Writing a Script Calling a Third Party Tool » History » Version 12
Sarah Guthrie, 04/06/2016 08:46 PM
1 | 1 | Sarah Guthrie | {{>toc}} |
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3 | h1. Writing a Script Calling a Third Party Tool |
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5 | Case study: FastQC |
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6 | |||
7 | Good tips include: |
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8 | * Keep the Dockerfile in the git repository |
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9 | |||
10 | h3. Writing a Dockerfile |
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12 | 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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14 | 1 | Sarah Guthrie | Docker has some wonderful documentation for building Dockerfiles: |
15 | * A reference for Dockerfiles: https://docs.docker.com/engine/reference/builder/ |
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16 | * Dockerfile best practices: https://docs.docker.com/engine/userguide/eng-image/dockerfile_best-practices/ |
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17 | |||
18 | From Docker: |
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19 | |||
20 | """ |
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21 | 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. |
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23 | 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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24 | """ |
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25 | |||
26 | <pre> |
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27 | FROM arvados/jobs |
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28 | |||
29 | USER root |
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30 | |||
31 | RUN apt-get -q update && apt-get -qy install \ |
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32 | fontconfig \ |
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33 | openjdk-6-jre-headless \ |
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34 | perl \ |
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35 | unzip \ |
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36 | wget |
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37 | |||
38 | USER crunch |
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39 | |||
40 | RUN mkdir /home/crunch/fastqc |
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41 | RUN cd /home/crunch/fastqc && \ |
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42 | wget --quiet http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.4.zip && \ |
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43 | unzip /home/crunch/fastqc/fastqc_v0.11.4.zip |
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44 | |||
45 | </pre> |
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46 | |||
47 | h3. How to build a docker image from a Dockerfile |
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48 | |||
49 | <pre> |
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50 | docker build -t username/imagename path/to/Dockerfile/ |
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51 | </pre> |
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52 | |||
53 | h3. How to upload a docker image to Arvados |
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54 | |||
55 | <pre> |
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56 | arv keep put username/imagename |
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57 | </pre> |
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58 | |||
59 | h3. How to call an external tool from a crunch script |
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60 | |||
61 | 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. |
62 | 1 | Sarah Guthrie | |
63 | <pre> |
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64 | import subprocess |
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65 | 2 | Sarah Guthrie | foo = subprocess.check_output(['echo','foo']) |
66 | 1 | Sarah Guthrie | </pre> |
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68 | 3 | Sarah Guthrie | If the output is big, @subprocess.check_call@ can redirect it to a file while ensuring the tool completed successfully. |
69 | 1 | Sarah Guthrie | |
70 | <pre> |
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71 | import subprocess |
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72 | with open('foo', 'w') as outfile: |
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73 | subprocess.check_call(['head', '-c', '1234567', '/dev/urandom'], stdout=outfile) |
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74 | </pre> |
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75 | 2 | Sarah Guthrie | |
76 | 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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77 | |||
78 | <pre> |
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79 | import subprocess |
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80 | import arvados |
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81 | |||
82 | #Grab the file path pointing to the file to run fastqc on |
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83 | fastq_file = arvados.getjobparam('input_fastq_file') |
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84 | |||
85 | cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc', fastq_file] |
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86 | subprocess.check_call(cmd) |
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87 | </pre> |
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88 | 1 | Sarah Guthrie | |
89 | h3. Where to put temporary files |
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90 | 6 | Sarah Guthrie | |
91 | 5 | Sarah Guthrie | <pre> |
92 | import arvados |
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93 | |||
94 | task = arvados.current_task() |
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95 | tmpdir = task.tmpdir |
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96 | </pre> |
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97 | |||
98 | Inside the code: |
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99 | 1 | Sarah Guthrie | |
100 | <pre> |
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101 | 4 | Sarah Guthrie | import subprocess |
102 | 1 | Sarah Guthrie | import arvados |
103 | 4 | Sarah Guthrie | |
104 | 1 | Sarah Guthrie | task = arvados.current_task() |
105 | tmpdir = task.tmpdir |
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106 | |||
107 | 4 | Sarah Guthrie | #Grab the file path pointing to the file to run fastqc on |
108 | fastq_file = arvados.getjobparam('input_fastq_file') |
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109 | |||
110 | cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc', fastq_file, '-o', tmpdir] |
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111 | subprocess.check_call(cmd) |
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112 | |||
113 | 1 | Sarah Guthrie | </pre> |
114 | |||
115 | h3. How to write data directly to Keep (Using TaskOutputDir) |
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116 | |||
117 | <pre> |
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118 | 8 | Sarah Guthrie | import arvados |
119 | import arvados.crunch |
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120 | |||
121 | outdir = arvados.crunch.TaskOutputDir() |
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122 | |||
123 | # Write to outdir.path |
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124 | |||
125 | arvados.task_set_output(outdir.manifest_text()) |
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126 | </pre> |
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127 | |||
128 | Inside the code: |
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129 | |||
130 | <pre> |
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131 | 7 | Sarah Guthrie | import subprocess |
132 | 1 | Sarah Guthrie | import arvados |
133 | import arvados.crunch |
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134 | 7 | Sarah Guthrie | |
135 | 1 | Sarah Guthrie | outdir = arvados.crunch.TaskOutputDir() |
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137 | 7 | Sarah Guthrie | #Grab the file path pointing to the file to run fastqc on |
138 | fastq_file = arvados.getjobparam('input_fastq_file') |
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139 | |||
140 | cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc', fastq_file, '-o', outdir.path] |
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141 | subprocess.check_call(cmd) |
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142 | 1 | Sarah Guthrie | |
143 | arvados.task_set_output(outdir.manifest_text()) |
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144 | </pre> |
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145 | |||
146 | h3. When TaskOutputDir is not the correct choice |
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147 | |||
148 | * If the tool writes symbolic links or named pipes, which are not supported by fuse |
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149 | * If the I/O access patterns are not performant with fuse |
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150 | ** This occurs in Tophat, which opens 20 file handles on multiple files that it writes out |
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151 | 9 | Sarah Guthrie | |
152 | Open a collection writer, write files and/or directory trees: |
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153 | |||
154 | 1 | Sarah Guthrie | <pre> |
155 | import arvados |
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156 | 9 | Sarah Guthrie | |
157 | collection_writer = arvados.collection.CollectionWriter() |
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158 | collection_writer.write_file('foo.txt') |
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159 | collection_writer.write_directory_tree(bar_directory_path) |
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160 | arvados.task_set_output(collection_writer.finish()) |
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161 | </pre> |
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162 | |||
163 | Inside the code: |
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164 | |||
165 | <pre> |
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166 | import subprocess |
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167 | import arvados |
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168 | 1 | Sarah Guthrie | import os |
169 | 9 | Sarah Guthrie | |
170 | 1 | Sarah Guthrie | task = arvados.current_task() |
171 | tmpdir = task.tmpdir |
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172 | |||
173 | 9 | Sarah Guthrie | outdir_path = os.path.join(tmpdir, 'out') |
174 | os.mkdir(outdir_path) |
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175 | 1 | Sarah Guthrie | |
176 | 9 | Sarah Guthrie | #Grab the file path pointing to the file to run fastqc on |
177 | fastq_file = arvados.getjobparam('input_fastq_file') |
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178 | |||
179 | cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc', fastq_file, '-o', outdir_path] |
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180 | subprocess.check_call(cmd) |
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181 | 1 | Sarah Guthrie | |
182 | collection_writer = arvados.collection.CollectionWriter() |
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183 | 10 | Sarah Guthrie | collection_writer.write_file('foo.txt') |
184 | collection_writer.write_directory_tree(outdir_path) |
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185 | 1 | Sarah Guthrie | arvados.task_set_output(collection_writer.finish()) |
186 | |||
187 | </pre> |
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188 | |||
189 | h3. Putting it all together |
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190 | |||
191 | <pre> |
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192 | import subprocess |
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193 | 11 | Sarah Guthrie | import arvados |
194 | import arvados.crunch |
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195 | 1 | Sarah Guthrie | |
196 | 11 | Sarah Guthrie | outdir = arvados.crunch.TaskOutputDir() |
197 | 1 | Sarah Guthrie | |
198 | 11 | Sarah Guthrie | #Grab the file path pointing to the file to run fastqc on |
199 | fastq_file = arvados.getjobparam('input_fastq_file') |
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200 | 1 | Sarah Guthrie | |
201 | 11 | Sarah Guthrie | #Grab the number of threads available |
202 | num_threads = multiprocessing.cpu_count() |
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203 | |||
204 | cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc', fastq_file, '-o', outdir.path, '-t', str(num_threads)] |
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205 | subprocess.check_call(cmd) |
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206 | |||
207 | arvados.task_set_output(outdir.manifest_text()) |
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208 | 1 | Sarah Guthrie | </pre> |