Writing a Script Calling a Third Party Tool » History » Version 14
Sarah Guthrie, 04/06/2016 08:47 PM
1 | 1 | Sarah Guthrie | {{>toc}} |
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3 | h1. Writing a Script Calling a Third Party Tool |
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4 | |||
5 | Case study: FastQC |
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6 | |||
7 | h3. Writing a Dockerfile |
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8 | |||
9 | 12 | Sarah Guthrie | We strongly recommend keeping your Dockerfiles in the git repository with the crunch scripts that run inside the docker images created by them. |
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11 | 1 | Sarah Guthrie | Docker has some wonderful documentation for building Dockerfiles: |
12 | * A reference for Dockerfiles: https://docs.docker.com/engine/reference/builder/ |
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13 | * Dockerfile best practices: https://docs.docker.com/engine/userguide/eng-image/dockerfile_best-practices/ |
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14 | |||
15 | From Docker: |
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16 | |||
17 | 14 | Sarah Guthrie | > Docker can build images automatically by reading the instructions from a Dockerfile. A Dockerfile is a text document that contains all the commands a user could call on the command line to assemble an image. Using docker build users can create an automated build that executes several command-line instructions in succession. |
18 | > |
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19 | > This page describes the commands you can use in a Dockerfile. When you are done reading this page, refer to the Dockerfile Best Practices (https://docs.docker.com/engine/userguide/eng-image/dockerfile_best-practices/) for a tip-oriented guide. |
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20 | > |
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21 | 1 | Sarah Guthrie | |
22 | <pre> |
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23 | FROM arvados/jobs |
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24 | |||
25 | USER root |
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26 | |||
27 | RUN apt-get -q update && apt-get -qy install \ |
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28 | fontconfig \ |
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29 | openjdk-6-jre-headless \ |
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30 | perl \ |
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31 | unzip \ |
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32 | wget |
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33 | |||
34 | USER crunch |
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35 | |||
36 | RUN mkdir /home/crunch/fastqc |
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37 | RUN cd /home/crunch/fastqc && \ |
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38 | wget --quiet http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.4.zip && \ |
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39 | unzip /home/crunch/fastqc/fastqc_v0.11.4.zip |
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40 | |||
41 | </pre> |
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42 | |||
43 | h3. How to build a docker image from a Dockerfile |
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44 | |||
45 | <pre> |
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46 | docker build -t username/imagename path/to/Dockerfile/ |
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47 | </pre> |
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48 | |||
49 | h3. How to upload a docker image to Arvados |
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50 | |||
51 | <pre> |
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52 | arv keep put username/imagename |
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53 | </pre> |
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54 | |||
55 | h3. How to call an external tool from a crunch script |
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56 | |||
57 | 3 | Sarah Guthrie | We strongly recommend using the @subprocess@ module for calling external tools. If the output is small and written to standard out, using @subprocess.check_output@ will ensure the tool completed successfully and return the standard output. |
58 | 1 | Sarah Guthrie | |
59 | <pre> |
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60 | import subprocess |
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61 | 2 | Sarah Guthrie | foo = subprocess.check_output(['echo','foo']) |
62 | 1 | Sarah Guthrie | </pre> |
63 | |||
64 | 3 | Sarah Guthrie | If the output is big, @subprocess.check_call@ can redirect it to a file while ensuring the tool completed successfully. |
65 | 1 | Sarah Guthrie | |
66 | <pre> |
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67 | import subprocess |
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68 | with open('foo', 'w') as outfile: |
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69 | subprocess.check_call(['head', '-c', '1234567', '/dev/urandom'], stdout=outfile) |
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70 | </pre> |
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71 | 2 | Sarah Guthrie | |
72 | FastQC writes to the current output directory or the output directory specified by the @-o@ flag, so we can use @subprocess.check_call@ |
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73 | |||
74 | <pre> |
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75 | import subprocess |
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76 | import arvados |
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77 | |||
78 | #Grab the file path pointing to the file to run fastqc on |
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79 | fastq_file = arvados.getjobparam('input_fastq_file') |
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80 | |||
81 | cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc', fastq_file] |
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82 | subprocess.check_call(cmd) |
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83 | </pre> |
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84 | 1 | Sarah Guthrie | |
85 | h3. Where to put temporary files |
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86 | 6 | Sarah Guthrie | |
87 | 5 | Sarah Guthrie | <pre> |
88 | import arvados |
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89 | |||
90 | task = arvados.current_task() |
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91 | tmpdir = task.tmpdir |
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92 | </pre> |
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93 | |||
94 | Inside the code: |
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95 | 1 | Sarah Guthrie | |
96 | <pre> |
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97 | 4 | Sarah Guthrie | import subprocess |
98 | 1 | Sarah Guthrie | import arvados |
99 | 4 | Sarah Guthrie | |
100 | 1 | Sarah Guthrie | task = arvados.current_task() |
101 | tmpdir = task.tmpdir |
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102 | |||
103 | 4 | Sarah Guthrie | #Grab the file path pointing to the file to run fastqc on |
104 | fastq_file = arvados.getjobparam('input_fastq_file') |
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105 | |||
106 | cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc', fastq_file, '-o', tmpdir] |
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107 | subprocess.check_call(cmd) |
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108 | |||
109 | 1 | Sarah Guthrie | </pre> |
110 | |||
111 | h3. How to write data directly to Keep (Using TaskOutputDir) |
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112 | |||
113 | <pre> |
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114 | 8 | Sarah Guthrie | import arvados |
115 | import arvados.crunch |
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116 | |||
117 | outdir = arvados.crunch.TaskOutputDir() |
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118 | |||
119 | # Write to outdir.path |
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120 | |||
121 | arvados.task_set_output(outdir.manifest_text()) |
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122 | </pre> |
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123 | |||
124 | Inside the code: |
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125 | |||
126 | <pre> |
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127 | 7 | Sarah Guthrie | import subprocess |
128 | 1 | Sarah Guthrie | import arvados |
129 | import arvados.crunch |
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130 | 7 | Sarah Guthrie | |
131 | 1 | Sarah Guthrie | outdir = arvados.crunch.TaskOutputDir() |
132 | |||
133 | 7 | Sarah Guthrie | #Grab the file path pointing to the file to run fastqc on |
134 | fastq_file = arvados.getjobparam('input_fastq_file') |
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135 | |||
136 | cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc', fastq_file, '-o', outdir.path] |
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137 | subprocess.check_call(cmd) |
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138 | 1 | Sarah Guthrie | |
139 | arvados.task_set_output(outdir.manifest_text()) |
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140 | </pre> |
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141 | |||
142 | h3. When TaskOutputDir is not the correct choice |
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143 | |||
144 | * If the tool writes symbolic links or named pipes, which are not supported by fuse |
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145 | * If the I/O access patterns are not performant with fuse |
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146 | ** This occurs in Tophat, which opens 20 file handles on multiple files that it writes out |
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147 | 9 | Sarah Guthrie | |
148 | Open a collection writer, write files and/or directory trees: |
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149 | |||
150 | 1 | Sarah Guthrie | <pre> |
151 | import arvados |
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152 | 9 | Sarah Guthrie | |
153 | collection_writer = arvados.collection.CollectionWriter() |
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154 | collection_writer.write_file('foo.txt') |
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155 | collection_writer.write_directory_tree(bar_directory_path) |
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156 | arvados.task_set_output(collection_writer.finish()) |
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157 | </pre> |
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158 | |||
159 | Inside the code: |
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160 | |||
161 | <pre> |
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162 | import subprocess |
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163 | import arvados |
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164 | 1 | Sarah Guthrie | import os |
165 | 9 | Sarah Guthrie | |
166 | 1 | Sarah Guthrie | task = arvados.current_task() |
167 | tmpdir = task.tmpdir |
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168 | |||
169 | 9 | Sarah Guthrie | outdir_path = os.path.join(tmpdir, 'out') |
170 | os.mkdir(outdir_path) |
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171 | 1 | Sarah Guthrie | |
172 | 9 | Sarah Guthrie | #Grab the file path pointing to the file to run fastqc on |
173 | fastq_file = arvados.getjobparam('input_fastq_file') |
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174 | |||
175 | cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc', fastq_file, '-o', outdir_path] |
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176 | subprocess.check_call(cmd) |
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177 | 1 | Sarah Guthrie | |
178 | collection_writer = arvados.collection.CollectionWriter() |
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179 | 10 | Sarah Guthrie | collection_writer.write_file('foo.txt') |
180 | collection_writer.write_directory_tree(outdir_path) |
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181 | 1 | Sarah Guthrie | arvados.task_set_output(collection_writer.finish()) |
182 | |||
183 | </pre> |
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184 | |||
185 | h3. Putting it all together |
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186 | |||
187 | <pre> |
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188 | import subprocess |
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189 | 11 | Sarah Guthrie | import arvados |
190 | import arvados.crunch |
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191 | 1 | Sarah Guthrie | |
192 | 11 | Sarah Guthrie | outdir = arvados.crunch.TaskOutputDir() |
193 | 1 | Sarah Guthrie | |
194 | 11 | Sarah Guthrie | #Grab the file path pointing to the file to run fastqc on |
195 | fastq_file = arvados.getjobparam('input_fastq_file') |
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196 | 1 | Sarah Guthrie | |
197 | 11 | Sarah Guthrie | #Grab the number of threads available |
198 | num_threads = multiprocessing.cpu_count() |
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199 | |||
200 | cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc', fastq_file, '-o', outdir.path, '-t', str(num_threads)] |
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201 | subprocess.check_call(cmd) |
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202 | |||
203 | arvados.task_set_output(outdir.manifest_text()) |
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204 | 1 | Sarah Guthrie | </pre> |