diff --git a/CGATPipelines/Report.py b/CGATPipelines/Report.py index f3f911890..2704c2931 100644 --- a/CGATPipelines/Report.py +++ b/CGATPipelines/Report.py @@ -55,9 +55,9 @@ def run_report(clean=True, # from R plots. xvfb_command = IOTools.which("xvfb-run") - # permit multiple servers using -a option + # permit multiple servers using -d option if xvfb_command: - xvfb_command += " -a " + xvfb_command += " -d " else: xvfb_command = "" diff --git a/CGATPipelines/pipeline_enrichment.py b/CGATPipelines/pipeline_enrichment.py index ef1e147a6..60d613197 100644 --- a/CGATPipelines/pipeline_enrichment.py +++ b/CGATPipelines/pipeline_enrichment.py @@ -412,7 +412,7 @@ def runGsea(infile, outfile): resultsdir, output_fn = os.path.split(outfile) statement = ("cd {resultsdir} && " - "xvfb-run " + "xvfb-run -d " "cgat runGSEA " "-f ../{infile} -g {geneset} -m {min_size} -x {max_size} " "-s {seed} -n {no} -d {p_no} -l {l_no} " diff --git a/CGATPipelines/pipeline_testing.py b/CGATPipelines/pipeline_testing.py index ddaa36870..7d15dd2fc 100644 --- a/CGATPipelines/pipeline_testing.py +++ b/CGATPipelines/pipeline_testing.py @@ -259,12 +259,13 @@ def run_test(infile, outfile): #to_cluster = False template_statement = ( - "(cd %%(track)s.dir; " - "cgatflow %%(pipeline_name)s " + "cd %%(track)s.dir; " + "xvfb-run -d cgatflow %%(pipeline_name)s " "%%(pipeline_options)s " - "%%(workflow_options)s make %s) " - "1> %%(outfile)s " - "2> %%(outfile)s.stderr") + "%%(workflow_options)s make %s " + "-L ../%%(outfile)s " + "-S ../%%(outfile)s.stdout " + "-E ../%%(outfile)s.stderr") if len(pipeline_targets) == 1: statement = template_statement % pipeline_targets[0] @@ -302,8 +303,12 @@ def run_reports(infile, outfile): pipeline_name = PARAMS.get("%s_pipeline" % track, track[len("test_"):]) statement = ''' - (cd %(track)s.dir; cgatflow %(pipeline_name)s - %(pipeline_options)s %(workflow_options)s make build_report) 1> %(outfile)s 2> %(outfile)s.stderr + cd %(track)s.dir; + xvfb-run -d cgatflow %(pipeline_name)s + %(pipeline_options)s %(workflow_options)s make build_report + -L ../%(outfile)s + -S ../%(outfile)s.stdout + -E ../%(outfile)s.stderr ''' P.run(statement, ignore_errors=True)