Contents

require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
require 'rbbt/hpc/slurm'
require 'rbbt/workflow'

Workflow.require_workflow "Sample"
Workflow.require_workflow "HTS"
class TestSLURM < Test::Unit::TestCase

  def _test_template
    job = Sample.job(:mutect2, "small", :reference => "hg38")

    TmpFile.with_file do |batch_dir|

      template = HPC::SLURM.job_template(job, :batch_dir => batch_dir, :batch_modules => 'java')
      ppp template

    end
  end

  def test_run_job
    job = Sample.job(:mutect2, "small", :reference => "hg38")

    job.clean

    jobid = HPC::SLURM.run_job(job, :workflows => "HTS", :batch_modules => 'java', :env_cmd => '_JAVA_OPTIONS="-Xms1g -Xmx${MAX_MEMORY}m"', :queue => :debug, :time => '01:00:00', :config_keys => "HTS_light", :task_cpus => '10', :tail => true, :clean_task => "HTS#mutect2")
    iii jobid
  end

end

Version data entries

99 entries across 99 versions & 1 rubygems

Version	Path
rbbt-util-5.33.18	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.17	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.16	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.15	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.14	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.13	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.12	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.11	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.9	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.8	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.7	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.6	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.5	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.4	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.3	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.2	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.1	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.33.0	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.32.30	test/rbbt/hpc/test_slurm.rb
rbbt-util-5.32.28	test/rbbt/hpc/test_slurm.rb