib/site_perl ${TMP_INST}/lib/perl5
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${RM} -f ${TMP_INST}/bin/canu.defaults
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do-install:
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cd ${TMP_INST}/bin && ${PAX} -wr * ${DESTDIR}${PREFIX}/bin
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cd ${TMP_INST}/lib && ${PAX} -wr * ${DESTDIR}${PREFIX}/lib
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cd ${TMP_INST}/lib/perl5 && ${PAX} -wr * ${DESTDIR}${PREFIX}/lib/perl5
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cd ${TMP_INST}/share && ${PAX} -wr * ${DESTDIR}${PREFIX}/share
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.include "../../devel/boost-libs/buildlink3.mk"
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@ -3,7 +3,6 @@ bin/alignGFA
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bin/bogart
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bin/bogus
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bin/canu
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bin/canu.defaults
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bin/correctOverlaps
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bin/dumpBlob
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bin/edalign
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@ -54,7 +53,6 @@ bin/tgTigDisplay
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bin/trimReads
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bin/utgcns
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bin/wtdbgConvert
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lib/libcanu.a
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lib/perl5/site_perl/canu/Configure.pm
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lib/perl5/site_perl/canu/Consensus.pm
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lib/perl5/site_perl/canu/CorrectReads.pm
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@ -4,7 +4,7 @@ SHA1 (canu-1.8.tar.gz) = 7dd79415aa5ecb95f05109f0d8d58f7cbfc336e9
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RMD160 (canu-1.8.tar.gz) = 78d4872b4034f526037ce225c699debd910bd586
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SHA512 (canu-1.8.tar.gz) = 650bc96675f371596f8e7748d4ab2d229f0262bf84cee8fed59af43d534d76095a72e4ba0b4a5ce9f561992268c317964cda2f6c89ee514f4920e2ba47fbc86c
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Size (canu-1.8.tar.gz) = 2465314 bytes
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SHA1 (patch-Makefile) = 9b86a5697e3752c55a35fcff9dd14a11de25a5f9
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SHA1 (patch-pipelines_canu_Defaults.pm) = 987c1e370bc81381824f86001f70da66ea251524
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SHA1 (patch-pipelines_canu_Execution.pm) = 4c8ad9a3be08a8e5885e3ef35dca33e85c344547
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SHA1 (patch-utility_objectStore.C) = 9b466edcfdc608345c5f9128bdd416209e08e33a
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SHA1 (patch-Makefile) = aa83003677cbb12558e438c776402ec48df0598d
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SHA1 (patch-pipelines_canu_Defaults.pm) = 55a4631d86abb1881b0cc997514d44c536209ea6
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SHA1 (patch-pipelines_canu_Execution.pm) = fbb080c06ea5d2393d1835a61771715d2aef0274
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SHA1 (patch-utility_objectStore.C) = c8407de79abbaf296f027f704080cc7e878b85f4
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@ -1,6 +1,7 @@
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$NetBSD$
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# Requires platform-specific defaults
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# Template Makefile requires platform-specific defaults for each OS
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# To be sent upstream following commit
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--- Makefile.orig 2018-10-22 16:47:31.000000000 +0000
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+++ Makefile
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@ -1,6 +1,7 @@
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$NetBSD$
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# Add resource limits for SLURM
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# Upstream is considering a scheduler-independent approach to this feature
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--- pipelines/canu/Defaults.pm.orig 2018-06-22 08:20:52.000000000 +0000
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+++ pipelines/canu/Defaults.pm
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@ -1,6 +1,7 @@
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$NetBSD$
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# Add resource limits for SLURM
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# Upstream is considering a scheduler-independent approach to this feature
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--- pipelines/canu/Execution.pm.orig 2018-06-22 08:20:52.000000000 +0000
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+++ pipelines/canu/Execution.pm
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@ -1,6 +1,8 @@
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$NetBSD$
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# Portability
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# NetBSD does not provide WEXITED
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# Empty bitmask should suffice in this case
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--- utility/objectStore.C.orig 2018-12-23 01:57:06.000000000 +0000
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+++ utility/objectStore.C
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@@ -286,6 +286,11 @@ fetchFromObjectStore(char *requested) {
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