Mercurial > repos > davidvanzessen > argalaxy_tools
comparison tests/test_imgt.py @ 57:33412e85e669 draft
"planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"
author | rhpvorderman |
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date | Wed, 02 Feb 2022 10:50:01 +0000 |
parents | 7ae6b6b5d890 |
children |
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56:7ae6b6b5d890 | 57:33412e85e669 |
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75 clonality_method | 75 clonality_method |
76 ] | 76 ] |
77 docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}", | 77 docker_cmd = ["docker", "run", "-v", f"{temp_dir}:{temp_dir}", |
78 "-v", f"{sample}:{sample}", | 78 "-v", f"{sample}:{sample}", |
79 "-w", str(working_dir), | 79 "-w", str(working_dir), |
80 # Run as current user which allows deletion of files. | |
81 # It also mitigates some security considerations | |
82 "-u", f"{os.getuid()}:{os.getgid()}", | |
83 # Run with default seccomp profile to mitigate mitigation slowdown | |
84 # http://mamememo.blogspot.com/2020/05/cpu-intensive-rubypython-code-runs.html | |
85 "--security-opt", "seccomp=unconfined", | |
80 get_container()] + cmd | 86 get_container()] + cmd |
81 with open(temp_dir / "stderr", "wt") as stderr_file: | 87 with open(temp_dir / "stderr", "wt") as stderr_file: |
82 with open(temp_dir / "stdout", "wt") as stdout_file: | 88 with open(temp_dir / "stdout", "wt") as stdout_file: |
83 subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file, | 89 subprocess.run(docker_cmd, cwd=working_dir, stdout=stdout_file, |
84 stderr=stderr_file, check=True) | 90 stderr=stderr_file, check=True) |