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| author | Jason W. Bacon <jwb@FreeBSD.org> | 2020-09-15 06:27:37 +0800 |
|---|---|---|
| committer | Jason W. Bacon <jwb@FreeBSD.org> | 2020-09-15 06:27:37 +0800 |
| commit | 719076a220d704c365135ed875088f08ac1ec795 (patch) | |
| tree | 95a1d43d7d362477d6afd00f7980b52dc686b97b /biology/canu/files | |
| parent | fafc1b8e311ddca5d2126ce29f1eb88bcd125bc2 (diff) | |
| download | freebsd-ports-gnome-719076a220d704c365135ed875088f08ac1ec795.tar.gz freebsd-ports-gnome-719076a220d704c365135ed875088f08ac1ec795.tar.zst freebsd-ports-gnome-719076a220d704c365135ed875088f08ac1ec795.zip | |
biology/canu: Upgrade to 2.1
Numerous functional improvements for ease of use and output quality
A few bug fixes
Reported by: portscout
Diffstat (limited to 'biology/canu/files')
| -rw-r--r-- | biology/canu/files/patch-pipelines_canu_Execution.pm | 24 |
1 files changed, 7 insertions, 17 deletions
diff --git a/biology/canu/files/patch-pipelines_canu_Execution.pm b/biology/canu/files/patch-pipelines_canu_Execution.pm index 4b489761931c..66fd808d5f48 100644 --- a/biology/canu/files/patch-pipelines_canu_Execution.pm +++ b/biology/canu/files/patch-pipelines_canu_Execution.pm @@ -1,17 +1,6 @@ ---- pipelines/canu/Execution.pm.orig 2018-10-22 16:47:31 UTC +--- pipelines/canu/Execution.pm.orig 2020-09-07 19:08:24 UTC +++ pipelines/canu/Execution.pm -@@ -333,10 +333,6 @@ sub resetIteration ($) { - sub getInstallDirectory () { - my $installDir = $FindBin::RealBin; - -- if ($installDir =~ m!^(.*)/\w+-\w+/bin$!) { -- $installDir = $1; -- } -- - return($installDir); - } - -@@ -784,8 +780,8 @@ sub submitScript ($$) { +@@ -762,8 +762,8 @@ sub submitScript ($$) { @@ -22,7 +11,7 @@ my $off = 0; # In some grids (SGE) this is the maximum size of an array job. -@@ -823,8 +819,42 @@ sub buildGridArray ($$$$) { +@@ -803,9 +803,43 @@ sub buildGridArray ($$$$) { $off = "-F \"$off\""; } @@ -35,7 +24,7 @@ + elsif( $opt =~ m/(ARRAY_JOBS)/ ) + { + $opt =~ s/$1/$bgn-$end/; # Replace ARRAY_JOBS with 'bgn-end' -+ + + if( lc( getGlobal( 'gridEngine' ) ) eq 'slurm' && $end > 1 ) + { + if( $name =~ m/^cormhap_/i && defined getGlobal( 'slurmCormhapCoreLimit' ) ) @@ -64,10 +53,11 @@ + } + } + } - ++ return($opt, $off); } -@@ -973,7 +1003,7 @@ sub buildGridJob ($$$$$$$$$) { + +@@ -951,7 +985,7 @@ sub buildGridJob ($$$$$$$$$) { my $jobNameT = makeUniqueJobName($jobType, $asm); my ($jobName, $jobOff) = buildGridArray($jobNameT, $bgnJob, $endJob, getGlobal("gridEngineArrayName")); |