svn commit: r484077 - in head/biology/canu: . files
Jason W. Bacon
jwb at FreeBSD.org
Sun Nov 4 14:29:05 UTC 2018
Author: jwb
Date: Sun Nov 4 14:29:02 2018
New Revision: 484077
URL: https://svnweb.freebsd.org/changeset/ports/484077
Log:
biology/canu: Upgrade to 1.8, add experimental SLURM integration
Solves build issue with gcc8.
PR: 232930
Reported by: gerald
Approved by: jrm (mentor, implicit)
Added:
head/biology/canu/files/patch-pipelines_canu_Defaults.pm (contents, props changed)
Modified:
head/biology/canu/Makefile
head/biology/canu/distinfo
head/biology/canu/files/patch-pipelines_canu_Execution.pm
head/biology/canu/pkg-plist
Modified: head/biology/canu/Makefile
==============================================================================
--- head/biology/canu/Makefile Sun Nov 4 14:27:06 2018 (r484076)
+++ head/biology/canu/Makefile Sun Nov 4 14:29:02 2018 (r484077)
@@ -2,8 +2,7 @@
PORTNAME= canu
DISTVERSIONPREFIX= v
-DISTVERSION= 1.7
-PORTREVISION= 2
+DISTVERSION= 1.8
CATEGORIES= biology java perl5
MAINTAINER= jwb at FreeBSD.org
@@ -21,9 +20,10 @@ RUN_DEPENDS= gnuplot:math/gnuplot
USES= compiler:openmp gmake perl5
USE_JAVA= yes
+USE_GITHUB= yes
+
JAVA_RUN= yes
JAVA_VERSION= 1.8+
-USE_GITHUB= yes
GH_ACCOUNT= marbl
WRKSRC_SUBDIR= src
@@ -44,12 +44,12 @@ post-patch:
# Upstream does not want to use lib/perl5/site_perl
post-build:
- ${MKDIR} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5
+ @${MKDIR} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5
${MV} ${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/site_perl \
${WRKSRC}${PREFIX}/FreeBSD-${ARCH}/lib/perl5
do-install:
- ${MKDIR} ${STAGEDIR}${PREFIX}
+ @${MKDIR} ${STAGEDIR}${PREFIX}
(cd ${WRKSRC}${PREFIX}/FreeBSD-${ARCH} && \
${COPYTREE_BIN} bin ${STAGEDIR}${PREFIX})
# STRIP_CMD fails without this on 11.1 under poudriere
Modified: head/biology/canu/distinfo
==============================================================================
--- head/biology/canu/distinfo Sun Nov 4 14:27:06 2018 (r484076)
+++ head/biology/canu/distinfo Sun Nov 4 14:29:02 2018 (r484077)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1524325169
-SHA256 (marbl-canu-v1.7_GH0.tar.gz) = c5be54b0ad20729093413e7e722a19637d32e966dc8ecd2b579ba3e4958d378a
-SIZE (marbl-canu-v1.7_GH0.tar.gz) = 2533016
+TIMESTAMP = 1540317173
+SHA256 (marbl-canu-v1.8_GH0.tar.gz) = 30ecfe574166f54f79606038830f68927cf0efab33bdc3c6e43fd1448fa0b2e4
+SIZE (marbl-canu-v1.8_GH0.tar.gz) = 2465314
Added: head/biology/canu/files/patch-pipelines_canu_Defaults.pm
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/canu/files/patch-pipelines_canu_Defaults.pm Sun Nov 4 14:29:02 2018 (r484077)
@@ -0,0 +1,19 @@
+--- pipelines/canu/Defaults.pm.orig 2018-06-19 17:20:30 UTC
++++ 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'");
Modified: head/biology/canu/files/patch-pipelines_canu_Execution.pm
==============================================================================
--- head/biology/canu/files/patch-pipelines_canu_Execution.pm Sun Nov 4 14:27:06 2018 (r484076)
+++ head/biology/canu/files/patch-pipelines_canu_Execution.pm Sun Nov 4 14:29:02 2018 (r484077)
@@ -1,8 +1,6 @@
-$NetBSD$
-
---- pipelines/canu/Execution.pm.orig 2017-04-17 19:32:38 UTC
+--- pipelines/canu/Execution.pm.orig 2018-06-18 02:42:11 UTC
+++ pipelines/canu/Execution.pm
-@@ -293,10 +293,6 @@ sub skipStage ($$@) {
+@@ -303,10 +303,6 @@ sub skipStage ($$@) {
sub getInstallDirectory () {
my $installDir = $FindBin::RealBin;
@@ -12,4 +10,69 @@ $NetBSD$
-
return($installDir);
}
+
+@@ -694,8 +690,8 @@ sub submitScript ($$) {
+
+
+
+-sub buildGridArray ($$$$) {
+- my ($name, $bgn, $end, $opt) = @_;
++sub buildGridArray (@) {
++ my ( $name, $bgn, $end, $opt, $thr ) = @_;
+ my $off = 0;
+
+ # In some grids (SGE) this is the maximum size of an array job.
+@@ -725,8 +721,42 @@ sub buildGridArray ($$$$) {
+ $off = "-F \"$off\"";
+ }
+
+- $opt =~ s/ARRAY_NAME/$name/g; # Replace ARRAY_NAME with 'job name'
+- $opt =~ s/ARRAY_JOBS/$bgn-$end/g; # Replace ARRAY_JOBS with 'bgn-end'
++ if( $opt =~ m/(ARRAY_NAME)/ )
++ {
++ $opt =~ s/$1/$name/; # Replace ARRAY_NAME with 'job name'
++ }
++ elsif( $opt =~ m/(ARRAY_JOBS)/ )
++ {
++ $opt =~ s/$1/$bgn-$end/; # Replace ARRAY_JOBS with 'bgn-end'
++
++ if( lc( getGlobal( 'gridEngine' ) ) eq 'slurm' && $end > 1 )
++ {
++ if( $name =~ m/^cormhap_/i && defined getGlobal( 'slurmCormhapCoreLimit' ) )
++ {
++ $opt .= '%' . int( getGlobal( 'slurmCormhapCoreLimit' ) / $thr );
++ }
++ elsif( $name =~ m/^ovb_/i && defined getGlobal( 'slurmOvbCoreLimit' ) )
++ {
++ $opt .= '%' . getGlobal( 'slurmOvbCoreLimit' );
++ }
++ elsif( $name =~ m/^ovs_/i && defined getGlobal( 'slurmOvsCoreLimit' ) )
++ {
++ $opt .= '%' . getGlobal( 'slurmOvsCoreLimit' );
++ }
++ elsif( $name =~ m/^red_/i && defined getGlobal( 'slurmRedCoreLimit' ) )
++ {
++ $opt .= '%' . int( getGlobal( 'slurmRedCoreLimit' ) / $thr );
++ }
++ elsif( defined getGlobal( 'slurmArrayTaskLimit' ) )
++ {
++ $opt .= '%' . getGlobal( 'slurmArrayTaskLimit' );
++ }
++ elsif( defined getGlobal( 'slurmArrayCoreLimit' ) )
++ {
++ $opt .= '%' . int( getGlobal( 'slurmArrayCoreLimit' ) / $thr );
++ }
++ }
++ }
+
+ return($opt, $off);
+ }
+@@ -870,7 +900,7 @@ sub buildGridJob ($$$$$$$$$) {
+ my $jobNameT = makeUniqueJobName($jobType, $asm);
+
+ my ($jobName, $jobOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayName"));
+- my ($arrayOpt, $arrayOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayOption"));
++ my ( $arrayOpt, $arrayOff ) = buildGridArray( $jobNameT, $bgnJob, $endJob, getGlobal( "gridEngineArrayOption" ), $thr );
+
+ my $outputOption = buildOutputOption($path, $script);
Modified: head/biology/canu/pkg-plist
==============================================================================
--- head/biology/canu/pkg-plist Sun Nov 4 14:27:06 2018 (r484076)
+++ head/biology/canu/pkg-plist Sun Nov 4 14:29:02 2018 (r484077)
@@ -4,14 +4,9 @@ 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
@@ -21,21 +16,16 @@ bin/filterCorrectionLayouts
bin/filterCorrectionOverlaps
bin/findErrors
bin/findErrors-Dump
-bin/gatekeeperCreate
-bin/gatekeeperDumpFASTQ
-bin/gatekeeperDumpMetaData
-bin/gatekeeperPartition
bin/generateCorrectionLayouts
-bin/leaff
bin/loadCorrectedReads
+bin/loadErates
bin/loadTrimmedReads
-bin/maskMers
-bin/merTrim
bin/meryl
bin/mhapConvert
bin/mmapConvert
bin/ovStoreBucketizer
bin/ovStoreBuild
+bin/ovStoreConfig
bin/ovStoreDump
bin/ovStoreIndexer
bin/ovStoreSorter
@@ -45,14 +35,15 @@ 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/sqStoreCreate
+bin/sqStoreCreatePartition
+bin/sqStoreDumpFASTQ
+bin/sqStoreDumpMetaData
bin/tgStoreCompress
bin/tgStoreCoverageStat
bin/tgStoreDump
@@ -60,17 +51,14 @@ bin/tgStoreFilter
bin/tgStoreLoad
bin/tgTigDisplay
bin/trimReads
-bin/trioCanu
bin/utgcns
+bin/wtdbgConvert
lib/libcanu.a
-lib/libleaff.a
%%SITE_PERL%%/canu/Configure.pm
%%SITE_PERL%%/canu/Consensus.pm
%%SITE_PERL%%/canu/CorrectReads.pm
%%SITE_PERL%%/canu/Defaults.pm
-%%SITE_PERL%%/canu/ErrorEstimate.pm
%%SITE_PERL%%/canu/Execution.pm
-%%SITE_PERL%%/canu/Gatekeeper.pm
%%SITE_PERL%%/canu/Grid.pm
%%SITE_PERL%%/canu/Grid_Cloud.pm
%%SITE_PERL%%/canu/Grid_DNANexus.pm
@@ -88,5 +76,6 @@ lib/libleaff.a
%%SITE_PERL%%/canu/OverlapMhap.pm
%%SITE_PERL%%/canu/OverlapStore.pm
%%SITE_PERL%%/canu/Report.pm
+%%SITE_PERL%%/canu/SequenceStore.pm
%%SITE_PERL%%/canu/Unitig.pm
%%JAVAJARDIR%%/mhap-2.1.3.jar
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