[ENSCORESW-550]. Made the pipeline run on the new farm infrastructure by...

[ENSCORESW-550]. Made the pipeline run on the new farm infrastructure by editting memory requirements.

The original version had memory requirements in KB. New farm infrastructure says we
specify in MB. This is good so now all memory requirement params are all in the
same order of magnitude. The final collection job now specifies its memory
requirements. This is a good thing again. Currently this is set to 5MB.

misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateBasic.pm

@@ -123,7 +123,7 @@ sub resubmit_exonerate {
 
   my $queue = $self->mapper->farm_queue || 'long';
   
-  my $usage = '-M 1500000 -R"select[mem>1500] rusage[tmp='.$disk_space_needed.', mem=1500]" -J "'.$unique_name.'" -q '.$queue;
+  my $usage = '-M 1500 -R"select[mem>1500] rusage[tmp='.$disk_space_needed.', mem=1500]" -J "'.$unique_name.'" -q '.$queue;
 
 
   my $com = "bsub $usage -o $root_dir/$outfile -e $root_dir/$errfile ".$exe_file;
@@ -265,7 +265,7 @@ EON
   my $queue = $self->mapper->farm_queue || 'long';
 
 
-  my $usage = "-q $queue ".'-M 1500000 -R"select[mem>1500] rusage[tmp='.$disk_space_needed.', mem=1500]" '.'-J "'.$unique_name.'[1-'.$num_jobs.']%200" -o '.$prefix.'.%J-%I.out -e  '.$prefix.'.%J-%I.err';
+  my $usage = "-q $queue ".'-M 1500 -R"select[mem>1500] rusage[tmp='.$disk_space_needed.', mem=1500]" '.'-J "'.$unique_name.'[1-'.$num_jobs.']%200" -o '.$prefix.'.%J-%I.out -e  '.$prefix.'.%J-%I.err';
 
 
   my $command = $exe." ".$query." ".$target.' --querychunkid $LSB_JOBINDEX --querychunktotal '.$num_jobs.' --showvulgar false --showalignment FALSE --ryo "xref:%qi:%ti:%ei:%ql:%tl:%qab:%qae:%tab:%tae:%C:%s\n" '.$options_str;
@@ -301,7 +301,7 @@ EON
   } 
   else{
     # write details of job to database
-    my $command = "$exonerate_path $query $target --querychunkid \$LSB_JOBINDEX --querychunktotal $num_jobs --showvulgar false --showalignment FALSE --ryo ".
+    my $command = "$exe $query $target --querychunkid \$LSB_JOBINDEX --querychunktotal $num_jobs --showvulgar false --showalignment FALSE --ryo ".
       '"xref:%qi:%ti:%ei:%ql:%tl:%qab:%qae:%tab:%tae:%C:%s\\\n"'." $options_str | grep ".'"'."^xref".'"'." > $root_dir/$output";
 
     my $sth = $mapper->xref->dbc->prepare("insert into process_status (status, date) values('mapping_submitted',now())");

misc-scripts/xref_mapping/XrefMapper/SubmitMapper.pm

@@ -1033,8 +1033,8 @@ sub submit_depend_job {
 #  push @depend_bsub, ('-q', $queue, '-o', "$root_dir/depend.out", '-e', "$root_dir/depend.err");
 
   my $jobid = 0;
-
-  my $com = "bsub -K -q ".$queue." -o $root_dir/depend.out -e $root_dir/depend.err $ended_str /bin/true";
+  my $memory_resources = q{-M 5 -R"select[mem>5] rusage[mem=5]"}
+  my $com = "bsub -K -q $queue $memory_resources -o $root_dir/depend.out -e $root_dir/depend.err $ended_str /bin/true";
 
 
   my $line = `$com`;