Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/tool_util/deps/singularity_util.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 import os |
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2 import shlex |
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3 |
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4 DEFAULT_WORKING_DIRECTORY = None |
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5 DEFAULT_SINGULARITY_COMMAND = "singularity" |
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6 DEFAULT_SUDO = False |
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7 DEFAULT_SUDO_COMMAND = "sudo" |
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8 DEFAULT_RUN_EXTRA_ARGUMENTS = None |
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9 |
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10 |
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11 def pull_mulled_singularity_command(docker_image_identifier, |
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12 cache_directory, |
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13 namespace=None, |
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14 singularity_cmd=DEFAULT_SINGULARITY_COMMAND, |
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15 sudo=DEFAULT_SUDO, |
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16 sudo_cmd=DEFAULT_SUDO_COMMAND): |
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17 command_parts = [] |
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18 command_parts += _singularity_prefix( |
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19 singularity_cmd=singularity_cmd, |
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20 sudo=sudo, |
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21 sudo_cmd=sudo_cmd, |
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22 ) |
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23 save_path = docker_image_identifier |
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24 if namespace: |
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25 prefix = "docker://quay.io/%s/" % namespace |
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26 if docker_image_identifier.startswith(prefix): |
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27 save_path = docker_image_identifier[len(prefix):] |
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28 command_parts.extend(["build", os.path.join(cache_directory, save_path), docker_image_identifier]) |
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29 return command_parts |
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30 |
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31 |
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32 def build_singularity_run_command( |
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33 container_command, |
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34 image, |
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35 volumes=None, |
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36 env=None, |
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37 working_directory=DEFAULT_WORKING_DIRECTORY, |
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38 singularity_cmd=DEFAULT_SINGULARITY_COMMAND, |
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39 run_extra_arguments=DEFAULT_RUN_EXTRA_ARGUMENTS, |
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40 sudo=DEFAULT_SUDO, |
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41 sudo_cmd=DEFAULT_SUDO_COMMAND, |
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42 guest_ports=False, |
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43 container_name=None |
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44 ): |
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45 volumes = volumes or [] |
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46 env = env or [] |
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47 command_parts = [] |
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48 # http://singularity.lbl.gov/docs-environment-metadata |
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49 home = None |
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50 for (key, value) in env: |
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51 if key == 'HOME': |
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52 home = value |
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53 command_parts.extend([f"SINGULARITYENV_{key}={value}"]) |
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54 command_parts += _singularity_prefix( |
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55 singularity_cmd=singularity_cmd, |
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56 sudo=sudo, |
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57 sudo_cmd=sudo_cmd, |
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58 ) |
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59 command_parts.append("-s") |
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60 command_parts.append("exec") |
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61 for volume in volumes: |
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62 command_parts.extend(["-B", str(volume)]) |
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63 if home is not None: |
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64 command_parts.extend(["--home", f"{home}:{home}"]) |
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65 if run_extra_arguments: |
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66 command_parts.append(run_extra_arguments) |
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67 full_image = image |
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68 command_parts.append(shlex.quote(full_image)) |
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69 command_parts.append(container_command) |
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70 return " ".join(command_parts) |
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71 |
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72 |
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73 def _singularity_prefix( |
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74 singularity_cmd=DEFAULT_SINGULARITY_COMMAND, |
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75 sudo=DEFAULT_SUDO, |
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76 sudo_cmd=DEFAULT_SUDO_COMMAND, |
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77 **kwds |
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78 ): |
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79 """Prefix to issue a singularity command.""" |
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80 command_parts = [] |
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81 if sudo: |
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82 command_parts.append(sudo_cmd) |
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83 command_parts.append(singularity_cmd) |
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84 return command_parts |
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85 |
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86 |
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87 __all__ = ("build_singularity_run_command", "pull_mulled_singularity_command") |