Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/schemas/v1.1/invocation.md @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 # Running a Command
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2
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3 To accommodate the enormous variety in syntax and semantics for input, runtime
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4 environment, invocation, and output of arbitrary programs, a CommandLineTool
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5 defines an "input binding" that describes how to translate abstract input
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6 parameters to an concrete program invocation, and an "output binding" that
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7 describes how to generate output parameters from program output.
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8
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9 ## Input binding
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10
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11 The tool command line is built by applying command line bindings to the
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12 input object. Bindings are listed either as part of an [input
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13 parameter](#CommandInputParameter) using the `inputBinding` field, or
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14 separately using the `arguments` field of the CommandLineTool.
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15
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16 The algorithm to build the command line is as follows. In this algorithm,
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17 the sort key is a list consisting of one or more numeric or string
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18 elements. Strings are sorted lexicographically based on UTF-8 encoding.
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19
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20 1. Collect `CommandLineBinding` objects from `arguments`. Assign a sorting
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21 key `[position, i]` where `position` is
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22 [`CommandLineBinding.position`](#CommandLineBinding) and `i`
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23 is the index in the `arguments` list.
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24
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25 2. Collect `CommandLineBinding` objects from the `inputs` schema and
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26 associate them with values from the input object. Where the input type
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27 is a record, array, or map, recursively walk the schema and input object,
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28 collecting nested `CommandLineBinding` objects and associating them with
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29 values from the input object.
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30
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31 3. Create a sorting key by taking the value of the `position` field at
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32 each level leading to each leaf binding object. If `position` is not
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33 specified, it is not added to the sorting key. For bindings on arrays
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34 and maps, the sorting key must include the array index or map key
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35 following the position. If and only if two bindings have the same sort
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36 key, the tie must be broken using the ordering of the field or parameter
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37 name immediately containing the leaf binding.
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38
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39 4. Sort elements using the assigned sorting keys. Numeric entries sort
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40 before strings.
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41
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42 5. In the sorted order, apply the rules defined in
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43 [`CommandLineBinding`](#CommandLineBinding) to convert bindings to actual
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44 command line elements.
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45
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46 6. Insert elements from `baseCommand` at the beginning of the command
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47 line.
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48
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49 ## Runtime environment
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50
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51 All files listed in the input object must be made available in the runtime
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52 environment. The implementation may use a shared or distributed file
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53 system or transfer files via explicit download to the host. Implementations
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54 may choose not to provide access to files not explicitly specified in the input
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55 object or process requirements.
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56
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57 Output files produced by tool execution must be written to the
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58 **designated output directory**. The initial current working
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59 directory when executing the tool must be the designated output
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60 directory. The designated output directory should be empty, except
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61 for files or directories specified using
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62 [InitialWorkDirRequirement](InitialWorkDirRequirement).
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63
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64 Files may also be written to the **designated temporary directory**. This
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65 directory must be isolated and not shared with other processes. Any files
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66 written to the designated temporary directory may be automatically deleted by
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67 the workflow platform immediately after the tool terminates.
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68
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69 For compatibility, files may be written to the **system temporary directory**
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70 which must be located at `/tmp`. Because the system temporary directory may be
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71 shared with other processes on the system, files placed in the system temporary
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72 directory are not guaranteed to be deleted automatically. A tool
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73 must not use the system temporary directory as a backchannel communication with
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74 other tools. It is valid for the system temporary directory to be the same as
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75 the designated temporary directory.
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76
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77 When executing the tool, the tool must execute in a new, empty environment
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78 with only the environment variables described below; the child process must
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79 not inherit environment variables from the parent process except as
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80 specified or at user option.
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81
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82 * `HOME` must be set to the designated output directory.
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83 * `TMPDIR` must be set to the designated temporary directory.
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84 * `PATH` may be inherited from the parent process, except when run in a
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85 container that provides its own `PATH`.
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86 * Variables defined by [EnvVarRequirement](#EnvVarRequirement)
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87 * The default environment of the container, such as when using
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88 [DockerRequirement](#DockerRequirement)
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89
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90 An implementation may forbid the tool from writing to any location in the
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91 runtime environment file system other than the designated temporary directory,
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92 system temporary directory, and designated output directory. An implementation
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93 may provide read-only input files, and disallow in-place update of input files.
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94 The designated temporary directory, system temporary directory and designated
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95 output directory may each reside on different mount points on different file
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96 systems.
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97
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98 An implementation may forbid the tool from directly accessing network
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99 resources. Correct tools must not assume any network access. Future versions
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100 of the specification may incorporate optional process requirements that
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101 describe the networking needs of a tool.
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102
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103 The `runtime` section available in [parameter references](#Parameter_references)
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104 and [expressions](#Expressions) contains the following fields. As noted
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105 earlier, an implementation may perform deferred resolution of runtime fields by providing
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106 opaque strings for any or all of the following fields; parameter references
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107 and expressions may only use the literal string value of the field and must
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108 not perform computation on the contents.
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109
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110 * `runtime.outdir`: an absolute path to the designated output directory
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111 * `runtime.tmpdir`: an absolute path to the designated temporary directory
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112 * `runtime.cores`: number of CPU cores reserved for the tool process
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113 * `runtime.ram`: amount of RAM in mebibytes (2\*\*20) reserved for the tool process
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114 * `runtime.outdirSize`: reserved storage space available in the designated output directory
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115 * `runtime.tmpdirSize`: reserved storage space available in the designated temporary directory
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116
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117 For `cores`, `ram`, `outdirSize` and `tmpdirSize`, if an implementation can't
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118 provide the actual number of reserved cores during the expression evaluation time,
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119 it should report back the minimal requested amount.
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120
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121 See [ResourceRequirement](#ResourceRequirement) for details on how to
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122 describe the hardware resources required by a tool.
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123
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124 The standard input stream and standard output stream may be redirected as
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125 described in the `stdin` and `stdout` fields.
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126
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127 ## Execution
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128
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129 Once the command line is built and the runtime environment is created, the
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130 actual tool is executed.
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131
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132 The standard error stream and standard output stream (unless redirected by
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133 setting `stdout` or `stderr`) may be captured by platform logging facilities
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134 for storage and reporting.
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135
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136 Tools may be multithreaded or spawn child processes; however, when the
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137 parent process exits, the tool is considered finished regardless of whether
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138 any detached child processes are still running. Tools must not require any
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139 kind of console, GUI, or web based user interaction in order to start and
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140 run to completion.
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141
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142 The exit code of the process indicates if the process completed
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143 successfully. By convention, an exit code of zero is treated as success
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144 and non-zero exit codes are treated as failure. This may be customized by
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145 providing the fields `successCodes`, `temporaryFailCodes`, and
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146 `permanentFailCodes`. An implementation may choose to default unspecified
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147 non-zero exit codes to either `temporaryFailure` or `permanentFailure`.
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148
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149 The exit code of the process is available to expressions in
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150 `outputEval` as `runtime.exitCode`.
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151
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152 ## Output binding
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153
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154 If the output directory contains a file named "cwl.output.json", that file
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155 must be loaded and used as the output object. Otherwise, the output object
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156 must be generated by walking the parameters listed in `outputs` and
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157 applying output bindings to the tool output. Output bindings are
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158 associated with output parameters using the `outputBinding` field. See
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159 [`CommandOutputBinding`](#CommandOutputBinding) for details.