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Pipeline template template » History » Version 3

Bryan Cosca, 05/21/2015 05:25 PM

1 1 Bryan Cosca
h1. Pipeline template template
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h2. Run-Command Template
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h2. Crunch Script Template
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<pre>
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#!/usr/bin/env python
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import arvados
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import subprocess
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import os
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import sys
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import re
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from arvados.collection import Collection as coll
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import arvados_tools
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import shutil
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arvados_tools.spawn_new_task_per_file('input','.*realigned.bqsrCal.bam$',if_sequence=0, and_end_task=True)
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this_job = arvados.current_job()
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this_task = arvados.current_task()
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tmpdir = arvados.current_task().tmpdir
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input_1 = this_task['parameters']['input_1']
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input_1_path = os.path.join(arvados.get_job_param_mount("input"),input_1)
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tmp_input_1_path = os.path.join(tmpdir,input_1) # If we need to copy to tmpdir
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shutil.copyfile(input_1_path,tmp_input_1_path) # If we need to copy to tmpdir
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</pre> 
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<pre>
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samtools_path = arvados_tools.get_file_path('samtools','^samtools$')
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gatk_path = arvados_tools.get_file_path('gatk_jar','^GenomeAnalysisTK.jar$')
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reference_path = arvados_tools.get_file_path('reference','.*f(ast)?a(.gz)?$')
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dbsnp_path = arvados_tools.get_file_path('dbsnp','^dbsnp.*vcf$')
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</pre>
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<pre>
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gatk_inserttool_args = []
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gatk_inserttool_output_name
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gatk_inserttool_output_path
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gatk_inserttool_pipe = subprocess.check_output()
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</pre>
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<pre>
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samtools_inserttool_args = []
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</pre>
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h2. Script Parameter Template
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h2. Latest arvados_sdk_version: 
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https://arvados.org/projects/arvados/repository/revisions/master/show/sdk/python