Mercurial > repos > romaingred > pirna_pipeline
changeset 21:2bd100775c36 draft
Uploaded
| author | romaingred |
|---|---|
| date | Fri, 20 Oct 2017 08:34:50 -0400 |
| parents | 509d95c26dab |
| children | b9cf69322742 |
| files | bin/piPipe.pl |
| diffstat | 1 files changed, 9 insertions(+), 9 deletions(-) [+] |
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--- a/bin/piPipe.pl Fri Oct 20 08:34:35 2017 -0400 +++ b/bin/piPipe.pl Fri Oct 20 08:34:50 2017 -0400 @@ -20,7 +20,7 @@ my ( $ref, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $exons, $TE ); my ( $si_min, $si_max, $pi_min, $pi_max ); my ( $build_index, $build_tRNAs, $build_rRNAs, $build_snRNAs, $build_miRNAs, $build_exons, $build_TE ); -my $max_procs = 4; +my $max_procs = 8; ( $build_index, $build_tRNAs, $build_rRNAs, $build_snRNAs, $build_miRNAs, $build_exons, $build_TE ) = (0,0,0,0,0,0,0); ( $min, $max, $mis, $misTE, $si_min, $si_max, $pi_min, $pi_max, $dir ) = ( 18, 29, 0, 3, 21, 21, 23, 29 ); @@ -73,9 +73,9 @@ to_build ( \%toBuild, $report ); my $proc_child = ceil($max_procs / scalar(@fastq)); -my $proc_grand_child = ceil($proc_child/5); +my $proc_grand_child = ceil($proc_child/4); my $pm = Parallel::ForkManager->new($max_procs); -my $pm3 = Parallel::ForkManager->new($proc_grand_child); +my $pm2 = Parallel::ForkManager->new($proc_grand_child); $pm->run_on_finish( sub { my ($pid, $exit_code, $ident) = @_; @@ -87,13 +87,13 @@ my ($pid,$ident)=@_; print $report "Fastq fork : $ident started, pid: $pid\n"; }); -$pm3->run_on_finish( sub { +$pm2->run_on_finish( sub { my ($pid, $exit_code, $ident) = @_; print $report "** Subgroup fork $ident just finished ". "with PID $pid and exit code: $exit_code\n"; die "Something went wrong!\n" if $exit_code != 0; }); -$pm3->run_on_start( sub { +$pm2->run_on_start( sub { my ($pid,$ident)=@_; print $report "** Subgroup fork $ident started, pid: $pid\n"; }); @@ -182,7 +182,7 @@ my $type_dir = $group_dir.$types_names[$grand_child].'/'; my $type_prefix = $types_names[$grand_child].'-'; mkdir $type_dir; - + $pm2->start($types[$grand_child]) and next; my ( $type_sam_genome, $type_sam_TEs, $type_sam_exons ) = ( $type_dir.$type_prefix.'genome.sam', $type_dir.$type_prefix.'TEs.sam', $type_dir.$type_prefix.'exons.sam' ); my ( $type_sam_uni_genome, $type_sam_uni_TEs, $type_sam_uni_exons ) = ( $type_dir.$type_prefix.'genome_unique.sam', $type_dir.$type_prefix.'TEs_unique.sam', $type_dir.$type_prefix.'exons_unique.sam' ); my ( $type_uni_genome_fastq, $type_uni_TEs_fastq, $type_uni_exons_fastq ) = ( $fq_collection.$type_prefix.'genome_uni.fastq', $fq_collection.$type_prefix.'TEs_uni.fastq', $fq_collection.$type_prefix.'exons_uni.fastq'); @@ -240,9 +240,9 @@ my $prefix_details_pages = $dir.$fastq_n[$child].'-'.$types_names[$grand_child]; details_pages ( $type_dir, $prefix_details_pages, \@fastq_n, $fastq_n[$child], $misTE, $dir ); - $pm3->finish($grand_child); + $pm2->finish(); } - $pm3->wait_all_children; + $pm2->wait_all_children; if ( $Pcheck eq 'true' ) { @@ -261,7 +261,7 @@ my $menu_page = $dir.$fastq_n[$child].'-sub.html'; menu_page ( $group_dir, $menu_page, \@fastq_n, $fastq_n[$child], $min, $max, $si_min, $si_max, $pi_min, $pi_max, $dir ); - $pm->finish($child); # pass an exit code to finish + $pm->finish(); # pass an exit code to finish } $pm->wait_all_children;