Arvados

Pipeline template template » History » Revision 3

Revision 2 (Bryan Cosca, 05/21/2015 05:24 PM) → Revision 3/25 (Bryan Cosca, 05/21/2015 05:25 PM)

h1. Pipeline template template 

 h2. Run-Command Template 


 h2. Crunch Script Template 
 <pre> 
 #!/usr/bin/env python 

 import arvados 
 import subprocess 
 import os 
 import sys 
 import re 
 from arvados.collection import Collection as coll 
 import arvados_tools 
 import shutil 

 arvados_tools.spawn_new_task_per_file('input','.*realigned.bqsrCal.bam$',if_sequence=0, and_end_task=True) 

 this_job = arvados.current_job() 
 this_task = arvados.current_task() 
 tmpdir = arvados.current_task().tmpdir 

 input_1 = this_task['parameters']['input_1'] 
 input_1_path = os.path.join(arvados.get_job_param_mount("input"),input_1) 
 tmp_input_1_path = os.path.join(tmpdir,input_1) # If we need to copy to tmpdir 
 shutil.copyfile(input_1_path,tmp_input_1_path) # If we need to copy to tmpdir 
 </pre>  


 <pre> 
 samtools_path = arvados_tools.get_file_path('samtools','^samtools$') 
 gatk_path = arvados_tools.get_file_path('gatk_jar','^GenomeAnalysisTK.jar$') 
 reference_path = arvados_tools.get_file_path('reference','.*f(ast)?a(.gz)?$') 
 dbsnp_path = arvados_tools.get_file_path('dbsnp','^dbsnp.*vcf$') 
 </pre> 

 <pre> 
 gatk_inserttool_args = [] 
 gatk_inserttool_output_name 
 gatk_inserttool_output_path 
 gatk_inserttool_pipe = subprocess.check_output() 
 </pre> 

 <pre> 
 samtools_inserttool_args = [] 
 </pre> 

 

 h2. Script Parameter Template 


 h2. h3. Latest arvados_sdk_version:  

 https://arvados.org/projects/arvados/repository/revisions/master/show/sdk/python