Writing a Script Calling a Third Party Tool » History » Version 6
Sarah Guthrie, 04/06/2016 08:11 PM
1 | 1 | Sarah Guthrie | {{>toc}} |
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2 | |||
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 | 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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11 | |||
12 | Docker has some wonderful documentation for building Dockerfiles: |
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13 | * A reference for Dockerfiles: https://docs.docker.com/engine/reference/builder/ |
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14 | * Dockerfile best practices: https://docs.docker.com/engine/userguide/eng-image/dockerfile_best-practices/ |
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15 | |||
16 | From Docker: |
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17 | |||
18 | """ |
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19 | 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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21 | 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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22 | """ |
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23 | |||
24 | <pre> |
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25 | FROM arvados/jobs |
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26 | |||
27 | USER root |
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28 | |||
29 | RUN apt-get -q update && apt-get -qy install \ |
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30 | fontconfig \ |
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31 | openjdk-6-jre-headless \ |
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32 | perl \ |
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33 | unzip \ |
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34 | wget |
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35 | |||
36 | USER crunch |
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37 | |||
38 | RUN mkdir /home/crunch/fastqc |
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39 | RUN cd /home/crunch/fastqc && \ |
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40 | wget --quiet http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.4.zip && \ |
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41 | unzip /home/crunch/fastqc/fastqc_v0.11.4.zip |
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42 | |||
43 | </pre> |
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44 | |||
45 | h3. How to build a docker image from a Dockerfile |
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46 | |||
47 | <pre> |
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48 | docker build -t username/imagename path/to/Dockerfile/ |
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49 | </pre> |
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50 | |||
51 | h3. How to upload a docker image to Arvados |
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52 | |||
53 | <pre> |
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54 | arv keep put username/imagename |
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55 | </pre> |
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56 | |||
57 | h3. How to call an external tool from a crunch script |
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58 | |||
59 | 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. |
60 | 1 | Sarah Guthrie | |
61 | <pre> |
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62 | import subprocess |
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63 | 2 | Sarah Guthrie | foo = subprocess.check_output(['echo','foo']) |
64 | 1 | Sarah Guthrie | </pre> |
65 | |||
66 | 3 | Sarah Guthrie | If the output is big, @subprocess.check_call@ can redirect it to a file while ensuring the tool completed successfully. |
67 | 1 | Sarah Guthrie | |
68 | <pre> |
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69 | import subprocess |
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70 | with open('foo', 'w') as outfile: |
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71 | subprocess.check_call(['head', '-c', '1234567', '/dev/urandom'], stdout=outfile) |
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72 | </pre> |
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73 | 2 | Sarah Guthrie | |
74 | 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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75 | |||
76 | <pre> |
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77 | import subprocess |
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78 | import arvados |
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79 | |||
80 | #Grab the file path pointing to the file to run fastqc on |
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81 | fastq_file = arvados.getjobparam('input_fastq_file') |
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82 | |||
83 | cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc', fastq_file] |
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84 | subprocess.check_call(cmd) |
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85 | </pre> |
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86 | 1 | Sarah Guthrie | |
87 | h3. Where to put temporary files |
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88 | 6 | Sarah Guthrie | |
89 | 5 | Sarah Guthrie | <pre> |
90 | import arvados |
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91 | |||
92 | task = arvados.current_task() |
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93 | tmpdir = task.tmpdir |
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94 | </pre> |
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95 | |||
96 | Inside the code: |
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97 | 1 | Sarah Guthrie | |
98 | <pre> |
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99 | 4 | Sarah Guthrie | import subprocess |
100 | 1 | Sarah Guthrie | import arvados |
101 | 4 | Sarah Guthrie | |
102 | 1 | Sarah Guthrie | task = arvados.current_task() |
103 | tmpdir = task.tmpdir |
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104 | |||
105 | 4 | Sarah Guthrie | #Grab the file path pointing to the file to run fastqc on |
106 | fastq_file = arvados.getjobparam('input_fastq_file') |
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107 | |||
108 | cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc', fastq_file, '-o', tmpdir] |
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109 | subprocess.check_call(cmd) |
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110 | |||
111 | 1 | Sarah Guthrie | </pre> |
112 | |||
113 | h3. How to write data directly to Keep (Using TaskOutputDir) |
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114 | |||
115 | <pre> |
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116 | import arvados |
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117 | import arvados.crunch |
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118 | import os |
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119 | outdir = arvados.crunch.TaskOutputDir() |
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120 | |||
121 | with open(os.path.join(outdir.path, 'foo'), 'w') as outfile: |
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122 | subprocess.check_call(['head', '-c', '1234567', '/dev/urandom'], stdout=outfile) |
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123 | |||
124 | arvados.task_set_output(outdir.manifest_text()) |
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125 | </pre> |
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126 | |||
127 | h3. When TaskOutputDir is not the correct choice |
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128 | |||
129 | * If the tool writes symbolic links or named pipes, which are not supported by fuse |
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130 | * If the I/O access patterns are not performant with fuse |
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131 | ** This occurs in Tophat, which opens 20 file handles on multiple files that it writes out |
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132 | |||
133 | <pre> |
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134 | import arvados |
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135 | import os |
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136 | task = arvados.current_task() |
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137 | tmpdir = task.tmpdir |
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138 | |||
139 | os.mkdir(os.path.join(tmpdir, 'out')) |
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140 | |||
141 | with open(os.path.join(tmpdir, 'out', 'foo.txt'), 'w') as out: |
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142 | subprocess.check_call(['head', '-c', '1234567', '/dev/urandom'], stdout=outfile) |
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143 | |||
144 | collection_writer = arvados.collection.CollectionWriter() |
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145 | collection_writer.write_file('random_file.txt') |
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146 | collection_writer.write_directory_tree(os.path.join(tmpdir, 'out')) |
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147 | arvados.task_set_output(collection_writer.finish()) |
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148 | |||
149 | </pre> |
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150 | |||
151 | h3. Putting it all together |
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152 | |||
153 | <pre> |
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154 | import subprocess |
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155 | |||
156 | cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc'] |
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157 | fq_files = sorted(glob.glob('*.fq*')) |
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158 | fastq_files = sorted(glob.glob('*.fastq*')) |
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159 | cmd.extend(fq_files+fastq_files) |
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160 | cmd.extend(['-o', outdirpath, '-t', str(num_threads)]) |
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161 | fastqc_pipe = subprocess.Popen(cmd) |
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162 | fastqc_pipe.wait() |
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163 | |||
164 | coll_writer = arvados.CollectionWriter() |
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165 | coll_writer.write_directory_tree(outdirpath) |
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166 | pdh = coll_writer.finish() |
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167 | |||
168 | body = {'output':pdh, 'success':fastqc_pipe.returncode==0, 'progress':1.0} |
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169 | arvados.api('v1').job_tasks().update(uuid=this_task['uuid'], body=body).execute() |
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170 | </pre> |