Arvados

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

h3. Latest arvados_sdk_version: https://arvados.org/projects/arvados/repository/revisions/master/show/sdk/python