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redefining chrom_list in global throws an error and dies. #11

Closed jerowe closed 7 years ago

jerowe commented 7 years ago 
#!/usr/bin/env bash

#
# Generated at: 2017-06-08T08:16:24
# This file was generated with the following options
#       run
#       -w      resequencing-human-complete-part5_african_genome.yml
#       --stdout        --select_rules
#       split_by_chrom  --samples
#       151215_FR07958690
#

[2017/06/08 12:16:24] Loading workflow /scratch/gencore/Youssef_data/resequencing-human-complete-part5_african_genome.yml ... 
[2017/06/08 12:16:24] Your workflow is valid

You cannot overwrite a locally defined method (all_chrom_lists) with a delegation at /scratch/gencore/.local/easybuild/software/gencore_dev/1.0/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi/Class/MOP/Class.pm line 899
        Class::MOP::Class::try {...}  at /scratch/gencore/.local/easybuild/software/gencore_dev/1.0/lib/perl5/site_perl/5.22.0/Try/Tiny.pm line 103
        eval {...} at /scratch/gencore/.local/easybuild/software/gencore_dev/1.0/lib/perl5/site_perl/5.22.0/Try/Tiny.pm line 94
        Try::Tiny::try('CODE(0x5ea0780)', 'Try::Tiny::Catch=REF(0x5eaa490)') called at /scratch/gencore/.local/easybuild/software/gencore_dev/1.0/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi/Class/MOP/Class.pm line 904
        Class::MOP::Class::_post_add_attribute('Moose::Meta::Class=HASH(0x4f43420)', 'Moose::Meta::Class::__ANON__::SERIAL::1=HASH(0x5ed9b80)') called at /scratch/gencore/.local/easybuild/software/gencore_dev/1.0/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi/Class/MOP/Mixin/HasAttributes.pm line 39
        Class::MOP::Mixin::HasAttributes::add_attribute('Moose::Meta::Class=HASH(0x4f43420)', 'Moose::Meta::Class::__ANON__::SERIAL::1=HASH(0x5ed9b80)') called at /scratch/gencore/.local/easybuild/software/gencore_dev/1.0/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi/Moose/Meta/Class.pm line 572
        Moose::Meta::Class::add_attribute('Moose::Meta::Class=HASH(0x4f43420)', 'chrom_list', 'traits', 'ARRAY(0x5eaa478)', 'isa', 'ArrayRef', 'is', 'rw', 'clearer', 'clear_chrom_list', 'default', 'CODE(0x51238b8)', 'handles', 'HASH(0x5ea9f38)') called at /scratch/gencore/.local/easybuild/software/gencore_dev/1.0/lib/perl5/site_perl/5.22.0/BioX/Workflow/Command/run/Utils/Directives.pm line 471
        BioX::Workflow::Command::run::Utils::Directives::create_ARRAY_attr('BioX::Workflow::Command::run::Utils::Directives=HASH(0x5e33e80)', 'Moose::Meta::Class=HASH(0x4f43420)', 'chrom_list') called at /scratch/gencore/.local/easybuild/software/gencore_dev/1.0/lib/perl5/site_perl/5.22.0/BioX/Workflow/Command/run/Utils/Directives.pm line 579
        BioX::Workflow::Command::run::Utils::Directives::create_ITERABLE_attr('BioX::Workflow::Command::run::Utils::Directives=HASH(0x5e33e80)', 'Moose::Meta::Class=HASH(0x4f43420)', 'chrom_list') called at /scratch/gencore/.local/easybuild/software/gencore_dev/1.0/lib/perl5/site_perl/5.22.0/BioX/Workflow/Command/run/Utils/Directives.pm line 426
        BioX::Workflow::Command::run::Utils::Directives::create_attr('BioX::Workflow::Command::run::Utils::Directives=HASH(0x5e33e80)', 'ARRAY(0x5d4d260)') called at /scratch/gencore/.local/easybuild/software/gencore_dev/1.0/lib/perl5/site_perl/5.22.0/BioX/Workflow/Command/run/Utils/Attributes.pm line 217
        BioX::Workflow::Command::run::Utils::Attributes::apply_global_attributes('BioX::Workflow::Command::run=HASH(0x50d8528)') called at /scratch/gencore/.local/easybuild/software/gencore_dev/1.0/lib/perl5/site_perl/5.22.0/BioX/Workflow/Command/run.pm line 52
        BioX::Workflow::Command::run::execute('BioX::Workflow::Command::run=HASH(0x50d8528)') called at /scratch/gencore/.local/easybuild/software/gencore_dev/1.0/bin/biox line 8
jerowe commented 7 years ago

This was resolved in 2.1.12