Arvados

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h1. Writing a Script Calling a Third Party Tool

h2. Case study: FastQC

# Building an environment able to run FastQC

## Writing a Dockerfile 

## Building a docker image from the Dockerfile

## Uploading the docker image to an Arvados instance

# Writing a crunch script that runs FastQC (in the docker image)

## Calling FastQC

## Where to place temporary files

## Writing output data

# Writing a pipeline template to run the crunch script

h3. Writing a Dockerfile

Dockerfiles, as explained by 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 (https://docs.docker.com/engine/reference/builder/) 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.

Docker has some wonderful documentation for building Dockerfiles which we recommend you look at for instructions on getting the finished product below:

* 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/

We strongly recommend keeping your Dockerfiles in the git repository with the crunch scripts that run inside the docker images created by them. 

Dockerfile that installs FastQC:

<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

Once you have a Dockerfile, you can use the @docker build@ command to build the image using the Dockerfile instructions.

<pre>

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

</pre>

h3. How to upload a docker image to Arvados

Once the docker image is built, you can use the arvados cli (http://doc.arvados.org/sdk/cli/index.html) command @arv keep docker@ to upload the image to an Arvados cluster.

<pre>

arv keep docker 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

outdir = arvados.crunch.TaskOutputDir()

# Write to outdir.path

arvados.task_set_output(outdir.manifest_text())

</pre>

Inside the code:

<pre>

import subprocess

import arvados

import arvados.crunch

outdir = arvados.crunch.TaskOutputDir()

#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', outdir.path]

subprocess.check_call(cmd)

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

Open a collection writer, write files and/or directory trees:

<pre>

import arvados

collection_writer = arvados.collection.CollectionWriter()

collection_writer.write_file('foo.txt')

collection_writer.write_directory_tree(bar_directory_path)

arvados.task_set_output(collection_writer.finish())

</pre>

Inside the code:

<pre>

import subprocess

import arvados

import os

task = arvados.current_task()

tmpdir = task.tmpdir

outdir_path = os.path.join(tmpdir, 'out')

os.mkdir(outdir_path)

#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', outdir_path]

subprocess.check_call(cmd)

collection_writer = arvados.collection.CollectionWriter()

collection_writer.write_file('foo.txt')

collection_writer.write_directory_tree(outdir_path)

arvados.task_set_output(collection_writer.finish())

</pre>

h3. The final crunch script

<pre>

import subprocess

import arvados

import arvados.crunch

outdir = arvados.crunch.TaskOutputDir()

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

fastq_file = arvados.getjobparam('input_fastq_file')

#Grab the number of threads available

num_threads = multiprocessing.cpu_count()

cmd = ['perl', '/home/crunch/fastqc/FastQC/fastqc', fastq_file, '-o', outdir.path, '-t', str(num_threads)]

subprocess.check_call(cmd)

arvados.task_set_output(outdir.manifest_text())

</pre>

h3. Writing a pipeline template to run the crunch script

...