5 title: "Crunch utility libraries"
9 h1. Crunch utility libraries
11 Several utility libraries are included with Arvados. They are intended to make it quicker and easier to write your own crunch scripts.
15 The Python SDK adds some convenience features that are particularly useful in crunch scripts, in addition to the standard set of API calls.
19 In a crunch job, the environment variables @ARVADOS_API_HOST@ and @ARVADOS_API_TOKEN@ will be set up so the job has the privileges of the user who submitted the job.
24 my_user = arvados.api().users().current().execute()
25 my_uuid = my_user['uuid']
28 h4. Get the current job and task parameters
30 @arvados.current_job()@ and @arvados.current_task()@ are convenient ways to retrieve the current Job and Task, using the @JOB_UUID@ and @TASK_UUID@ environment variables provided to each crunch task process.
33 this_job = arvados.current_job()
34 this_task = arvados.current_task()
35 this_job_input = this_job['script_parameters']['input']
36 this_task_input = this_task['parameters']['input']
39 h4(#one_task_per_input). Queue a task for each input file
41 A common pattern for a crunch job is to run one task to scan the input, and one task per input file to do the work.
43 The @one_task_per_input_file()@ function implements this pattern. Pseudocode:
46 if this is the job's first (default) task:
47 for each file in the 'input' collection:
48 queue a new task, with parameters['input'] = file
58 arvados.job_setup.one_task_per_input_file(if_sequence=0, and_end_task=True)
60 # Now do the work on a single file
61 my_input = this_task['parameters']['input']
64 h4. Set the current task's output and success flag
66 Each task in a crunch job must make an API call to record its output and set its @success@ attribute to True. The object returned by @current_task()@ has a @set_output()@ method to make the process more succinct.
69 arvados.current_task().set_output(my_output_locator)
76 Manage child processes and FIFOs (pipes).
80 This module makes it easier to check the exit status of every child process you start, and close the unused end of each FIFO at the appropriate time.
83 from arvados_ipc import *
88 pipe_setup(pipes, 'hellopipe')
89 if 0 == named_fork(children, 'child_a'):
90 pipe_closeallbut(pipes, ('hellopipe', 'w'))
91 os.write(pipes['hellopipe', 'w'], "Hello, parent.")
94 pipe_closeallbut(pipes, ('hellopipe', 'r'))
95 with os.fdopen(pipes['hellopipe', 'r'], 'rb') as f:
97 sys.stderr.write("Child says: " + message + "\n")
99 if not waitpid_and_check_children(children):
100 raise Exception("Child process exited non-zero.")
103 The "crunch scripts" included with Arvados include some more examples of using the arvados_ipc module.
109 The following *arvados-∗.py* modules provide "extract, build, run" helpers to make it easy to incorporate common analysis tools in your crunch scripts.
113 Build and run the "bwa":http://bio-bwa.sourceforge.net/bwa.shtml program.
115 <div class="offset1">
117 The module retrieves the bwa source code from Keep, using the job's @bwa_tbz@ parameter.
121 arvados_bwa.run('aln', [ref_basename, '-'],
122 stdin=open(fastq_filename,'rb'),
123 stdout=open(aln_filename,'wb'))
126 On qr1hi.arvadosapi.com, the source distribution @bwa-0.7.5a.tar.bz2@ is available in the collection @8b6e2c4916133e1d859c9e812861ce13+70@.
130 "script_parameters":{
131 "bwa_tbz":"8b6e2c4916133e1d859c9e812861ce13+70",
142 Extract and run the "Genome Analysis Toolkit":http://www.broadinstitute.org/gatk/ programs.
144 <div class="offset1">
146 The module retrieves the binary distribution tarball from Keep, using the job's @gatk_tbz@ parameter.
152 '-T', 'BaseRecalibrator',
153 '-R', ref_fasta_files[0],
154 '-I', input_bam_files[0],
159 On qr1hi.arvadosapi.com, the binary distribution @GenomeAnalysisTK-2.6-4.tar.bz2@ is available in the collection @5790482512cf6d5d6dfd50b7fd61e1d1+86@.
161 The GATK data bundle is available in the collection @d237a90bae3870b3b033aea1e99de4a9+10820@.
165 "script_parameters":{
166 "gatk_tbz":"7e0a277d6d2353678a11f56bab3b13f2+87",
167 "gatk_bundle":"d237a90bae3870b3b033aea1e99de4a9+10820",
176 h4. arvados_samtools.py
178 Build and run the "samtools":http://samtools.sourceforge.net/samtools.shtml program.
180 <div class="offset1">
182 The module retrieves the samtools source code from Keep, using the job's @samtools_tgz@ parameter.
185 import arvados_samtools
186 arvados_samtools.run('view', ['-S', '-b', '-'],
187 stdin=open(sam_filename,'rb'),
188 stdout=open(bam_filename,'wb'))
191 On qr1hi.arvadosapi.com, the source distribution @samtools-0.1.19.tar.gz@ is available in the collection @c777e23cf13e5d5906abfdc08d84bfdb+74@.
195 "script_parameters":{
196 "samtools_tgz":"c777e23cf13e5d5906abfdc08d84bfdb+74",
205 h4. arvados_picard.py
207 Build and run the "picard":http://picard.sourceforge.net/command-line-overview.shtml program.
209 <div class="offset1">
211 The module retrieves the picard binary distribution from Keep, using the job's @picard_zip@ parameter.
214 import arvados_picard
216 'FixMateInformation',
222 'validation_stringency': 'LENIENT',
223 'compression_level': 0
225 stdout=open('out.bam','wb'))
228 On qr1hi.arvadosapi.com, the binary distribution @picard-tools-1.82.zip@ is available in the collection @687f74675c6a0e925dec619cc2bec25f+77@.
232 "script_parameters":{
233 "picard_zip":"687f74675c6a0e925dec619cc2bec25f+77",