---
layout: default
navsection: userguide
title: "Crunch utility libraries"
navorder: 31
---

h1. Crunch utility libraries

Several utility libraries are included with Arvados. They are intended to make it quicker and easier to write your own crunch scripts.

h4. Python SDK extras

The Python SDK adds some convenience features that are particularly useful in crunch scripts, in addition to the standard set of API calls.

<div class="offset1">

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.

<pre>
import arvados

my_user = arvados.api().users().current().execute()
my_uuid = my_user['uuid']
</pre>

h4. Get the current job and task parameters

@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.

<pre>
this_job = arvados.current_job()
this_task = arvados.current_task()
this_job_input = this_job['script_parameters']['input']
this_task_input = this_task['parameters']['input']
</pre>

h4. Queue a task for each input file

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.

The @one_task_per_input_file()@ function implements this pattern. Pseudocode:

<pre>
if this is the job's first (default) task:
    for each file in the 'input' collection:
        queue a new task, with parameters['input'] = file
    exit
else:
    return
</pre>

Usage:

<pre>
import arvados
arvados.job_setup.one_task_per_input_file(if_sequence=0, and_end_task=True)

# Now do the work on a single file
my_input = this_task['parameters']['input']
</pre>

h4. Set the current task's output and success flag

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.

<pre>
arvados.current_task().set_output(my_output_locator)
</pre>

</div>

h4. arvados_ipc.py

Manage child processes and FIFOs (pipes).

<div class="offset1">

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.

<pre>
from arvados_ipc import *

children = {}
pipes = {}

pipe_setup(pipes, 'hellopipe')
if 0 == named_fork(children, 'child_a'):
    pipe_closeallbut(pipes, ('hellopipe', 'w'))
    os.write(pipes['hellopipe', 'w'], "Hello, parent.")
    os._exit(0)

pipe_closeallbut(pipes, ('hellopipe', 'r'))
with os.fdopen(pipes['hellopipe', 'r'], 'rb') as f:
    message = f.read()
    sys.stderr.write("Child says: " + message + "\n")

if not waitpid_and_check_children(children):
    raise Exception("Child process exited non-zero.")
</pre>

The "crunch scripts" included with Arvados include some more examples of using the arvados_ipc module.

</div>

h3. Toolkit wrappers

The following *arvados-&lowast;.py* modules provide "extract, build, run" helpers to make it easy to incorporate common analysis tools in your crunch scripts.

h4. arvados_bwa.py

Build and run the "bwa":http://bio-bwa.sourceforge.net/bwa.shtml program.

<div class="offset1">

The module retrieves the bwa source code from Keep, using the job's @bwa_tbz@ parameter.

<pre>
import arvados_bwa
arvados_bwa.run('aln', [ref_basename, '-'],
                stdin=open(fastq_filename,'rb'),
                stdout=open(aln_filename,'wb'))
</pre>

On qr1hi.arvadosapi.com, the source distribution @bwa-0.7.5a.tar.bz2@ is available in the collection @8b6e2c4916133e1d859c9e812861ce13+70@.

<pre>
{
 "script_parameters":{
  "bwa_tbz":"8b6e2c4916133e1d859c9e812861ce13+70",
  ...
 },
 ...
}
</pre>

</div>

h4. arvados_gatk2.py

Extract and run the "Genome Analysis Toolkit":http://www.broadinstitute.org/gatk/ programs.

<div class="offset1">

The module retrieves the binary distribution tarball from Keep, using the job's @gatk_tbz@ parameter.

<pre>
arvados_gatk2.run(
    args=[
        '-nct', 8,
        '-T', 'BaseRecalibrator',
        '-R', ref_fasta_files[0],
        '-I', input_bam_files[0],
        '-o', recal_file,
        ])
</pre>

On qr1hi.arvadosapi.com, the binary distribution @GenomeAnalysisTK-2.6-4.tar.bz2@ is available in the collection @5790482512cf6d5d6dfd50b7fd61e1d1+86@.

The GATK data bundle is available in the collection @d237a90bae3870b3b033aea1e99de4a9+10820@.

<pre>
{
 "script_parameters":{
  "gatk_tbz":"7e0a277d6d2353678a11f56bab3b13f2+87",
  "gatk_bundle":"d237a90bae3870b3b033aea1e99de4a9+10820",
  ...
 },
 ...
}
</pre>

</div>

h4. arvados_samtools.py

Build and run the "samtools":http://samtools.sourceforge.net/samtools.shtml program.

<div class="offset1">

The module retrieves the samtools source code from Keep, using the job's @samtools_tgz@ parameter.

<pre>
import arvados_samtools
arvados_samtools.run('view', ['-S', '-b', '-'],
                     stdin=open(sam_filename,'rb'),
                     stdout=open(bam_filename,'wb'))
</pre>

On qr1hi.arvadosapi.com, the source distribution @samtools-0.1.19.tar.gz@ is available in the collection @c777e23cf13e5d5906abfdc08d84bfdb+74@.

<pre>
{
 "script_parameters":{
  "samtools_tgz":"c777e23cf13e5d5906abfdc08d84bfdb+74",
  ...
 },
 ...
}
</pre>

</div>

h4. arvados_picard.py

Build and run the "picard":http://picard.sourceforge.net/command-line-overview.shtml program.

<div class="offset1">

The module retrieves the picard binary distribution from Keep, using the job's @picard_zip@ parameter.

<pre>
import arvados_picard
arvados_picard.run(
    'FixMateInformation',
    params={
        'i': input_bam_path,
        'o': '/dev/stdout',
        'quiet': 'true',
        'so': 'coordinate',
        'validation_stringency': 'LENIENT',
        'compression_level': 0
        },
    stdout=open('out.bam','wb'))
</pre>

On qr1hi.arvadosapi.com, the binary distribution @picard-tools-1.82.zip@ is available in the collection @687f74675c6a0e925dec619cc2bec25f+77@.

<pre>
{
 "script_parameters":{
  "picard_zip":"687f74675c6a0e925dec619cc2bec25f+77",
  ...
 },
 ...
}
</pre>

</div>

