Merge pull request #440 from sanger-pathogens/thouio

Revert "thouio removal"

Author: seretol

lib/VertRes/Pipelines/Import.pm

@@ -37,7 +37,7 @@ our $options =
     # Executables
     'fastqcheck'      => 'fastqcheck',
     'mpsa'            => '/software/solexa/bin/mpsa_download',
-    'bsub_opts'       => "-q normal -R 'select[type==X86_64]'",
+    'bsub_opts'       => "-q normal -R 'select[type==X86_64] rusage[thouio=1]'",
     'local_bam_dir'     => '',
 };
 

lib/VertRes/Pipelines/Import_Bam.pm

@@ -34,7 +34,7 @@ our @actions =
 our $options = 
 {
     'bamcheck'        => 'bamcheck -q 20',
-    'bsub_opts'       => "-q normal -R 'select[type==X86_64]'",
+    'bsub_opts'       => "-q normal -R 'select[type==X86_64] rusage[thouio=1]'",
     'local_bam_dir'   => '',
 };
 

lib/VertRes/Pipelines/Import_iRODS.pm

@@ -34,7 +34,7 @@ our @actions =
 our $options = 
 {
     'bamcheck'        => 'bamcheck -q 20',
-    'bsub_opts'       => " -q normal -R 'select[type==X86_64]' ",
+    'bsub_opts'       => " -q normal -R 'select[type==X86_64] rusage[thouio=1]' ",
 };
 
 

lib/VertRes/Pipelines/Import_iRODS_fastq.pm

@@ -109,7 +109,7 @@ our @actions =
 our $options = 
 {
     'bamcheck'        => 'bamcheck -q 20',
-    'bsub_opts'       => "-q normal -R 'select[type==X86_64]'",
+    'bsub_opts'       => "-q normal -R 'select[type==X86_64] rusage[thouio=1]'",
 };
 
 

lib/VertRes/Pipelines/SNPs.pm

@@ -35,10 +35,10 @@ data =>
 {
     task => 'mpileup,gatk,update_db,cleanup,pseudo_genome',
    
-    bsub_opts       => "-q normal -M3500 -R 'select[type==X86_64] select[mem>3500] rusage[mem=3500] rusage[tmp=16000]'",
-    bsub_opts_long  => "-q normal -M3500 -R 'select[type==X86_64 select[mem>3500] rusage[mem=3500] rusage[tmp=16000]'",
-    bsub_opts_qcall  => "-q normal -M3500 -R 'select[type==X86_64 select[mem>3500 && tmp>17000] rusage[mem=3500] rusage[tmp=17000]'",
-    bsub_opts_mpileup    => "-q normal -R 'select[type==X86_64]'",
+    bsub_opts       => "-q normal -M3500 -R 'select[type==X86_64] select[mem>3500] rusage[mem=3500] rusage[thouio=1] rusage[tmp=16000]'",
+    bsub_opts_long  => "-q normal -M3500 -R 'select[type==X86_64 select[mem>3500] rusage[mem=3500] rusage[thouio=1] rusage[tmp=16000]'",
+    bsub_opts_qcall  => "-q normal -M3500 -R 'select[type==X86_64 select[mem>3500 && tmp>17000] rusage[mem=3500] rusage[thouio=1] rusage[tmp=17000]'",
+    bsub_opts_mpileup    => "-q normal -R 'select[type==X86_64] rusage[thouio=1]'",
  
     split_size_mpileup   => 300_000_000,
     split_size_gatk      => 100_000_000,         
@@ -221,9 +221,9 @@ our @actions =
 our $options = 
 {
     bcftools        => 'bcftools',
-    bsub_opts_varfilter  => "-q normal -R 'select[type==X86_64]'",
-    bsub_opts_mpileup    => "-q normal -R 'select[type==X86_64]'",
-    bsub_opts_qcall      => "-q normal -R 'select[type==X86_64]'",
+    bsub_opts_varfilter  => "-q normal -R 'select[type==X86_64] rusage[thouio=1]'",
+    bsub_opts_mpileup    => "-q normal -R 'select[type==X86_64] rusage[thouio=1]'",
+    bsub_opts_qcall      => "-q normal -R 'select[type==X86_64] rusage[thouio=1]'",
     bsub_opts_gatk       => "-q normal -M3000 -R 'select[mem>3000] rusage[mem=3000]'",
     chunks_overlap  => 250,
     fai_chr_regex   => '\d+|x|y',

lib/VertRes/Pipelines/TrackQC_Bam.pm

@@ -90,7 +90,7 @@ our $options =
 
     'adapters'        => '/software/pathogen/projects/protocols/ext/solexa-adapters.fasta',
     'bsub_opts'       => "-q normal -M5000 -R 'select[type==X86_64] select[mem>5000] rusage[mem=5000]'",
-    'bsub_opts_merge' => "-q normal -M5000 -R 'select[type==X86_64] select[mem>5000] rusage[mem=5000]'",
+    'bsub_opts_merge' => "-q normal -M5000 -R 'select[type==X86_64] select[mem>5000] rusage[mem=5000] rusage[thouio=5]'",
     'gc_depth_bin'    => 20000,
     'gtype_confidence'=> 5.0,
     'mapstat_id'      => 'mapstat_id.txt',
@@ -131,7 +131,7 @@ our $options =
                     adapters        .. the location of .fa with adapter sequences
                     assembly        .. e.g. NCBI36
                     bsub_opts       .. LSF bsub options for jobs
-                    bsub_opts_merge .. LSF bsub options for the rename_and_merge task 
+                    bsub_opts_merge .. LSF bsub options for the rename_and_merge task (thouio=50)
                     bwa_ref         .. the prefix to reference files, as required by bwa
                     clean_fastqs    .. If set, .fastq files will be deleted as the last step in update_db
                     do_samtools_rmdup .. If set, pipes the bam through samtools rmdup to get stats without duplicates

lib/VertRes/Pipelines/TrackQC_ExomeBam.pm

@@ -133,7 +133,7 @@ our $options = {
 
     'adapters'        => '/software/pathogen/projects/protocols/ext/solexa-adapters.fasta',
     'bsub_opts'       => "-q normal -M5000 -R 'select[mem>5000] rusage[mem=5000]'",
-    'bsub_opts_merge' => "-q normal -M5000 -R 'select[mem>5000] rusage[mem=5000]'",
+    'bsub_opts_merge' => "-q normal -M5000 -R 'select[mem>5000] rusage[mem=5000]' -R 'rusage[thouio=5]'",
     'bsub_opts_stats' => "-q normal -M3500 -R 'select[mem>3500] rusage[mem=3500]'",
     'gc_depth_bin'    => 20000,
     'gtype_confidence'=> 5.0,

lib/VertRes/Utils/Mapping.pm

@@ -271,10 +271,10 @@ sub _bsub_opts {
         $bsub_opts{bsub_opts} .= ' -q normal -M5100 -R \'select[mem>5100] rusage[mem=5100]\'';
     }
     elsif ($action && $action =~ /map|merge/) {
-        $bsub_opts{bsub_opts} .= ' -M1000 -R \'select[mem>1000] rusage[mem=1000]\'';
+        $bsub_opts{bsub_opts} .= ' -R \'rusage[thouio=5]\' -M1000 -R \'select[mem>1000] rusage[mem=1000]\'';
     }
     elsif ($action && $action =~ /split/) {
-        $bsub_opts{bsub_opts} .= '-n 2  -R \'span[hosts=1]\' -M1000 -R \'select[mem>1000] rusage[mem=1000]\'';
+        $bsub_opts{bsub_opts} .= '-n 2  -R \'span[hosts=1]\' -R \'rusage[thouio=5]\' -M1000 -R \'select[mem>1000] rusage[mem=1000]\'';
     }
 
     return \%bsub_opts;