diff --git a/bacterial_mobile_elem/ncbi_crisper_wnode.cwl b/bacterial_mobile_elem/ncbi_crisper_wnode.cwl index d8e53f1..c0b4a96 100644 --- a/bacterial_mobile_elem/ncbi_crisper_wnode.cwl +++ b/bacterial_mobile_elem/ncbi_crisper_wnode.cwl @@ -16,7 +16,7 @@ inputs: prefix: -input-jobs crisper_path: type: string? - default: /opt/crispr/1.02/bin/ + default: /opt/crispr/1.03/bin/ inputBinding: prefix: -ncbi-crisper-path output_dir: diff --git a/scripts/pgap.py b/scripts/pgap.py index 4493d97..e82db79 100755 --- a/scripts/pgap.py +++ b/scripts/pgap.py @@ -219,6 +219,8 @@ def __init__(self, params, local_input, pipeline): def make_docker_cmd(self): self.cmd = [self.params.docker_cmd, 'run', '-i', '--rm' ] + self.cmd.extend(['--platform', 'linux/amd64']) + if self.params.docker_user_remap: self.cmd.extend(['--user', str(os.getuid()) + ":" + str(os.getgid())]) self.cmd.extend([ @@ -531,11 +533,13 @@ def launch(self): for line in fIn: f.write(line) f.write("--- End YAML Input ---\n\n") - # Show runtime parameters in the log - f.write("--- Start Runtime Report ---\n") - self.record_runtime(f) - f.write("\n--- End Runtime Report ---\n\n") - f.flush() + + if platform.system() != "Darwin": + # Show runtime parameters in the log + f.write("--- Start Runtime Report ---\n") + self.record_runtime(f) + f.write("\n--- End Runtime Report ---\n\n") + try: proc = subprocess.Popen(self.cmd, stdout=f, stderr=subprocess.STDOUT) proc.wait()