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- #!/usr/bin/env perl
- #
- # Client JSV script from Mark Lundie for running cellranger
- # pipeline
- #
- # Strips "-pe smp.pe 1" lines from job submission scripts
- # (requests for >1 core will be kept unchanged)
- #
- # Include in qsub commands using -jsv PATH/TO/sge.strip_pe.pl
- use strict;
- use warnings;
- no warnings qw/uninitialized/;
- use Env qw(SGE_ROOT);
- use lib "$SGE_ROOT/util/resources/jsv";
- use JSV qw( :DEFAULT jsv_send_env jsv_log_info);
- jsv_on_start(sub {
- jsv_send_env();
- });
- jsv_on_verify(sub {
- my %params = jsv_get_param_hash();
- if (exists $params{pe_name}) {
- my $nslots = $params{pe_min};
- if ($nslots lt 2) {
- jsv_del_param('pe_name');
- jsv_correct('Stripped PE from serial job.');
- }
- }
- jsv_accept();
- });
- jsv_main();
- #!/usr/bin/env perl
- use strict;
- use warnings;
- no warnings qw/uninitialized/;
- use Env qw(SGE_ROOT);
- use lib "$SGE_ROOT/util/resources/jsv";
- use JSV qw( :DEFAULT jsv_send_env jsv_log_info);
- jsv_on_start(sub {
- jsv_send_env();
- });
- jsv_on_verify(sub {
- my %params = jsv_get_param_hash();
- if (exists $params{pe_name}) {
- my $nslots = $params{pe_min};
- if ($nslots lt 2) {
- jsv_del_param('pe_name');
- jsv_correct('Stripped PE from serial job.');
- }
- }
- jsv_accept();
- });
- jsv_main();
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