Arvados

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h1. Writing a Script Calling a Third Party Tool

Case study: FastQC

Good tips include:

* Keep the Dockerfile in the git repository

h3. Writing a Dockerfile

Docker has some wonderful documentation for building Dockerfiles:

* A reference for Dockerfiles: https://docs.docker.com/engine/reference/builder/

* Dockerfile best practices: https://docs.docker.com/engine/userguide/eng-image/dockerfile_best-practices/

From Docker:

"""

Docker can build images automatically by reading the instructions from a Dockerfile. A Dockerfile is a text document that contains all the commands a user could call on the command line to assemble an image. Using docker build users can create an automated build that executes several command-line instructions in succession.

This page describes the commands you can use in a Dockerfile. When you are done reading this page, refer to the Dockerfile Best Practices (https://docs.docker.com/engine/userguide/eng-image/dockerfile_best-practices/) for a tip-oriented guide.

"""

<pre>

FROM arvados/jobs

USER root

RUN apt-get -q update && apt-get -qy install \

  fontconfig \

  openjdk-6-jre-headless \

  perl \

  unzip \

  wget

USER crunch

RUN mkdir /home/crunch/fastqc

RUN cd /home/crunch/fastqc && \

    wget --quiet http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.4.zip && \

    unzip /home/crunch/fastqc/fastqc_v0.11.4.zip

</pre>

h3. How to build a docker image from a Dockerfile

<pre>

docker build -t username/imagename path/to/Dockerfile/

</pre>

h3. How to upload a docker image to Arvados

<pre>

arv keep put username/imagename

</pre>

h3. How to call an external tool from a crunch script

We strongly recommend using the @subprocess@ module for calling external tools. If the output is small and written to standard out, using @subprocess.check_output@ will ensure the tool completed successfully and return the standard output.

<pre>

import subprocess

foo = subprocess.check_output(['echo','foo'])

</pre>

If the output is big, @subprocess.check_call@ can redirect it to a file while ensuring the tool completed successfully.

<pre>

import subprocess

with open('foo', 'w') as outfile:

    subprocess.check_call(['head', '-c', '1234567', '/dev/urandom'], stdout=outfile)

</pre>

FastQC writes to the current output directory or the output directory specified by the @-o@ flag, so we can use @subprocess.check_call@

<pre>

import subprocess

import arvados

#Grab the file path pointing to the file to run fastqc on 

fastq_file = arvados.getjobparam('input_fastq_file')

cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc', fastq_file]

subprocess.check_call(cmd)

</pre>

h3. Where to put temporary files

<pre>

import arvados

task = arvados.current_task()

tmpdir = task.tmpdir

</pre>

Inside the code:

<pre>

import subprocess

import arvados

task = arvados.current_task()

tmpdir = task.tmpdir

#Grab the file path pointing to the file to run fastqc on 

fastq_file = arvados.getjobparam('input_fastq_file')

cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc', fastq_file, '-o', tmpdir]

subprocess.check_call(cmd)

</pre>

h3. How to write data directly to Keep (Using TaskOutputDir)

<pre>

import arvados

import arvados.crunch

import os

outdir = arvados.crunch.TaskOutputDir()

with open(os.path.join(outdir.path, 'foo'), 'w') as outfile:

    subprocess.check_call(['head', '-c', '1234567', '/dev/urandom'], stdout=outfile)

arvados.task_set_output(outdir.manifest_text())

</pre>

h3. When TaskOutputDir is not the correct choice

* If the tool writes symbolic links or named pipes, which are not supported by fuse

* If the I/O access patterns are not performant with fuse

** This occurs in Tophat, which opens 20 file handles on multiple files that it writes out

<pre>

import arvados

import os

task = arvados.current_task()

tmpdir = task.tmpdir

os.mkdir(os.path.join(tmpdir, 'out'))

with open(os.path.join(tmpdir, 'out', 'foo.txt'), 'w') as out:

    subprocess.check_call(['head', '-c', '1234567', '/dev/urandom'], stdout=outfile)

collection_writer = arvados.collection.CollectionWriter()

collection_writer.write_file('random_file.txt')

collection_writer.write_directory_tree(os.path.join(tmpdir, 'out'))

arvados.task_set_output(collection_writer.finish())

</pre>

h3. Putting it all together

<pre>

import subprocess

cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc']

fq_files = sorted(glob.glob('*.fq*'))

fastq_files = sorted(glob.glob('*.fastq*'))

cmd.extend(fq_files+fastq_files)

cmd.extend(['-o', outdirpath, '-t', str(num_threads)])

fastqc_pipe = subprocess.Popen(cmd)

fastqc_pipe.wait()

coll_writer = arvados.CollectionWriter()

coll_writer.write_directory_tree(outdirpath)

pdh = coll_writer.finish()

body = {'output':pdh, 'success':fastqc_pipe.returncode==0, 'progress':1.0}

arvados.api('v1').job_tasks().update(uuid=this_task['uuid'], body=body).execute()

</pre>