Running a basic workflow¶

A Toil workflow can be run with just two steps:

from toil.common import Toil
from toil.job import Job
def helloWorld(message, memory="1G", cores=1, disk="1G"):


    return "Hello, world!, here's a message: %s" % message
if __name__ == "__main__":


    parser = Job.Runner.getDefaultArgumentParser()


    options = parser.parse_args()


    options.clean = "always"


    with Toil(options) as toil:


        output = toil.start(Job.wrapFn(helloWorld, "You did it!"))


    print(output)

python helloWorld.py file:my-job-store

Congratulations! You've run your first Toil workflow using the default Batch System, singleMachine, using the file job store.

Toil uses batch systems to manage the jobs it creates.

The singleMachine batch system is primarily used to prepare and debug workflows on a local machine. Once validated, try running them on a full-fledged batch system (see batchsysteminterface). Toil supports many different batch systems such as Apache Mesos and Grid Engine; its versatility makes it easy to run your workflow in all kinds of places.

Toil is totally customizable! Run python helloWorld.py --help to see a complete list of available options.

For something beyond a "Hello, world!" example, refer to A (more) real-world example.

Running a basic CWL workflow¶

The Common Workflow Language (CWL) is an emerging standard for writing workflows that are portable across multiple workflow engines and platforms. Running CWL workflows using Toil is easy.

cwlVersion: v1.0
class: CommandLineTool
baseCommand: echo
stdout: output.txt
inputs:


  message:


    type: string


    inputBinding:


      position: 1
outputs:


  output:


    type: stdout

message: Hello world!

$ toil-cwl-runner example.cwl example-job.yaml

$ cat output.txt
Hello world!

To learn more about CWL, see the CWL User Guide (from where this example was shamelessly borrowed).

To run this workflow on an AWS cluster have a look at Running a CWL Workflow on AWS.

For information on using CWL with Toil see the section cwl

Running a basic WDL workflow¶

The Workflow Description Language (WDL) is another emerging language for writing workflows that are portable across multiple workflow engines and platforms. Running WDL workflows using Toil is still in alpha, and currently experimental. Toil currently supports basic workflow syntax (see wdl for more details and examples). Here we go over running a basic WDL helloworld workflow.

    workflow write_simple_file {


      call write_file


    }


    task write_file {


      String message


      command { echo ${message} > wdl-helloworld-output.txt }


      output { File test = "wdl-helloworld-output.txt" }


    }
and this code into ``wdl-helloworld.json``::


    {


      "write_simple_file.write_file.message": "Hello world!"


    }

$ toil-wdl-runner wdl-helloworld.wdl wdl-helloworld.json

$ cat wdl-helloworld-output.txt
Hello world!

To learn more about WDL, see the main WDL website .

A (more) real-world example¶

For a more detailed example and explanation, we've developed a sample pipeline that merge-sorts a temporary file. This is not supposed to be an efficient sorting program, rather a more fully worked example of what Toil is capable of.

Running the example¶

$ python sort.py file:jobStore

NOTE:

$ python sort.py file:jobStore \


             --numLines=5000 \


             --lineLength=10 \


             --overwriteOutput=True \


             --workDir=/tmp/

Describing the source code¶

To understand the details of what's going on inside. Let's start with the main() function. It looks like a lot of code, but don't worry---we'll break it down piece by piece.

def main(options=None):


    if not options:


        # deal with command line arguments


        parser = ArgumentParser()


        Job.Runner.addToilOptions(parser)


        parser.add_argument('--numLines', default=defaultLines, help='Number of lines in file to sort.', type=int)


        parser.add_argument('--lineLength', default=defaultLineLen, help='Length of lines in file to sort.', type=int)


        parser.add_argument("--fileToSort", help="The file you wish to sort")


        parser.add_argument("--outputFile", help="Where the sorted output will go")


        parser.add_argument("--overwriteOutput", help="Write over the output file if it already exists.", default=True)


        parser.add_argument("--N", dest="N",


                            help="The threshold below which a serial sort function is used to sort file. "


                                 "All lines must of length less than or equal to N or program will fail",


                            default=10000)


        parser.add_argument('--downCheckpoints', action='store_true',


                            help='If this option is set, the workflow will make checkpoints on its way through'


                                 'the recursive "down" part of the sort')


        parser.add_argument("--sortMemory", dest="sortMemory",


                        help="Memory for jobs that sort chunks of the file.",


                        default=None)


    


        parser.add_argument("--mergeMemory", dest="mergeMemory",


                        help="Memory for jobs that collate results.",


                        default=None)


        options = parser.parse_args()


    if not hasattr(options, "sortMemory") or not options.sortMemory:


        options.sortMemory = sortMemory


    if not hasattr(options, "mergeMemory") or not options.mergeMemory:


        options.mergeMemory = sortMemory


    # do some input verification


    sortedFileName = options.outputFile or "sortedFile.txt"


    if not options.overwriteOutput and os.path.exists(sortedFileName):


        print(f'Output file {sortedFileName} already exists.  '


              f'Delete it to run the sort example again or use --overwriteOutput=True')


        exit()


    fileName = options.fileToSort


    if options.fileToSort is None:


        # make the file ourselves


        fileName = 'fileToSort.txt'


        if os.path.exists(fileName):


            print(f'Sorting existing file: {fileName}')


        else:


            print(f'No sort file specified. Generating one automatically called: {fileName}.')


            makeFileToSort(fileName=fileName, lines=options.numLines, lineLen=options.lineLength)


    else:


        if not os.path.exists(options.fileToSort):


            raise RuntimeError("File to sort does not exist: %s" % options.fileToSort)


    if int(options.N) <= 0:


        raise RuntimeError("Invalid value of N: %s" % options.N)


    # Now we are ready to run


    with Toil(options) as workflow:


        sortedFileURL = 'file://' + os.path.abspath(sortedFileName)


        if not workflow.options.restart:


            sortFileURL = 'file://' + os.path.abspath(fileName)


            sortFileID = workflow.importFile(sortFileURL)


            sortedFileID = workflow.start(Job.wrapJobFn(setup,


                                                        sortFileID,


                                                        int(options.N),


                                                        options.downCheckpoints,


                                                        options=options,


                                                        memory=sortMemory))


        else:


            sortedFileID = workflow.restart()


        workflow.exportFile(sortedFileID, sortedFileURL)

First we make a parser to process command line arguments using the argparse module. It's important that we add the call to Job.Runner.addToilOptions() to initialize our parser with all of Toil's default options. Then we add the command line arguments unique to this workflow, and parse the input. The help message listed with the arguments should give you a pretty good idea of what they can do.

Next we do a little bit of verification of the input arguments. The option --fileToSort allows you to specify a file that needs to be sorted. If this option isn't given, it's here that we make our own file with the call to makeFileToSort().

Finally we come to the context manager that initializes the workflow. We create a path to the input file prepended with 'file://' as per the documentation for toil.common.Toil() when staging a file that is stored locally. Notice that we have to check whether or not the workflow is restarting so that we don't import the file more than once. Finally we can kick off the workflow by calling toil.common.Toil.start() on the job setup. When the workflow ends we capture its output (the sorted file's fileID) and use that in toil.common.Toil.exportFile() to move the sorted file from the job store back into "userland".

Next let's look at the job that begins the actual workflow, setup.

def setup(job, inputFile, N, downCheckpoints, options):


    """


    Sets up the sort.


    Returns the FileID of the sorted file


    """


    RealtimeLogger.info("Starting the merge sort")


    return job.addChildJobFn(down,


                             inputFile, N, 'root',


                             downCheckpoints,


                             options = options,


                             preemptable=True,


                             memory=sortMemory).rv()

setup really only does two things. First it writes to the logs using Job.log() and then calls addChildJobFn(). Child jobs run directly after the current job. This function turns the 'job function' down into an actual job and passes in the inputs including an optional resource requirement, memory. The job doesn't actually get run until the call to Job.rv(). Once the job down finishes, its output is returned here.

Now we can look at what down does.

def down(job, inputFileStoreID, N, path, downCheckpoints, options, memory=sortMemory):


    """


    Input is a file, a subdivision size N, and a path in the hierarchy of jobs.


    If the range is larger than a threshold N the range is divided recursively and


    a follow on job is then created which merges back the results else


    the file is sorted and placed in the output.


    """


    


    RealtimeLogger.info("Down job starting: %s" % path)


    


    # Read the file


    inputFile = job.fileStore.readGlobalFile(inputFileStoreID, cache=False)


    length = os.path.getsize(inputFile)


    if length > N:


        # We will subdivide the file


        RealtimeLogger.critical("Splitting file: %s of size: %s"


                % (inputFileStoreID, length))


        # Split the file into two copies


        midPoint = getMidPoint(inputFile, 0, length)


        t1 = job.fileStore.getLocalTempFile()


        with open(t1, 'w') as fH:


            fH.write(copySubRangeOfFile(inputFile, 0, midPoint+1))


        t2 = job.fileStore.getLocalTempFile()


        with open(t2, 'w') as fH:


            fH.write(copySubRangeOfFile(inputFile, midPoint+1, length))


        # Call down recursively. By giving the rv() of the two jobs as inputs to the follow-on job, up,


        # we communicate the dependency without hindering concurrency.


        result = job.addFollowOnJobFn(up,


                                    job.addChildJobFn(down, job.fileStore.writeGlobalFile(t1), N, path + '/0',


                                                      downCheckpoints, checkpoint=downCheckpoints, options=options,


                                                      preemptable=True, memory=options.sortMemory).rv(),


                                    job.addChildJobFn(down, job.fileStore.writeGlobalFile(t2), N, path + '/1',


                                                      downCheckpoints, checkpoint=downCheckpoints, options=options,


                                                      preemptable=True, memory=options.mergeMemory).rv(),


                                    path + '/up', preemptable=True, options=options, memory=options.sortMemory).rv()


    else:


        # We can sort this bit of the file


        RealtimeLogger.critical("Sorting file: %s of size: %s"


                % (inputFileStoreID, length))


        # Sort the copy and write back to the fileStore


        shutil.copyfile(inputFile, inputFile + '.sort')


        sort(inputFile + '.sort')


        result = job.fileStore.writeGlobalFile(inputFile + '.sort')


        


    RealtimeLogger.info("Down job finished: %s" % path)


    return result

Down is the recursive part of the workflow. First we read the file into the local filestore by calling job.fileStore.readGlobalFile(). This puts a copy of the file in the temp directory for this particular job. This storage will disappear once this job ends. For a detailed explanation of the filestore, job store, and their interfaces have a look at managingFiles.

Next down checks the base case of the recursion: is the length of the input file less than N (remember N was an option we added to the workflow in main)? In the base case, we just sort the file, and return the file ID of this new sorted file.

If the base case fails, then the file is split into two new tempFiles using job.fileStore.getLocalTempFile() and the helper function copySubRangeOfFile. Finally we add a follow on Job up with job.addFollowOnJobFn(). We've already seen child jobs. A follow-on Job is a job that runs after the current job and all of its children (and their children and follow-ons) have completed. Using a follow-on makes sense because up is responsible for merging the files together and we don't want to merge the files together until we know they are sorted. Again, the return value of the follow-on job is requested using Job.rv().

Looking at up

def up(job, inputFileID1, inputFileID2, path, options, memory=sortMemory):


    """


    Merges the two files and places them in the output.


    """


    


    RealtimeLogger.info("Up job starting: %s" % path)


    


    with job.fileStore.writeGlobalFileStream() as (fileHandle, outputFileStoreID):


        fileHandle = codecs.getwriter('utf-8')(fileHandle)


        with job.fileStore.readGlobalFileStream(inputFileID1) as inputFileHandle1:


            inputFileHandle1 = codecs.getreader('utf-8')(inputFileHandle1)


            with job.fileStore.readGlobalFileStream(inputFileID2) as inputFileHandle2:


                inputFileHandle2 = codecs.getreader('utf-8')(inputFileHandle2)


                RealtimeLogger.info("Merging %s and %s to %s"


                    % (inputFileID1, inputFileID2, outputFileStoreID))


                merge(inputFileHandle1, inputFileHandle2, fileHandle)


        # Cleanup up the input files - these deletes will occur after the completion is successful.


        job.fileStore.deleteGlobalFile(inputFileID1)


        job.fileStore.deleteGlobalFile(inputFileID2)


        


        RealtimeLogger.info("Up job finished: %s" % path)


        


        return outputFileStoreID

we see that the two input files are merged together and the output is written to a new file using job.fileStore.writeGlobalFileStream(). After a little cleanup, the output file is returned.

Once the final up finishes and all of the rv() promises are fulfilled, main receives the sorted file's ID which it uses in exportFile to send it to the user.

There are other things in this example that we didn't go over such as checkpoints and the details of much of the api.

At the end of the script the lines

if __name__ == '__main__'


    main()

are included to ensure that the main function is only run once in the '__main__' process invoked by you, the user. In Toil terms, by invoking the script you created the leader process in which the main() function is run. A worker process is a separate process whose sole purpose is to host the execution of one or more jobs defined in that script. In any Toil workflow there is always one leader process, and potentially many worker processes.

When using the single-machine batch system (the default), the worker processes will be running on the same machine as the leader process. With full-fledged batch systems like Mesos the worker processes will typically be started on separate machines. The boilerplate ensures that the pipeline is only started once---on the leader---but not when its job functions are imported and executed on the individual workers.

Typing python sort.py --help will show the complete list of arguments for the workflow which includes both Toil's and ones defined inside sort.py. A complete explanation of Toil's arguments can be found in commandRef.

Logging¶

By default, Toil logs a lot of information related to the current environment in addition to messages from the batch system and jobs. This can be configured with the --logLevel flag. For example, to only log CRITICAL level messages to the screen:

$ python sort.py file:jobStore \


             --logLevel=critical \


             --overwriteOutput=True

This hides most of the information we get from the Toil run. For more detail, we can run the pipeline with --logLevel=debug to see a comprehensive output. For more information, see workflowOptions.

Error Handling and Resuming Pipelines¶

With Toil, you can recover gracefully from a bug in your pipeline without losing any progress from successfully completed jobs. To demonstrate this, let's add a bug to our example code to see how Toil handles a failure and how we can resume a pipeline after that happens. Add a bad assertion at line 52 of the example (the first line of down()):

def down(job, inputFileStoreID, N, downCheckpoints, memory=sortMemory):


    ...


    assert 1 == 2, "Test error!"

When we run the pipeline, Toil will show a detailed failure log with a traceback:

$ python sort.py file:jobStore
...
---TOIL WORKER OUTPUT LOG---
...
m/j/jobonrSMP    Traceback (most recent call last):
m/j/jobonrSMP      File "toil/src/toil/worker.py", line 340, in main
m/j/jobonrSMP        job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore)
m/j/jobonrSMP      File "toil/src/toil/job.py", line 1270, in _runner
m/j/jobonrSMP        returnValues = self._run(jobGraph, fileStore)
m/j/jobonrSMP      File "toil/src/toil/job.py", line 1217, in _run
m/j/jobonrSMP        return self.run(fileStore)
m/j/jobonrSMP      File "toil/src/toil/job.py", line 1383, in run
m/j/jobonrSMP        rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs)
m/j/jobonrSMP      File "toil/example.py", line 30, in down
m/j/jobonrSMP        assert 1 == 2, "Test error!"
m/j/jobonrSMP    AssertionError: Test error!

If we try and run the pipeline again, Toil will give us an error message saying that a job store of the same name already exists. By default, in the event of a failure, the job store is preserved so that the workflow can be restarted, starting from the previously failed jobs. We can restart the pipeline by running

$ python sort.py file:jobStore \


             --restart \


             --overwriteOutput=True

We can also change the number of times Toil will attempt to retry a failed job:

$ python sort.py file:jobStore \


             --retryCount 2 \


             --restart \


             --overwriteOutput=True

You'll now see Toil attempt to rerun the failed job until it runs out of tries. --retryCount is useful for non-systemic errors, like downloading a file that may experience a sporadic interruption, or some other non-deterministic failure.

To successfully restart our pipeline, we can edit our script to comment out line 30, or remove it, and then run

$ python sort.py file:jobStore \


             --restart \


             --overwriteOutput=True

The pipeline will run successfully, and the job store will be removed on the pipeline's completion.

Collecting Statistics¶

Please see the cli_status section for more on gathering runtime and resource info on jobs.

Launching a Toil Workflow in AWS¶

After having installed the aws extra for Toil during the installation-ref and set up AWS (see prepareAWS), the user can run the basic helloWorld.py script (Running a basic workflow) on a VM in AWS just by modifying the run command.

Note that when running in AWS, users can either run the workflow on a single instance or run it on a cluster (which is running across multiple containers on multiple AWS instances). For more information on running Toil workflows on a cluster, see runningAWS.

Also! Remember to use the destroyCluster command when finished to destroy the cluster! Otherwise things may not be cleaned up properly.

$ toil launch-cluster <cluster-name> \


             --keyPairName <AWS-key-pair-name> \


             --leaderNodeType t2.medium \


             --zone us-west-2a

$ toil rsync-cluster --zone us-west-2a <cluster-name> helloWorld.py :/tmp

$ toil ssh-cluster --zone us-west-2a <cluster-name>

$ python /tmp/helloWorld.py aws:us-west-2:my-S3-bucket

$ exit

$ toil destroy-cluster --zone us-west-2a <cluster-name>

Running a CWL Workflow on AWS¶

After having installed the aws and cwl extras for Toil during the installation-ref and set up AWS (see prepareAWS), the user can run a CWL workflow with Toil on AWS.

Also! Remember to use the destroyCluster command when finished to destroy the cluster! Otherwise things may not be cleaned up properly.

$ toil launch-cluster <cluster-name> \


             --keyPairName <AWS-key-pair-name> \


             --leaderNodeType t2.medium \


             --zone us-west-2a

toil rsync-cluster --zone us-west-2a <cluster-name> example.cwl :/tmp
toil rsync-cluster --zone us-west-2a <cluster-name> example-job.yaml :/tmp

$ toil ssh-cluster --zone us-west-2a <cluster-name>

sudo apt-get update
sudo apt-get -y upgrade
sudo apt-get -y dist-upgrade
sudo apt-get -y install git
sudo pip install mesos.cli

virtualenv --system-site-packages venv
source venv/bin/activate

(venv) $ toil-cwl-runner \


             --provisioner aws \


             --jobStore aws:us-west-2a:any-name \


             /tmp/example.cwl /tmp/example-job.yaml

$ toil destroy-cluster --zone us-west-2a <cluster-name>

Running a Workflow with Autoscaling - Cactus¶

Cactus is a reference-free, whole-genome multiple alignment program that can be run on any of the cloud platforms Toil supports.

NOTE:

Also! Remember to use the destroyCluster command when finished to destroy the cluster! Otherwise things may not be cleaned up properly.

(venv) $ toil launch-cluster <cluster-name> \


             --provisioner <aws, gce> \


             --keyPairName <key-pair-name> \


             --leaderNodeType <type> \


             --zone <zone>

$ export TOIL_AWS_ZONE=us-west-2c

$ toil ssh-cluster --provisioner <aws, gce> <cluster-name>
$ mkdir /root/cact_ex
$ exit

$ toil rsync-cluster --provisioner <aws, gce> <cluster-name> pestis-short-aws-seqFile.txt :/root/cact_ex
$ toil rsync-cluster --provisioner <aws, gce> <cluster-name> GCF_000169655.1_ASM16965v1_genomic.fna :/root/cact_ex
$ toil rsync-cluster --provisioner <aws, gce> <cluster-name> GCF_000006645.1_ASM664v1_genomic.fna :/root/cact_ex
$ toil rsync-cluster --provisioner <aws, gce> <cluster-name> GCF_000182485.1_ASM18248v1_genomic.fna :/root/cact_ex
$ toil rsync-cluster --provisioner <aws, gce> <cluster-name> GCF_000013805.1_ASM1380v1_genomic.fna :/root/cact_ex
$ toil rsync-cluster --provisioner <aws, gce> <cluster-name> setup_leaderNode.sh :/root/cact_ex
$ toil rsync-cluster --provisioner <aws, gce> <cluster-name> blockTrim1.xml :/root/cact_ex
$ toil rsync-cluster --provisioner <aws, gce> <cluster-name> blockTrim3.xml :/root/cact_ex

$ toil ssh-cluster --provisioner <aws, gce> <cluster-name>

$ bash /root/cact_ex/setup_leaderNode.sh
$ source cact_venv/bin/activate
(cact_venv) $ cd cactus
(cact_venv) $ pip install --upgrade .

(cact_venv) $ TOIL_APPLIANCE_SELF=quay.io/ucsc_cgl/toil:3.14.0 cactus \


                  --provisioner <aws, gce> \


                  --nodeType <type> \


                  --maxNodes 2 \


                  --minNodes 0 \


                  --retry 10 \


                  --batchSystem mesos \


                  --logDebug \


                  --logFile /logFile_pestis3 \


                  --configFile \


                  /root/cact_ex/blockTrim3.xml <aws, google>:<zone>:cactus-pestis \


                  /root/cact_ex/pestis-short-aws-seqFile.txt \


                  /root/cact_ex/pestis_output3.hal

(cact_venv) $ exit

(venv) $ toil rsync-cluster \


             --provisioner <aws, gce> <cluster-name> \


             :/root/cact_ex/pestis_output3.hal \


             <path-of-folder-on-local-machine>

(venv) $ toil destroy-cluster --provisioner <aws, gce> <cluster-name>

Job Store¶

The job store is a storage abstraction which contains all of the information used in a Toil run. This centralizes all of the files used by jobs in the workflow and also the details of the progress of the run. If a workflow crashes or fails, the job store contains all of the information necessary to resume with minimal repetition of work.

Several different job stores are supported, including the file job store and cloud job stores.

File Job Store¶

The file job store is for use locally, and keeps the workflow information in a directory on the machine where the workflow is launched. This is the simplest and most convenient job store for testing or for small runs.

For an example that uses the file job store, see quickstart.

Cloud Job Stores¶

Toil currently supports the following cloud storage systems as job stores:

These use cloud buckets to house all of the files. This is useful if there are several different worker machines all running jobs that need to access the job store.

Batch System¶

A Toil batch system is either a local single-machine (one computer) or a currently supported HPC cluster of computers (lsf, parasol, mesos, slurm, torque, htcondor, or grid_engine). Mesos is a special case, and is launched for cloud environments. These environments manage individual worker nodes under a leader node to process the work required in a workflow. The leader and its workers all coordinate their tasks and files through a centralized job store location.

See batchSystemInterface for a more detailed description of different batch systems.

Provisioner¶

The Toil provisioner provides a tool set for running a Toil workflow on a particular cloud platform.

The clusterRef are command line tools used to provision nodes in your desired cloud platform. They allows you to launch nodes, ssh to the leader, and rsync files back and forth.

For detailed instructions for using the provisioner see runningAWS or runningGCE.

The Job Store¶

Running toil scripts requires a filepath or url to a centralizing location for all of the files of the workflow. This is Toil's one required positional argument: the job store. To use the quickstart example, if you're on a node that has a large /scratch volume, you can specify that the jobstore be created there by executing: python HelloWorld.py /scratch/my-job-store, or more explicitly, python HelloWorld.py file:/scratch/my-job-store.

Syntax for specifying different job stores:

Different types of job store options can be found below.

Commandline Options¶

Core Toil Options

Logging Options

Toil hides stdout and stderr by default except in case of job failure. Log levels in toil are based on priority from the logging module:

Batch System Options

Autoscaling Options

Restart Option¶

In the event of failure, Toil can resume the pipeline by adding the argument --restart and rerunning the python script. Toil pipelines can even be edited and resumed which is useful for development or troubleshooting.

Running Workflows with Services¶

Toil supports jobs, or clusters of jobs, that run as services to other accessor jobs. Example services include server databases or Apache Spark Clusters. As service jobs exist to provide services to accessor jobs their runtime is dependent on the concurrent running of their accessor jobs. The dependencies between services and their accessor jobs can create potential deadlock scenarios, where the running of the workflow hangs because only service jobs are being run and their accessor jobs can not be scheduled because of too limited resources to run both simultaneously. To cope with this situation Toil attempts to schedule services and accessors intelligently, however to avoid a deadlock with workflows running service jobs it is advisable to use the following parameters:

Specifying these parameters so that at a maximum cluster size there will be sufficient resources to run accessors in addition to services will ensure that such a deadlock can not occur.

If too low a limit is specified then a deadlock can occur in which toil can not schedule sufficient service jobs concurrently to complete the workflow. Toil will detect this situation if it occurs and throw a toil.DeadlockException exception. Increasing the cluster size and these limits will resolve the issue.

Setting Options directly with the Toil Script¶

It's good to remember that commandline options can be overridden in the Toil script itself. For example, toil.job.Job.Runner.getDefaultOptions() can be used to run toil with all default options, and in this example, it will override commandline args to run the default options and always run with the "./toilWorkflow" directory specified as the jobstore:

options = Job.Runner.getDefaultOptions("./toilWorkflow") # Get the options object
with Toil(options) as toil:


    toil.start(Job())  # Run the script

However, each option can be explicitly set within the script by supplying arguments (in this example, we are setting logLevel = "DEBUG" (all log statements are shown) and clean="ALWAYS" (always delete the jobstore) like so:

options = Job.Runner.getDefaultOptions("./toilWorkflow") # Get the options object
options.logLevel = "DEBUG" # Set the log level to the debug level.
options.clean = "ALWAYS" # Always delete the jobStore after a run
with Toil(options) as toil:


    toil.start(Job())  # Run the script

However, the usual incantation is to accept commandline args from the user with the following:

parser = Job.Runner.getDefaultArgumentParser() # Get the parser
options = parser.parse_args() # Parse user args to create the options object
with Toil(options) as toil:


    toil.start(Job())  # Run the script

Which can also, of course, then accept script supplied arguments as before (which will overwrite any user supplied args):

parser = Job.Runner.getDefaultArgumentParser() # Get the parser
options = parser.parse_args() # Parse user args to create the options object
options.logLevel = "DEBUG" # Set the log level to the debug level.
options.clean = "ALWAYS" # Always delete the jobStore after a run
with Toil(options) as toil:


    toil.start(Job())  # Run the script

Introspecting the Jobstore¶

Note: Currently these features are only implemented for use locally (single machine) with the fileJobStore.

To view what files currently reside in the jobstore, run the following command:

$ toil debug-file file:path-to-jobstore-directory \


      --listFilesInJobStore

When run from the commandline, this should generate a file containing the contents of the job store (in addition to displaying a series of log messages to the terminal). This file is named "jobstore_files.txt" by default and will be generated in the current working directory.

If one wishes to copy any of these files to a local directory, one can run for example:

$ toil debug-file file:path-to-jobstore \


      --fetch overview.txt *.bam *.fastq \


      --localFilePath=/home/user/localpath

To fetch overview.txt, and all .bam and .fastq files. This can be used to recover previously used input and output files for debugging or reuse in other workflows, or use in general debugging to ensure that certain outputs were imported into the jobStore.

Stats and Status¶

See cli_status for more about gathering statistics about job success, runtime, and resource usage from workflows.

Using a Python debugger¶

If you execute a workflow using the --debugWorker flag, Toil will not fork in order to run jobs, which means you can either use pdb, or an IDE that supports debugging Python as you would normally. Note that the --debugWorker flag will only work with the singleMachine batch system (the default), and not any of the custom job schedulers.

Managing a Cluster of Virtual Machines (Provisioning)¶

Toil can launch and manage a cluster of virtual machines to run using the provisioner to run a workflow distributed over several nodes. The provisioner also has the ability to automatically scale up or down the size of the cluster to handle dynamic changes in computational demand (autoscaling). Currently we have working provisioners with AWS and GCE (Azure support has been deprecated).

Toil uses Apache Mesos as the batchSystemOverview.

See here for instructions for runningAWS.

See here for instructions for runningGCE.

Storage (Toil jobStore)¶

Toil can make use of cloud storage such as AWS or Google buckets to take care of storage needs.

This is useful when running Toil in single machine mode on any cloud platform since it allows you to make use of their integrated storage systems.

For an overview of the job store see jobStoreOverview.

For instructions configuring a particular job store see:

Running on Kubernetes¶

Kubernetes is a very popular container orchestration tool that has become a de facto cross-cloud-provider API for accessing cloud resources. Major cloud providers like Amazon, Microsoft, Kubernetes owner Google, and DigitalOcean have invested heavily in making Kubernetes work well on their platforms, by writing their own deployment documentation and developing provider-managed Kubernetes-based products. Using minikube, Kubernetes can even be run on a single machine.

Toil supports running Toil workflows against a Kubernetes cluster, either in the cloud or deployed on user-owned hardware.

Preparing your Kubernetes environment¶

apiVersion: rbac.authorization.k8s.io/v1
kind: Role
metadata:


  namespace: YOUR_NAMESPACE_HERE


  name: toil-user
rules:
- apiGroups: ["*"]


  resources: ["*"]


  verbs: ["explain", "get", "watch", "list", "describe", "logs", "attach", "exec", "port-forward", "proxy", "cp", "auth"]
- apiGroups: ["batch"]


  resources: ["*"]


  verbs: ["get", "watch", "list", "create", "run", "set", "delete"]
- apiGroups: [""]


  resources: ["secrets", "pods", "pods/attach", "podtemplates", "configmaps", "events", "services"]


  verbs: ["patch", "get", "update", "watch", "list", "create", "run", "set", "delete", "exec"]
- apiGroups: [""]


  resources: ["pods", "pods/log"]


  verbs: ["get", "list"]
- apiGroups: [""]


  resources: ["pods/exec"]


  verbs: ["create"]

apiVersion: rbac.authorization.k8s.io/v1
kind: ClusterRole
metadata:


  name: node-reader
rules:
- apiGroups: [""]


  resources: ["nodes"]


  verbs: ["get", "list", "describe"]
- apiGroups: [""]


  resources: ["namespaces"]


  verbs: ["get", "list", "describe"]
- apiGroups: ["metrics.k8s.io"]


  resources: ["*"]


  verbs: ["*"]

apiVersion: rbac.authorization.k8s.io/v1
kind: RoleBinding
metadata:


  name: toil-developer-member


  namespace: toil
subjects:
- kind: User


  name: YOUR_KUBERNETES_USERNAME_HERE


  apiGroup: rbac.authorization.k8s.io
- kind: ServiceAccount


  name: YOUR_SERVICE_ACCOUNT_NAME_HERE


  namespace: YOUR_NAMESPACE_HERE
roleRef:


  kind: Role


  name: toil-user


  apiGroup: rbac.authorization.k8s.io

apiVersion: rbac.authorization.k8s.io/v1
kind: ClusterRoleBinding
metadata:


  name: read-nodes
subjects:
- kind: User


  name: YOUR_KUBERNETES_USERNAME_HERE


  apiGroup: rbac.authorization.k8s.io
- kind: ServiceAccount


  name: YOUR_SERVICE_ACCOUNT_NAME_HERE


  namespace: YOUR_NAMESPACE_HERE
roleRef:


  kind: ClusterRole


  name: node-reader


  apiGroup: rbac.authorization.k8s.io

AWS Job Store for Kubernetes¶

Currently, the only job store, which is what Toil uses to exchange data between jobs, that works with jobs running on Kubernetes is the AWS Job Store. This requires that the Toil leader and Kubernetes jobs be able to connect to and use Amazon S3 and Amazon SimpleDB. It also requires that you have an Amazon Web Services account.

https://console.aws.amazon.com/iam/home?region=us-west-1#/home

$ aws configure

[default]
aws_access_key_id =  BLAH
aws_secret_access_key =  blahblahblah

$ cd ~/.aws

$ kubectl create secret generic aws-credentials --from-file credentials

Configuring Toil for your Kubernetes environment¶

To configure your workflow to run on Kubernetes, you will have to configure several environment variables, in addition to passing the --batchSystem kubernetes option. Doing the research to figure out what values to give these variables may require talking to your cluster provider.

Note that Docker containers cannot be run inside of unprivileged Kubernetes pods (which are themselves containers). The Docker daemon does not (yet) support this. Other tools, such as Singularity in its user-namespace mode, are able to run containers from within containers. If using Singularity to run containerized tools, and you want downloaded container images to persist between Toil jobs, you will also want to set TOIL_KUBERNETES_HOST_PATH and make sure that Singularity is downloading its containers under the Toil work directory (/var/lib/toil buy default) by setting SINGULARITY_CACHEDIR. However, you will need to make sure that no two jobs try to download the same container at the same time; Singularity has no synchronization or locking around its cache, but the cache is also not safe for simultaneous access by multiple Singularity invocations. Some Toil workflows use their own custom workaround logic for this problem; this work is likely to be made part of Toil in a future release.

Running workflows¶

To run the workflow, you will need to run the Toil leader process somewhere. It can either be run inside Kubernetes as a Kubernetes job, or outside Kubernetes as a normal command.

Option 1: Running the Leader Inside Kubernetes¶

Once you have determined a set of environment variable values for your workflow run, write a YAML file that defines a Kubernetes job to run your workflow with that configuration. Some configuration items (such as your username, and the name of your AWS credentials secret) need to be written into the YAML so that they can be used from the leader as well.

Note that the leader pod will need your workflow script, its other dependencies, and Toil all installed. An easy way to get Toil installed is to start with the Toil appliance image for the version of Toil you want to use. In this example, we use quay.io/ucsc_cgl/toil:4.1.0.

Here's an example YAML file to run a test workflow:

apiVersion: batch/v1
kind: Job
metadata:


  # It is good practice to include your username in your job name.


  # Also specify it in TOIL_KUBERNETES_OWNER


  name: demo-user-toil-test
# Do not try and rerun the leader job if it fails
spec:


 backoffLimit: 0


 template:


   spec:


     # Do not restart the pod when the job fails, but keep it around so the


     # log can be retrieved


     restartPolicy: Never


     volumes:


     - name: aws-credentials-vol


       secret:


         # Make sure the AWS credentials are available as a volume.


         # This should match TOIL_AWS_SECRET_NAME


         secretName: aws-credentials


     # You may need to replace this with a different service account name as


     # appropriate for your cluster.


     serviceAccountName: default


     containers:


     - name: main


       image: quay.io/ucsc_cgl/toil:4.1.0


       env:


       # Specify your username for inclusion in job names


       - name: TOIL_KUBERNETES_OWNER


         value: demo-user


       # Specify where to find the AWS credentials to access the job store with


       - name: TOIL_AWS_SECRET_NAME


         value: aws-credentials


       # Specify where per-host caches should be stored, on the Kubernetes hosts.


       # Needs to be set for Toil's caching to be efficient.


       - name: TOIL_KUBERNETES_HOST_PATH


         value: /data/scratch


       volumeMounts:


       # Mount the AWS credentials volume


       - mountPath: /root/.aws


         name: aws-credentials-vol


       resources:


         # Make sure to set these resource limits to values large enough


         # to accomodate the work your workflow does in the leader


         # process, but small enough to fit on your cluster.


         #


         # Since no request values are specified, the limits are also used


         # for the requests.


         limits:


           cpu: 2


           memory: "4Gi"


           ephemeral-storage: "10Gi"


       command:


       - /bin/bash


       - -c


       - |


         # This Bash script will set up Toil and the workflow to run, and run them.


         set -e


         # We make sure to create a work directory; Toil can't hot-deploy a


         # script from the root of the filesystem, which is where we start.


         mkdir /tmp/work


         cd /tmp/work


         # We make a virtual environment to allow workflow dependencies to be


         # hot-deployed.


         #


         # We don't really make use of it in this example, but for workflows


         # that depend on PyPI packages we will need this.


         #


         # We use --system-site-packages so that the Toil installed in the


         # appliance image is still available.


         virtualenv --python python3 --system-site-packages venv


         . venv/bin/activate


         # Now we install the workflow. Here we're using a demo workflow


         # script from Toil itself.


         wget https://raw.githubusercontent.com/DataBiosphere/toil/releases/4.1.0/src/toil/test/docs/scripts/tutorial_helloworld.py


         # Now we run the workflow. We make sure to use the Kubernetes batch


         # system and an AWS job store, and we set some generally useful


         # logging options. We also make sure to enable caching.


         python3 tutorial_helloworld.py \


             aws:us-west-2:demouser-toil-test-jobstore \


             --batchSystem kubernetes \


             --realTimeLogging \


             --logInfo \


             --disableCaching false

You can save this YAML as leader.yaml, and then run it on your Kubernetes installation with:

$ kubectl apply -f leader.yaml

To monitor the progress of the leader job, you will want to read its logs. If you are using a Kubernetes dashboard such as k9s, you can simply find the pod created for the job in the dashboard, and view its logs there. If not, you will need to locate the pod by hand.

Monitoring and Debugging Kubernetes Jobs and Pods¶

The following techniques are most useful for looking at the pod which holds the Toil leader, but they can also be applied to individual Toil jobs on Kubernetes, even when the leader is outside the cluster.

Kubernetes names pods for jobs by appending a short random string to the name of the job. You can find the name of the pod for your job by doing:

$ kubectl get pods | grep demo-user-toil-test
demo-user-toil-test-g5496                                         1/1     Running     0          2m

Assuming you have set TOIL_KUBERNETES_OWNER correctly, you should be able to find all of your workflow's pods by searching for your username:

$ kubectl get pods | grep demo-user

If the status of a pod is anything other than Pending, you will be able to view its logs with:

$ kubectl logs demo-user-toil-test-g5496

This will dump the pod's logs from the beginning to now and terminate. To follow along with the logs from a running pod, add the -f option:

$ kubectl logs -f demo-user-toil-test-g5496

A status of ImagePullBackoff suggests that you have requested to use an image that is not available. Check the image section of your YAML if you are looking at a leader, or the value of TOIL_APPLIANCE_SELF if you are delaying with a worker job. You also might want to check your Kubernetes node's Internet connectivity and DNS function; in Kubernetes, DNS depends on system-level pods which can be terminated or evicted in cases of resource oversubscription, just like user workloads.

If your pod seems to be stuck Pending, ContainerCreating, you can get information on what is wrong with it by using kubectl describe pod:

$ kubectl describe pod demo-user-toil-test-g5496

Pay particular attention to the Events: section at the end of the output. An indication that a job is too big for the available nodes on your cluster, or that your cluster is too busy for your jobs, is FailedScheduling events:

Type     Reason            Age                  From               Message
----     ------            ----                 ----               -------
Warning  FailedScheduling  13s (x79 over 100m)  default-scheduler  0/4 nodes are available: 1 Insufficient cpu, 1 Insufficient ephemeral-storage, 4 Insufficient memory.

If a pod is running but seems to be behaving erratically, or seems stuck, you can shell into it and look around:

$ kubectl exec -ti demo-user-toil-test-g5496 /bin/bash

One common cause of stuck pods is attempting to use more memory than allowed by Kubernetes (or by the Toil job's memory resource requirement), but in a way that does not trigger the Linux OOM killer to terminate the pod's processes. In these cases, the pod can remain stuck at nearly 100% memory usage more or less indefinitely, and attempting to shell into the pod (which needs to start a process within the pod, using some of its memory) will fail. In these cases, the recommended solution is to kill the offending pod and increase its (or its Toil job's) memory requirement, or reduce its memory needs by adapting user code.

When Things Go Wrong¶

The Toil Kubernetes batch system includes cleanup code to terminate worker jobs when the leader shuts down. However, if the leader pod is removed by Kubernetes, is forcibly killed or otherwise suffers a sudden existence failure, it can go away while its worker jobs live on. It is not recommended to restart a workflow in this state, as jobs from the previous invocation will remain running and will be trying to modify the job store concurrently with jobs from the new invocation.

To clean up dangling jobs, you can use the following snippet:

$ kubectl get jobs | grep demo-user | cut -f1 -d' ' | xargs -n10 kubectl delete job

This will delete all jobs with demo-user's username in their names, in batches of 10. You can also use the UUID that Toil assigns to a particular workflow invocation in the filter, to clean up only the jobs pertaining to that workflow invocation.

Option 2: Running the Leader Outside Kubernetes¶

If you don't want to run your Toil leader inside Kubernetes, you can run it locally instead. This can be useful when developing a workflow; files can be hot-deployed from your local machine directly to Kubernetes. However, your local machine will have to have (ideally role-assumption- and MFA-free) access to AWS, and access to Kubernetes. Real time logging will not work unless your local machine is able to listen for incoming UDP packets on arbitrary ports on the address it uses to contact the IPv4 Internet; Toil does no NAT traversal or detection.

Note that if you set TOIL_WORKDIR when running your workflow like this, it will need to be a directory that exists both on the host and in the Toil appliance.

Here is an example of running our test workflow leader locally, outside of Kubernetes:

$ export TOIL_KUBERNETES_OWNER=demo-user  # This defaults to your local username if not set
$ export TOIL_AWS_SECRET_NAME=aws-credentials
$ export TOIL_KUBERNETES_HOST_PATH=/data/scratch
$ virtualenv --python python3 --system-site-packages venv
$ . venv/bin/activate
$ wget https://raw.githubusercontent.com/DataBiosphere/toil/releases/4.1.0/src/toil/test/docs/scripts/tutorial_helloworld.py
$ python3 tutorial_helloworld.py \


      aws:us-west-2:demouser-toil-test-jobstore \


      --batchSystem kubernetes \


      --realTimeLogging \


      --logInfo \


      --disableCaching false

Running in AWS¶

Toil jobs can be run on a variety of cloud platforms. Of these, Amazon Web Services (AWS) is currently the best-supported solution. Toil provides the clusterRef to conveniently create AWS clusters, connect to the leader of the cluster, and then launch a workflow. The leader handles distributing the jobs over the worker nodes and autoscaling to optimize costs.

The Running a Workflow with Autoscaling section details how to create a cluster and run a workflow that will dynamically scale depending on the workflow's needs.

The Static Provisioning section explains how a static cluster (one that won't automatically change in size) can be created and provisioned (grown, shrunk, destroyed, etc.).

Preparing your AWS environment¶

To use Amazon Web Services (AWS) to run Toil or to just use S3 to host the files during the computation of a workflow, first set up and configure an account with AWS:

$ ssh-keygen -t rsa

~/.ssh/id_rsa

$ cat ~/.ssh/id_rsa.pub >> ~/.ssh/authorized_keys
$ eval `ssh-agent -s`
$ ssh-add

$ chmod 400 id_rsa

https://us-west-1.console.aws.amazon.com/ec2/v2/home?region=us-west-1#KeyPairs:sort=keyName

https://console.aws.amazon.com/iam/home?region=us-west-1#/home

$ pip install awscli --upgrade --user

$ aws configure

" AWS Access Key ID [****************Q65Q]: "
" AWS Secret Access Key [****************G0ys]: "
" Default region name [us-west-1]: "
" Default output format [json]: "

$ virtualenv venv
$ source venv/bin/activate
$ pip install toil[all]==3.12.0

$ TOIL_APPLIANCE_SELF=quay.io/ucsc_cgl/toil:3.12.0 \


      toil launch-cluster clustername \


      --leaderNodeType t2.medium \


      --zone us-west-1a \


      --keyPairName id_rsa

AWS Job Store¶

Using the AWS job store is straightforward after you've finished Preparing your AWS environment; all you need to do is specify the prefix for the job store name.

To run the sort example sort example with the AWS job store you would type

$ python sort.py aws:us-west-2:my-aws-sort-jobstore

Toil Provisioner¶

The Toil provisioner is included in Toil alongside the [aws] extra and allows us to spin up a cluster.

Getting started with the provisioner is simple:

The Toil provisioner is built around the Toil Appliance, a Docker image that bundles Toil and all its requirements (e.g. Mesos). This makes deployment simple across platforms, and you can even simulate a cluster locally (see appliance_dev for details).

For information on using the Toil Provisioner have a look at Running a Workflow with Autoscaling.

Details about Launching a Cluster in AWS¶

Using the provisioner to launch a Toil leader instance is simple using the launch-cluster command. For example, to launch a cluster named "my-cluster" with a t2.medium leader in the us-west-2a zone, run

(venv) $ toil launch-cluster my-cluster \


             --leaderNodeType t2.medium \


             --zone us-west-2a \


             --keyPairName <your-AWS-key-pair-name>

The cluster name is used to uniquely identify your cluster and will be used to populate the instance's Name tag. Also, the Toil provisioner will automatically tag your cluster with an Owner tag that corresponds to your keypair name to facilitate cost tracking. In addition, the ToilNodeType tag can be used to filter "leader" vs. "worker" nodes in your cluster.

The leaderNodeType is an EC2 instance type. This only affects the leader node.

The --zone parameter specifies which EC2 availability zone to launch the cluster in. Alternatively, you can specify this option via the TOIL_AWS_ZONE environment variable. Note: the zone is different from an EC2 region. A region corresponds to a geographical area like us-west-2 (Oregon), and availability zones are partitions of this area like us-west-2a.

By default, Toil creates an IAM role for each cluster with sufficient permissions to perform cluster operations (e.g. full S3, EC2, and SDB access). If the default permissions are not sufficient for your use case (e.g. if you need access to ECR), you may create a custom IAM role with all necessary permissions and set the --awsEc2ProfileArn parameter when launching the cluster. Note that your custom role must at least have these permissions in order for the Toil cluster to function properly.

In addition, Toil creates a new security group with the same name as the cluster name with default rules (e.g. opens port 22 for SSH access). If you require additional security groups, you may use the --awsEc2ExtraSecurityGroupId parameter when launching the cluster. Note: Do not use the same name as the cluster name for the extra security groups as any security group matching the cluster name will be deleted once the cluster is destroyed.

For more information on options try:

(venv) $ toil launch-cluster --help

Static Provisioning¶

Toil can be used to manage a cluster in the cloud by using the clusterRef. The cluster utilities also make it easy to run a toil workflow directly on this cluster. We call this static provisioning because the size of the cluster does not change. This is in contrast with Running a Workflow with Autoscaling.

To launch worker nodes alongside the leader we use the -w option:

(venv) $ toil launch-cluster my-cluster \


             --leaderNodeType t2.small -z us-west-2a \


             --keyPairName your-AWS-key-pair-name \


             --nodeTypes m3.large,t2.micro -w 1,4

This will spin up a leader node of type t2.small with five additional workers --- one m3.large instance and four t2.micro.

Currently static provisioning is only possible during the cluster's creation. The ability to add new nodes and remove existing nodes via the native provisioner is in development. Of course the cluster can always be deleted with the destroyCluster utility.

Uploading Workflows¶

Now that our cluster is launched, we use the rsyncCluster utility to copy the workflow to the leader. For a simple workflow in a single file this might look like

(venv) $ toil rsync-cluster -z us-west-2a my-cluster toil-workflow.py :/

NOTE:

Running a Workflow with Autoscaling¶

Autoscaling is a feature of running Toil in a cloud whereby additional cloud instances are launched to run the workflow. Autoscaling leverages Mesos containers to provide an execution environment for these workflows.

NOTE:

(venv) $ toil launch-cluster <cluster-name> \


             --keyPairName <AWS-key-pair-name> \


             --leaderNodeType t2.medium \


             --zone us-west-2a

(venv) $ toil rsync-cluster -z us-west-2a <cluster-name> sort.py :/root

(venv) $ toil ssh-cluster -z us-west-2a <cluster-name>

$ python /root/sort.py aws:us-west-2:<my-jobstore-name> \


      --provisioner aws \


      --nodeTypes c3.large \


      --maxNodes 2 \


      --batchSystem mesos

NOTE:

$ head fileToSort.txt

$ head sortedFile.txt

For more information on other autoscaling (and other) options have a look at workflowOptions and/or run

$ python my-toil-script.py --help

IMPORTANT:

Preemptability¶

Toil can run on a heterogeneous cluster of both preemptable and non-preemptable nodes. Being preemptable node simply means that the node may be shut down at any time, while jobs are running. These jobs can then be restarted later somewhere else.

A node type can be specified as preemptable by adding a spot bid to its entry in the list of node types provided with the --nodeTypes flag. If spot instance prices rise above your bid, the preemptable node whill be shut down.

While individual jobs can each explicitly specify whether or not they should be run on preemptable nodes via the boolean preemptable resource requirement, the --defaultPreemptable flag will allow jobs without a preemptable requirement to run on preemptable machines.

Finally, the --preemptableCompensation flag can be used to handle cases where preemptable nodes may not be available but are required for your workflow. With this flag enabled, the autoscaler will attempt to compensate for a shortage of preemptable nodes of a certain type by creating non-preemptable nodes of that type, if non-preemptable nodes of that type were specified in --nodeTypes.

Using MinIO and S3-Compatible object stores¶

Toil can be configured to access files stored in an S3-compatible object store such as MinIO. The following environment variables can be used to configure the S3 connection used:

Examples:

TOIL_S3_HOST=127.0.0.1
TOIL_S3_PORT=9010
TOIL_S3_USE_SSL=False

Dashboard¶

Toil provides a dashboard for viewing the RAM and CPU usage of each node, the number of issued jobs of each type, the number of failed jobs, and the size of the jobs queue. To launch this dashboard for a toil workflow, include the --metrics flag in the toil script command. The dashboard can then be viewed in your browser at localhost:3000 while connected to the leader node through toil ssh-cluster. On AWS, the dashboard keeps track of every node in the cluster to monitor CPU and RAM usage, but it can also be used while running a workflow on a single machine. The dashboard uses Grafana as the front end for displaying real-time plots, and Prometheus for tracking metrics exported by toil. In order to use the dashboard for a non-released toil version, you will have to build the containers locally with make docker, since the prometheus, grafana, and mtail containers used in the dashboard are tied to a specific toil version.

Running in Google Compute Engine (GCE)¶

Toil supports a provisioner with Google, and a Google Job Store. To get started, follow instructions for Preparing your Google environment.

Preparing your Google environment¶

Toil supports using the Google Cloud Platform. Setting this up is easy!

$ ssh-keygen -t rsa -f ~/.ssh/id_rsa -C [USERNAME]

$ chmod 400 ~/.ssh/id_rsa ~/.ssh/id_rsa.pub

For more details look at Google's instructions for adding SSH keys.

Google Job Store¶

To use the Google Job Store you will need to set the GOOGLE_APPLICATION_CREDENTIALS environment variable by following Google's instructions.

Then to run the sort example with the Google job store you would type

$ python sort.py google:my-project-id:my-google-sort-jobstore

Running a Workflow with Autoscaling¶

WARNING:

The steps to run a GCE workflow are similar to those of AWS (Autoscaling), except you will need to explicitly specify the --provisioner gce option which otherwise defaults to aws.

(venv) $ toil launch-cluster <CLUSTER-NAME> \


             --provisioner gce \


             --leaderNodeType n1-standard-1 \


             --keyPairName <SSH-KEYNAME> \


             --zone us-west1-a

(venv) $ toil rsync-cluster --provisioner gce <CLUSTER-NAME> sort.py :/root
(venv) $ toil ssh-cluster --provisioner gce <CLUSTER-NAME>

$ python /root/sort.py  google:<PROJECT-ID>:<JOBSTORE-NAME> \


      --provisioner gce \


      --batchSystem mesos \


      --nodeTypes n1-standard-2 \


      --maxNodes 2

$ exit  # this exits the ssh from the leader node
(venv) $ toil destroy-cluster --provisioner gce <CLUSTER-NAME>

Cluster Utilities¶

There are several utilities used for starting and managing a Toil cluster using the AWS provisioner. They are installed via the [aws] or [google] extra. For installation details see installProvisioner. The cluster utilities are used for runningAWS and are comprised of toil launch-cluster, toil rsync-cluster, toil ssh-cluster, and toil destroy-cluster entry points.

Cluster commands specific to toil are:

For information on a specific utility run:

toil launch-cluster --help

for a full list of its options and functionality.

The cluster utilities can be used for runningGCE and runningAWS.

TIP:

NOTE:

Stats Command¶

To use the stats command, a workflow must first be run using the --stats option. Using this command makes certain that toil does not delete the job store, no matter what other options are specified (i.e. normally the option --clean=always would delete the job, but --stats will override this).

An example of this would be running the following:

python discoverfiles.py file:my-jobstore --stats

Where discoverfiles.py is the following:

import os
import subprocess
from toil.common import Toil
from toil.job import Job
class discoverFiles(Job):


    """Views files at a specified path using ls."""


    def __init__(self, path, *args, **kwargs):


        self.path = path


        super(discoverFiles, self).__init__(*args, **kwargs)


    def run(self, fileStore):


        if os.path.exists(self.path):


            subprocess.check_call(["ls", self.path])
def main():


    options = Job.Runner.getDefaultArgumentParser().parse_args()


    options.clean = "always"


    job1 = discoverFiles(path="/sys/", displayName='sysFiles')


    job2 = discoverFiles(path=os.path.expanduser("~"), displayName='userFiles')


    job3 = discoverFiles(path="/tmp/")


    job1.addChild(job2)


    job2.addChild(job3)


    with Toil(options) as toil:


        if not toil.options.restart:


            toil.start(job1)


        else:


            toil.restart()
if __name__ == '__main__':


    main()

Notice the displayName key, which can rename a job, giving it an alias when it is finally displayed in stats. Running this workflow file should record three job names: sysFiles (job1), userFiles (job2), and discoverFiles (job3). To see the runtime and resources used for each job when it was run, type

toil stats file:my-jobstore

This should output the following:

Batch System: singleMachine
Default Cores: 1  Default Memory: 2097152K
Max Cores: 9.22337e+18
Total Clock: 0.56  Total Runtime: 1.01
Worker


    Count |                                    Time* |                                    Clock |                                     Wait |                                   Memory


        n |      min    med*     ave     max   total |      min     med     ave     max   total |      min     med     ave     max   total |      min     med     ave     max   total


        1 |     0.14    0.14    0.14    0.14    0.14 |     0.13    0.13    0.13    0.13    0.13 |     0.01    0.01    0.01    0.01    0.01 |      76K     76K     76K     76K     76K
Job


 Worker Jobs  |     min    med    ave    max


              |       3      3      3      3


    Count |                                    Time* |                                    Clock |                                     Wait |                                   Memory


        n |      min    med*     ave     max   total |      min     med     ave     max   total |      min     med     ave     max   total |      min     med     ave     max   total


        3 |     0.01    0.06    0.05    0.07    0.14 |     0.00    0.06    0.04    0.07    0.12 |     0.00    0.01    0.00    0.01    0.01 |      76K     76K     76K     76K    229K


 sysFiles


    Count |                                    Time* |                                    Clock |                                     Wait |                                   Memory


        n |      min    med*     ave     max   total |      min     med     ave     max   total |      min     med     ave     max   total |      min     med     ave     max   total


        1 |     0.01    0.01    0.01    0.01    0.01 |     0.00    0.00    0.00    0.00    0.00 |     0.01    0.01    0.01    0.01    0.01 |      76K     76K     76K     76K     76K


 userFiles


    Count |                                    Time* |                                    Clock |                                     Wait |                                   Memory


        n |      min    med*     ave     max   total |      min     med     ave     max   total |      min     med     ave     max   total |      min     med     ave     max   total


        1 |     0.06    0.06    0.06    0.06    0.06 |     0.06    0.06    0.06    0.06    0.06 |     0.01    0.01    0.01    0.01    0.01 |      76K     76K     76K     76K     76K


 discoverFiles


    Count |                                    Time* |                                    Clock |                                     Wait |                                   Memory


        n |      min    med*     ave     max   total |      min     med     ave     max   total |      min     med     ave     max   total |      min     med     ave     max   total


        1 |     0.07    0.07    0.07    0.07    0.07 |     0.07    0.07    0.07    0.07    0.07 |     0.00    0.00    0.00    0.00    0.00 |      76K     76K     76K     76K     76K

Once we're done, we can clean up the job store by running

toil clean file:my-jobstore

Status Command¶

Continuing the example from the stats section above, if we ran our workflow with the command

python discoverfiles.py file:my-jobstore --stats

We could interrogate our jobstore with the status command, for example:

toil status file:my-jobstore

If the run was successful, this would not return much valuable information, something like

2018-01-11 19:31:29,739 - toil.lib.bioio - INFO - Root logger is at level 'INFO', 'toil' logger at level 'INFO'.
2018-01-11 19:31:29,740 - toil.utils.toilStatus - INFO - Parsed arguments
2018-01-11 19:31:29,740 - toil.utils.toilStatus - INFO - Checking if we have files for Toil
The root job of the job store is absent, the workflow completed successfully.

Otherwise, the status command should return the following:

Clean Command¶

If a Toil pipeline didn't finish successfully, or was run using --clean=always or --stats, the job store will exist until it is deleted. toil clean <jobStore> ensures that all artifacts associated with a job store are removed. This is particularly useful for deleting AWS job stores, which reserves an SDB domain as well as an S3 bucket.

The deletion of the job store can be modified by the --clean argument, and may be set to always, onError, never, or onSuccess (default).

Temporary directories where jobs are running can also be saved from deletion using the --cleanWorkDir, which has the same options as --clean. This option should only be run when debugging, as intermediate jobs will fill up disk space.

Launch-Cluster Command¶

Running toil launch-cluster starts up a leader for a cluster. Workers can be added to the initial cluster by specifying the -w option. An example would be

$ toil launch-cluster my-cluster \


      --leaderNodeType t2.small -z us-west-2a \


      --keyPairName your-AWS-key-pair-name \


      --nodeTypes m3.large,t2.micro -w 1,4

Options are listed below. These can also be displayed by running

$ toil launch-cluster --help

launch-cluster's main positional argument is the clusterName. This is simply the name of your cluster. If it does not exist yet, Toil will create it for you.

Launch-Cluster Options

Logging Options

Ssh-Cluster Command¶

Toil provides the ability to ssh into the leader of the cluster. This can be done as follows:

$ toil ssh-cluster CLUSTER-NAME-HERE

This will open a shell on the Toil leader and is used to start an Autoscaling run. Issues with docker prevent using screen and tmux when sshing the cluster (The shell doesn't know that it is a TTY which prevents it from allocating a new screen session). This can be worked around via

$ script
$ screen

Simply running screen within script will get things working properly again.

Finally, you can execute remote commands with the following syntax:

$ toil ssh-cluster CLUSTER-NAME-HERE remoteCommand

It is not advised that you run your Toil workflow using remote execution like this unless a tool like nohup is used to ensure the process does not die if the SSH connection is interrupted.

For an example usage, see Autoscaling.

Rsync-Cluster Command¶

The most frequent use case for the rsync-cluster utility is deploying your Toil script to the Toil leader. Note that the syntax is the same as traditional rsync with the exception of the hostname before the colon. This is not needed in toil rsync-cluster since the hostname is automatically determined by Toil.

Here is an example of its usage:

$ toil rsync-cluster CLUSTER-NAME-HERE \


   ~/localFile :/remoteDestination

Destroy-Cluster Command¶

The destroy-cluster command is the advised way to get rid of any Toil cluster launched using the Launch-Cluster Command command. It ensures that all attached nodes, volumes, security groups, etc. are deleted. If a node or cluster is shut down using Amazon's online portal residual resources may still be in use in the background. To delete a cluster run

$ toil destroy-cluster CLUSTER-NAME-HERE

Kill Command¶

To kill all currently running jobs for a given jobstore, use the command

toil kill file:my-jobstore

Standard Output/Error from Batch System Jobs¶

Standard output and error from batch system jobs (except for the Parasol and Mesos batch systems) are redirected to files in the toil-<workflowID> directory created within the temporary directory specified by the --workDir option; see optionsRef. Each file is named as follows: toil_job_<Toil job ID>_batch_<name of batch system>_<job ID from batch system>_<file description>.log, where <file description> is std_output for standard output, and std_error for standard error. HTCondor will also write job event log files with <file description> = job_events.

If capturing standard output and error is desired, --workDir will generally need to be on a shared file system; otherwise if these are written to local temporary directories on each node (e.g. /tmp) Toil will not be able to retrieve them. Alternatively, the --noStdOutErr option forces Toil to discard all standard output and error from batch system jobs.

Running CWL Locally¶

The toil-cwl-runner command provides cwl-parsing functionality using cwltool, and leverages the job-scheduling and batch system support of Toil.

To run in local batch mode, provide the CWL file and the input object file:

$ toil-cwl-runner example.cwl example-job.yml

For a simple example of CWL with Toil see cwlquickstart.

Note for macOS + Docker + Toil¶

When invoking CWL documents that make use of Docker containers if you see errors that look like

docker: Error response from daemon: Mounts denied:
The paths /var/...tmp are not shared from OS X and are not known to Docker.

you may need to add

export TMPDIR=/tmp/docker_tmp

either in your startup file (.bashrc) or add it manually in your shell before invoking toil.

Detailed Usage Instructions¶

Help information can be found by using this toil command:

$ toil-cwl-runner -h

A more detailed example shows how we can specify both Toil and cwltool arguments for our workflow:

$ toil-cwl-runner \


    --singularity \


    --jobStore my_jobStore \


    --batchSystem lsf \


    --workDir `pwd` \


    --outdir `pwd` \


    --logFile cwltoil.log \


    --writeLogs `pwd` \


    --logLevel DEBUG \


    --retryCount 2 \


    --maxLogFileSize 20000000000 \


    --stats \


    standard_bam_processing.cwl \


    inputs.yaml

In this example, we set the following options, which are all passed to Toil:

--singularity: Specifies that all jobs with Docker fornat containers specified should be run using the Singularity container engine instead of the Docker container engine.

--jobStore: Path to a folder that already exists, which will contain the Toil jobstore and all related job-tracking information.

--batchSystem: Use the specified HPC or Cloud-based cluster platform.

--workDir: The directory where all temporary files will be created for the workflow. A subdirectory of this will be set as the $TMPDIR environment variable and this subdirectory can be referenced using the CWL parameter reference $(runtime.tmpdir) in CWL tools and workflows.

--outdir: Directory where final File and Directory outputs will be written. References to these and other output types will be in the JSON object printed to the stdout stream after workflow execution.

--logFile: Path to the main logfile with logs from all jobs.

--writeLogs: Directory where all job logs will be stored.

--retryCount: How many times to retry each Toil job.

--maxLogFileSize: Logs that get larger than this value will be truncated.

--stats: Save resources usages in json files that can be collected with the toil stats command after the workflow is done.

Running CWL in the Cloud¶

To run in cloud and HPC configurations, you may need to provide additional command line parameters to select and configure the batch system to use.

To run a CWL workflow in AWS with toil see awscwl.

Running CWL within Toil Scripts¶

A CWL workflow can be run indirectly in a native Toil script. However, this is not the standard way to run CWL workflows with Toil and doing so comes at the cost of job efficiency. For some use cases, such as running one process on multiple files, it may be useful. For example, if you want to run a CWL workflow with 3 YML files specifying different samples inputs, it could look something like:

import os
import subprocess
from toil.common import Toil
from toil.job import Job
def initialize_jobs(job):


    job.fileStore.logToMaster('initialize_jobs')
def runQC(job, cwl_file, cwl_filename, yml_file, yml_filename, outputs_dir, output_num):


    job.fileStore.logToMaster("runQC")


    tempDir = job.fileStore.getLocalTempDir()


    cwl = job.fileStore.readGlobalFile(cwl_file, userPath=os.path.join(tempDir, cwl_filename))


    yml = job.fileStore.readGlobalFile(yml_file, userPath=os.path.join(tempDir, yml_filename))


    subprocess.check_call(["toil-cwl-runner", cwl, yml])


    output_filename = "output.txt"


    output_file = job.fileStore.writeGlobalFile(output_filename)


    job.fileStore.readGlobalFile(output_file, userPath=os.path.join(outputs_dir, "sample_" + output_num + "_" + output_filename))


    return output_file
if __name__ == "__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    with Toil(options) as toil:


        # specify the folder where the cwl and yml files live


        inputs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "cwlExampleFiles")


        # specify where you wish the outputs to be written


        outputs_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)), "cwlExampleFiles")


        job0 = Job.wrapJobFn(initialize_jobs)


        cwl_filename = "hello.cwl"


        cwl_file = toil.importFile("file://" + os.path.abspath(os.path.join(inputs_dir, cwl_filename)))


        # add list of yml config inputs here or import and construct from file


        yml_files = ["hello1.yml", "hello2.yml", "hello3.yml"]


        i = 0


        for yml in yml_files:


            i = i + 1


            yml_file = toil.importFile("file://" + os.path.abspath(os.path.join(inputs_dir, yml)))


            yml_filename = yml


            job = Job.wrapJobFn(runQC, cwl_file, cwl_filename, yml_file, yml_filename, outputs_dir, output_num=str(i))


            job0.addChild(job)


        toil.start(job0)

Toil & CWL Tips¶

See logs for just one job by using the full log file

This requires knowing the job's toil-generated ID, which can be found in the log files.

cat cwltoil.log | grep jobVM1fIs

Grep for full tool commands from toil logs

This gives you a more concise view of the commands being run (note that this information is only available from Toil when running with --logDebug).

pcregrep -M "\[job .*\.cwl.*$\n(.*        .*$\n)*" cwltoil.log
#         ^allows for multiline matching

Find Bams that have been generated for specific step while pipeline is running:

find . | grep -P '^./out_tmpdir.*_MD\.bam$'

See what jobs have been run

cat log/cwltoil.log | grep -oP "\[job .*.cwl\]" | sort | uniq

or:

cat log/cwltoil.log | grep -i "issued job"

Get status of a workflow

$ toil status /home/johnsoni/TEST_RUNS_3/TEST_run/tmp/jobstore-09ae0acc-c800-11e8-9d09-70106fb1697e
<hostname> 2018-10-04 15:01:44,184 MainThread INFO toil.lib.bioio: Root logger is at level 'INFO', 'toil' logger at level 'INFO'.
<hostname> 2018-10-04 15:01:44,185 MainThread INFO toil.utils.toilStatus: Parsed arguments
<hostname> 2018-10-04 15:01:47,081 MainThread INFO toil.utils.toilStatus: Traversing the job graph gathering jobs. This may take a couple of minutes.
Of the 286 jobs considered, there are 179 jobs with children, 107 jobs ready to run, 0 zombie jobs, 0 jobs with services, 0 services, and 0 jobs with log files currently in file:/home/user/jobstore-09ae0acc-c800-11e8-9d09-70106fb1697e.

Toil Stats

You can get run statistics broken down by CWL file. This only works once the workflow is finished:

$ toil stats /path/to/jobstore

The output will contain CPU, memory, and walltime information for all CWL job types:

<hostname> 2018-10-15 12:06:19,003 MainThread INFO toil.lib.bioio: Root logger is at level 'INFO', 'toil' logger at level 'INFO'.
<hostname> 2018-10-15 12:06:19,004 MainThread INFO toil.utils.toilStats: Parsed arguments
<hostname> 2018-10-15 12:06:19,004 MainThread INFO toil.utils.toilStats: Checking if we have files for toil
<hostname> 2018-10-15 12:06:19,004 MainThread INFO toil.utils.toilStats: Checked arguments
Batch System: lsf
Default Cores: 1  Default Memory: 10485760K
Max Cores: 9.22337e+18
Total Clock: 106608.01  Total Runtime: 86634.11
Worker


    Count |                                       Time* |                                        Clock |                                              Wait |                                    Memory


        n |      min    med*     ave      max     total |      min     med      ave      max     total |        min      med       ave      max      total |      min     med     ave     max    total


     1659 |     0.00    0.80  264.87 12595.59 439424.40 |     0.00    0.46   449.05 42240.74 744968.80 |  -35336.69     0.16   -184.17  4230.65 -305544.39 |      48K    223K   1020K  40235K 1692300K
Job


 Worker Jobs  |     min    med    ave    max


              |    1077   1077   1077   1077


    Count |                                       Time* |                                        Clock |                                              Wait |                                    Memory


        n |      min    med*     ave      max     total |      min     med      ave      max     total |        min      med       ave      max      total |      min     med     ave     max    total


     1077 |     0.04    1.18  407.06 12593.43 438404.73 |     0.01    0.28   691.17 42240.35 744394.14 |  -35336.83     0.27   -284.11  4230.49 -305989.41 |     135K    268K   1633K  40235K 1759734K


 ResolveIndirect


    Count |                                       Time* |                                        Clock |                                              Wait |                                    Memory


        n |      min    med*     ave      max     total |      min     med      ave      max     total |        min      med       ave      max      total |      min     med     ave     max    total


      205 |     0.04    0.07    0.16     2.29     31.95 |     0.01    0.02     0.02     0.14      3.60 |       0.02     0.05      0.14     2.28      28.35 |     190K    266K    256K    314K   52487K


 CWLGather


    Count |                                       Time* |                                        Clock |                                              Wait |                                    Memory


        n |      min    med*     ave      max     total |      min     med      ave      max     total |        min      med       ave      max      total |      min     med     ave     max    total


       40 |     0.05    0.17    0.29     1.90     11.62 |     0.01    0.02     0.02     0.05      0.80 |       0.03     0.14      0.27     1.88      10.82 |     188K    265K    250K    316K   10039K


 CWLWorkflow


    Count |                                       Time* |                                        Clock |                                              Wait |                                    Memory


        n |      min    med*     ave      max     total |      min     med      ave      max     total |        min      med       ave      max      total |      min     med     ave     max    total


      205 |     0.09    0.40    0.98    13.70    200.82 |     0.04    0.15     0.16     1.08     31.78 |       0.04     0.26      0.82    12.62     169.04 |     190K    270K    257K    316K   52826K


 file:///home/johnsoni/pipeline_0.0.39/ACCESS-Pipeline/cwl_tools/expression_tools/group_waltz_files.cwl


    Count |                                       Time* |                                        Clock |                                              Wait |                                    Memory


        n |      min    med*     ave      max     total |      min     med      ave      max     total |        min      med       ave      max      total |      min     med     ave     max    total


       99 |     0.29    0.49    0.59     2.50     58.11 |     0.14    0.26     0.29     1.04     28.95 |       0.14     0.22      0.29     1.48      29.16 |     135K    135K    135K    136K   13459K


 file:///home/johnsoni/pipeline_0.0.39/ACCESS-Pipeline/cwl_tools/expression_tools/make_sample_output_dirs.cwl


    Count |                                       Time* |                                        Clock |                                              Wait |                                    Memory


        n |      min    med*     ave      max     total |      min     med      ave      max     total |        min      med       ave      max      total |      min     med     ave     max    total


       11 |     0.34    0.52    0.74     2.63      8.18 |     0.20    0.30     0.41     1.17      4.54 |       0.14     0.20      0.33     1.45       3.65 |     136K    136K    136K    136K    1496K


 file:///home/johnsoni/pipeline_0.0.39/ACCESS-Pipeline/cwl_tools/expression_tools/consolidate_files.cwl


    Count |                                       Time* |                                        Clock |                                              Wait |                                    Memory


        n |      min    med*     ave      max     total |      min     med      ave      max     total |        min      med       ave      max      total |      min     med     ave     max    total


        8 |     0.31    0.59    0.71     1.80      5.69 |     0.18    0.35     0.37     0.63      2.94 |       0.13     0.27      0.34     1.17       2.75 |     136K    136K    136K    136K    1091K


 file:///home/johnsoni/pipeline_0.0.39/ACCESS-Pipeline/cwl_tools/bwa-mem/bwa-mem.cwl


    Count |                                       Time* |                                        Clock |                                              Wait |                                    Memory


        n |      min    med*     ave      max     total |      min     med      ave      max     total |        min      med       ave      max      total |      min     med     ave     max    total


       22 |   895.76 3098.13 3587.34 12593.43  78921.51 |  2127.02 7910.31  8123.06 16959.13 178707.34 |  -11049.84 -3827.96  -4535.72    19.49  -99785.83 |    5659K   5950K   5854K   6128K  128807K

Understanding toil log files

There is a worker_log.txt file for each job, this file is written to while the job is running, and deleted after the job finishes. The contents are printed to the main log file and transferred to a log file in the --logDir folder once the job is completed successfully.

The new log file will be named something like:

file:<path to cwl tool>.cwl_<job ID>.log
file:---home-johnsoni-pipeline_1.1.14-ACCESS--Pipeline-cwl_tools-marianas-ProcessLoopUMIFastq.cwl_I-O-jobfGsQQw000.log

This is the toil job command with spaces replaced by dashes.

How to Run a WDL file in Toil¶

Recommended best practice when running wdl files is to first use the Broad's wdltool for syntax validation and generating the needed json input file. Full documentation can be found on the repository, and a precompiled jar binary can be downloaded here: wdltool (this requires java7).

That means two steps. First, make sure your wdl file is valid and devoid of syntax errors by running

java -jar wdltool.jar validate example_wdlfile.wdl

Second, generate a complementary json file if your wdl file needs one. This json will contain keys for every necessary input that your wdl file needs to run:

java -jar wdltool.jar inputs example_wdlfile.wdl

When this json template is generated, open the file, and fill in values as necessary by hand. WDL files all require json files to accompany them. If no variable inputs are needed, a json file containing only '{}' may be required.

Once a wdl file is validated and has an appropriate json file, workflows can be run in toil using:

toil-wdl-runner example_wdlfile.wdl example_jsonfile.json

See options below for more parameters.

ENCODE Example from ENCODE-DCC¶

To follow this example, you will need docker installed. The original workflow can be found here: https://github.com/ENCODE-DCC/pipeline-container

We've included the wdl file and data files in the toil repository needed to run this example. First, download the example code and unzip. The file needed is "testENCODE/encode_mapping_workflow.wdl".

Next, use wdltool (this requires java7) to validate this file:

java -jar wdltool.jar validate encode_mapping_workflow.wdl

Next, use wdltool to generate a json file for this wdl file:

java -jar wdltool.jar inputs encode_mapping_workflow.wdl

This json file once opened should look like this:

{
"encode_mapping_workflow.fastqs": "Array[File]",
"encode_mapping_workflow.trimming_parameter": "String",
"encode_mapping_workflow.reference": "File"
}

The trimming_parameter should be set to 'native'. Download the example code and unzip. Inside are two data files required for the run

ENCODE_data/reference/GRCh38_chr21_bwa.tar.gz ENCODE_data/ENCFF000VOL_chr21.fq.gz

Editing the json to include these as inputs, the json should now look something like this:

{
"encode_mapping_workflow.fastqs": ["/path/to/unzipped/ENCODE_data/ENCFF000VOL_chr21.fq.gz"],
"encode_mapping_workflow.trimming_parameter": "native",
"encode_mapping_workflow.reference": "/path/to/unzipped/ENCODE_data/reference/GRCh38_chr21_bwa.tar.gz"
}

The wdl and json files can now be run using the command

toil-wdl-runner encode_mapping_workflow.wdl encode_mapping_workflow.json

This should deposit the output files in the user's current working directory (to change this, specify a new directory with the '-o' option).

GATK Examples from the Broad¶

Simple examples of WDL can be found on the Broad's website as tutorials: https://software.broadinstitute.org/wdl/documentation/topic?name=wdl-tutorials.

One can follow along with these tutorials, write their own wdl files following the directions and run them using either cromwell or toil. For example, in tutorial 1, if you've followed along and named your wdl file 'helloHaplotypeCall.wdl', then once you've validated your wdl file using wdltool (this requires java7) using

java -jar wdltool.jar validate helloHaplotypeCaller.wdl

and generated a json file (and subsequently typed in appropriate filepaths* and variables) using

java -jar wdltool.jar inputs helloHaplotypeCaller.wdl

then the wdl script can be run using

toil-wdl-runner helloHaplotypeCaller.wdl helloHaplotypeCaller_inputs.json

toilwdl.py Options¶

'-o' or '-\-outdir': Specifies the output folder, and defaults to the current working directory if not specified by the user.

'-\-dev_mode': Creates "AST.out", which holds a printed AST of the wdl file and "mappings.out", which holds the printed task, workflow, csv, and tsv dictionaries generated by the parser. Also saves the compiled toil python workflow file for debugging.

Any number of arbitrary options may also be specified. These options will not be parsed immediately, but passed down as toil options once the wdl/json files are processed. For valid toil options, see the documentation: http://toil.readthedocs.io/en/latest/running/cliOptions.html

Running WDL within Toil Scripts¶

NOTE:

A WDL workflow can be run indirectly in a native Toil script. However, this is not the standard way to run WDL workflows with Toil and doing so comes at the cost of job efficiency. For some use cases, such as running one process on multiple files, it may be useful. For example, if you want to run a WDL workflow with 3 JSON files specifying different samples inputs, it could look something like:

import os
import subprocess
from toil.common import Toil
from toil.job import Job
def initialize_jobs(job):


    job.fileStore.logToMaster("initialize_jobs")
def runQC(job, wdl_file, wdl_filename, json_file, json_filename, outputs_dir, jar_loc,output_num):


    job.fileStore.logToMaster("runQC")


    tempDir = job.fileStore.getLocalTempDir()


    wdl = job.fileStore.readGlobalFile(wdl_file, userPath=os.path.join(tempDir, wdl_filename))


    json = job.fileStore.readGlobalFile(json_file, userPath=os.path.join(tempDir, json_filename))


    subprocess.check_call(["java","-jar",jar_loc,"run",wdl,"--inputs",json])


    output_filename = "output.txt"


    output_file = job.fileStore.writeGlobalFile(outputs_dir + output_filename)


    job.fileStore.readGlobalFile(output_file, userPath=os.path.join(outputs_dir, "sample_" + output_num + "_" + output_filename))


    return output_file
if __name__ == "__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    with Toil(options) as toil:


        # specify the folder where the wdl and json files live


        inputs_dir = "wdlExampleFiles/"


        # specify where you wish the outputs to be written


        outputs_dir = "wdlExampleFiles/"


        # specify the location of your cromwell jar


        jar_loc = os.path.abspath("wdlExampleFiles/cromwell-35.jar")


        job0 = Job.wrapJobFn(initialize_jobs)


        wdl_filename = "hello.wdl"


        wdl_file = toil.importFile("file://" + os.path.abspath(os.path.join(inputs_dir, wdl_filename)))


        # add list of yml config inputs here or import and construct from file


        json_files = ["hello1.json", "hello2.json", "hello3.json"]


        i = 0


        for json in json_files:


            i = i + 1


            json_file = toil.importFile("file://" + os.path.join(inputs_dir, json))


            json_filename = json


            job = Job.wrapJobFn(runQC, wdl_file, wdl_filename, json_file, json_filename, outputs_dir, jar_loc, output_num=str(i))


            job0.addChild(job)


        toil.start(job0)

WDL Specifications¶

WDL language specifications can be found here: https://github.com/broadinstitute/wdl/blob/develop/SPEC.md

Implementing support for more features is currently underway, but a basic roadmap so far is:

Scripting Quick Start¶

To begin, consider this short toil script which illustrates defining a workflow:

from toil.common import Toil
from toil.job import Job
def helloWorld(message, memory="2G", cores=2, disk="3G"):


    return "Hello, world!, here's a message: %s" % message
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "OFF"


    options.clean = "always"


    hello_job = Job.wrapFn(helloWorld, "Woot")


    with Toil(options) as toil:


        print(toil.start(hello_job)) #Prints Hello, world!, ...

The workflow consists of a single job. The resource requirements for that job are (optionally) specified by keyword arguments (memory, cores, disk). The script is run using toil.job.Job.Runner.getDefaultOptions(). Below we explain the components of this code in detail.

Job Basics¶

The atomic unit of work in a Toil workflow is a Job. User scripts inherit from this base class to define units of work. For example, here is a more long-winded class-based version of the job in the quick start example:

from toil.job import Job
class HelloWorld(Job):


    def __init__(self, message):


        Job.__init__(self,  memory="2G", cores=2, disk="3G")


        self.message = message


    def run(self, fileStore):


        return "Hello, world!, here's a message: %s" % self.message

In the example a class, HelloWorld, is defined. The constructor requests 2 gigabytes of memory, 2 cores and 3 gigabytes of local disk to complete the work.

The toil.job.Job.run() method is the function the user overrides to get work done. Here it just logs a message using toil.job.Job.log(), which will be registered in the log output of the leader process of the workflow.

Invoking a Workflow¶

We can add to the previous example to turn it into a complete workflow by adding the necessary function calls to create an instance of HelloWorld and to run this as a workflow containing a single job. This uses the toil.job.Job.Runner class, which is used to start and resume Toil workflows. For example:

from toil.common import Toil
from toil.job import Job
class HelloWorld(Job):


    def __init__(self, message):


        Job.__init__(self,  memory="2G", cores=2, disk="3G")


        self.message = message


    def run(self, fileStore):


        return "Hello, world!, here's a message: %s" % self.message
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "OFF"


    options.clean = "always"


    hello_job = HelloWorld("Woot")


    with Toil(options) as toil:


        print(toil.start(hello_job))

NOTE:

Alternatively, the more powerful toil.common.Toil class can be used to run and resume workflows. It is used as a context manager and allows for preliminary setup, such as staging of files into the job store on the leader node. An instance of the class is initialized by specifying an options object. The actual workflow is then invoked by calling the toil.common.Toil.start() method, passing the root job of the workflow, or, if a workflow is being restarted, toil.common.Toil.restart() should be used. Note that the context manager should have explicit if else branches addressing restart and non restart cases. The boolean value for these if else blocks is toil.options.restart.

For example:

from toil.common import Toil
from toil.job import Job
class HelloWorld(Job):


    def __init__(self, message):


        Job.__init__(self,  memory="2G", cores=2, disk="3G")


        self.message = message


    def run(self, fileStore):


        self.log("Hello, world!, I have a message: {}".format(self.message))
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    with Toil(options) as toil:


        if not toil.options.restart:


            job = HelloWorld("Woot!")


            toil.start(job)


        else:


            toil.restart()

The call to toil.job.Job.Runner.getDefaultOptions() creates a set of default options for the workflow. The only argument is a description of how to store the workflow's state in what we call a job-store. Here the job-store is contained in a directory within the current working directory called "toilWorkflowRun". Alternatively this string can encode other ways to store the necessary state, e.g. an S3 bucket object store location. By default the job-store is deleted if the workflow completes successfully.

The workflow is executed in the final line, which creates an instance of HelloWorld and runs it as a workflow. Note all Toil workflows start from a single starting job, referred to as the root job. The return value of the root job is returned as the result of the completed workflow (see promises below to see how this is a useful feature!).

Specifying Commandline Arguments¶

To allow command line control of the options we can use the toil.job.Job.Runner.getDefaultArgumentParser() method to create a argparse.ArgumentParser object which can be used to parse command line options for a Toil script. For example:

from toil.common import Toil
from toil.job import Job
class HelloWorld(Job):


    def __init__(self, message):


        Job.__init__(self,  memory="2G", cores=2, disk="3G")


        self.message = message


    def run(self, fileStore):


        return "Hello, world!, here's a message: %s" % self.message
if __name__=="__main__":


    parser = Job.Runner.getDefaultArgumentParser()


    options = parser.parse_args()


    options.logLevel = "OFF"


    options.clean = "always"


    hello_job = HelloWorld("Woot")


    with Toil(options) as toil:


        print(toil.start(hello_job))

Creates a fully fledged script with all the options Toil exposed as command line arguments. Running this script with "--help" will print the full list of options.

Alternatively an existing argparse.ArgumentParser or optparse.OptionParser object can have Toil script command line options added to it with the toil.job.Job.Runner.addToilOptions() method.

Resuming a Workflow¶

In the event that a workflow fails, either because of programmatic error within the jobs being run, or because of node failure, the workflow can be resumed. Workflows can only not be reliably resumed if the job-store itself becomes corrupt.

Critical to resumption is that jobs can be rerun, even if they have apparently completed successfully. Put succinctly, a user defined job should not corrupt its input arguments. That way, regardless of node, network or leader failure the job can be restarted and the workflow resumed.

To resume a workflow specify the "restart" option in the options object passed to toil.common.Toil.start(). If node failures are expected it can also be useful to use the integer "retryCount" option, which will attempt to rerun a job retryCount number of times before marking it fully failed.

In the common scenario that a small subset of jobs fail (including retry attempts) within a workflow Toil will continue to run other jobs until it can do no more, at which point toil.common.Toil.start() will raise a toil.leader.FailedJobsException exception. Typically at this point the user can decide to fix the script and resume the workflow or delete the job-store manually and rerun the complete workflow.

Functions and Job Functions¶

Defining jobs by creating class definitions generally involves the boilerplate of creating a constructor. To avoid this the classes toil.job.FunctionWrappingJob and toil.job.JobFunctionWrappingTarget allow functions to be directly converted to jobs. For example, the quick start example (repeated here):

from toil.common import Toil
from toil.job import Job
def helloWorld(message, memory="2G", cores=2, disk="3G"):


    return "Hello, world!, here's a message: %s" % message
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "OFF"


    options.clean = "always"


    hello_job = Job.wrapFn(helloWorld, "Woot")


    with Toil(options) as toil:


        print(toil.start(hello_job)) #Prints Hello, world!, ...

Is equivalent to the previous example, but using a function to define the job.

The function call:

Job.wrapFn(helloWorld, "Woot")

Creates the instance of the toil.job.FunctionWrappingTarget that wraps the function.

The keyword arguments memory, cores and disk allow resource requirements to be specified as before. Even if they are not included as keyword arguments within a function header they can be passed as arguments when wrapping a function as a job and will be used to specify resource requirements.

We can also use the function wrapping syntax to a job function, a function whose first argument is a reference to the wrapping job. Just like a self argument in a class, this allows access to the methods of the wrapping job, see toil.job.JobFunctionWrappingTarget. For example:

from toil.common import Toil
from toil.job import Job
def helloWorld(job, message):


    job.log("Hello world, I have a message: {}".format(message))
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    hello_job = Job.wrapJobFn(helloWorld, "Woot!")


    with Toil(options) as toil:


        toil.start(hello_job)

Here helloWorld() is a job function. It uses the toil.job.Job.log() to log a message that will be printed to the output console. Here the only subtle difference to note is the line:

hello_job = Job.wrapJobFn(helloWorld, "Woot")

Which uses the function toil.job.Job.wrapJobFn() to wrap the job function instead of toil.job.Job.wrapFn() which wraps a vanilla function.

Workflows with Multiple Jobs¶

A parent job can have child jobs and follow-on jobs. These relationships are specified by methods of the job class, e.g. toil.job.Job.addChild() and toil.job.Job.addFollowOn().

Considering a set of jobs the nodes in a job graph and the child and follow-on relationships the directed edges of the graph, we say that a job B that is on a directed path of child/follow-on edges from a job A in the job graph is a successor of A, similarly A is a predecessor of B.

A parent job's child jobs are run directly after the parent job has completed, and in parallel. The follow-on jobs of a job are run after its child jobs and their successors have completed. They are also run in parallel. Follow-ons allow the easy specification of cleanup tasks that happen after a set of parallel child tasks. The following shows a simple example that uses the earlier helloWorld() job function:

from toil.common import Toil
from toil.job import Job
def helloWorld(job, message, memory="2G", cores=2, disk="3G"):


    job.log("Hello world, I have a message: {}".format(message))
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    j1 = Job.wrapJobFn(helloWorld, "first")


    j2 = Job.wrapJobFn(helloWorld, "second or third")


    j3 = Job.wrapJobFn(helloWorld, "second or third")


    j4 = Job.wrapJobFn(helloWorld, "last")


    j1.addChild(j2)


    j1.addChild(j3)


    j1.addFollowOn(j4)


    with Toil(options) as toil:


        toil.start(j1)

In the example four jobs are created, first j1 is run, then j2 and j3 are run in parallel as children of j1, finally j4 is run as a follow-on of j1.

There are multiple short hand functions to achieve the same workflow, for example:

from toil.common import Toil
from toil.job import Job
def helloWorld(job, message, memory="2G", cores=2, disk="3G"):


    job.log("Hello world, I have a message: {}".format(message))
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    j1 = Job.wrapJobFn(helloWorld, "first")


    j2 = j1.addChildJobFn(helloWorld, "second or third")


    j3 = j1.addChildJobFn(helloWorld, "second or third")


    j4 = j1.addFollowOnJobFn(helloWorld, "last")


    with Toil(options) as toil:


        toil.start(j1)

Equivalently defines the workflow, where the functions toil.job.Job.addChildJobFn() and toil.job.Job.addFollowOnJobFn() are used to create job functions as children or follow-ons of an earlier job.

Jobs graphs are not limited to trees, and can express arbitrary directed acyclic graphs. For a precise definition of legal graphs see toil.job.Job.checkJobGraphForDeadlocks(). The previous example could be specified as a DAG as follows:

from toil.common import Toil
from toil.job import Job
def helloWorld(job, message, memory="2G", cores=2, disk="3G"):


    job.log("Hello world, I have a message: {}".format(message))
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    j1 = Job.wrapJobFn(helloWorld, "first")


    j2 = j1.addChildJobFn(helloWorld, "second or third")


    j3 = j1.addChildJobFn(helloWorld, "second or third")


    j4 = j2.addChildJobFn(helloWorld, "last")


    j3.addChild(j4)


    with Toil(options) as toil:


        toil.start(j1)

Note the use of an extra child edge to make j4 a child of both j2 and j3.

Dynamic Job Creation¶

The previous examples show a workflow being defined outside of a job. However, Toil also allows jobs to be created dynamically within jobs. For example:

from toil.common import Toil
from toil.job import Job
def binaryStringFn(job, depth, message=""):


    if depth > 0:


        job.addChildJobFn(binaryStringFn, depth-1, message + "0")


        job.addChildJobFn(binaryStringFn, depth-1, message + "1")


    else:


        job.log("Binary string: {}".format(message))
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    with Toil(options) as toil:


        toil.start(Job.wrapJobFn(binaryStringFn, depth=5))

The job function binaryStringFn logs all possible binary strings of length n (here n=5), creating a total of 2^(n+2) - 1 jobs dynamically and recursively. Static and dynamic creation of jobs can be mixed in a Toil workflow, with jobs defined within a job or job function being created at run time.

Promises¶

The previous example of dynamic job creation shows variables from a parent job being passed to a child job. Such forward variable passing is naturally specified by recursive invocation of successor jobs within parent jobs. This can also be achieved statically by passing around references to the return variables of jobs. In Toil this is achieved with promises, as illustrated in the following example:

from toil.common import Toil
from toil.job import Job
def fn(job, i):


    job.log("i is: %s" % i, level=100)


    return i+1
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    j1 = Job.wrapJobFn(fn, 1)


    j2 = j1.addChildJobFn(fn, j1.rv())


    j3 = j1.addFollowOnJobFn(fn, j2.rv())


    with Toil(options) as toil:


        toil.start(j1)

Running this workflow results in three log messages from the jobs: i is 1 from j1, i is 2 from j2 and i is 3 from j3.

The return value from the first job is promised to the second job by the call to toil.job.Job.rv() in the following line:

j2 = j1.addChildFn(fn, j1.rv())

The value of j1.rv() is a promise, rather than the actual return value of the function, because j1 for the given input has at that point not been evaluated. A promise (toil.job.Promise) is essentially a pointer to for the return value that is replaced by the actual return value once it has been evaluated. Therefore, when j2 is run the promise becomes 2.

Promises also support indexing of return values:

def parent(job):


    indexable = Job.wrapJobFn(fn)


    job.addChild(indexable)


    job.addFollowOnFn(raiseWrap, indexable.rv(2))
def raiseWrap(arg):


    raise RuntimeError(arg) # raises "2"
def fn(job):


    return (0, 1, 2, 3)

Promises can be quite useful. For example, we can combine dynamic job creation with promises to achieve a job creation process that mimics the functional patterns possible in many programming languages:

from toil.common import Toil
from toil.job import Job
def binaryStrings(job, depth, message=""):


    if depth > 0:


        s = [ job.addChildJobFn(binaryStrings, depth-1, message + "0").rv(),


              job.addChildJobFn(binaryStrings, depth-1, message + "1").rv() ]


        return job.addFollowOnFn(merge, s).rv()


    return [message]
def merge(strings):


    return strings[0] + strings[1]
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.loglevel = "OFF"


    options.clean = "always"


    with Toil(options) as toil:


        print(toil.start(Job.wrapJobFn(binaryStrings, depth=5)))

The return value l of the workflow is a list of all binary strings of length 10, computed recursively. Although a toy example, it demonstrates how closely Toil workflows can mimic typical programming patterns.

Promised Requirements¶

Promised requirements are a special case of Promises that allow a job's return value to be used as another job's resource requirements.

This is useful when, for example, a job's storage requirement is determined by a file staged to the job store by an earlier job:

import os
from toil.common import Toil
from toil.job import Job, PromisedRequirement
def parentJob(job):


    downloadJob = Job.wrapJobFn(stageFn, "File://"+os.path.realpath(__file__), cores=0.1, memory='32M', disk='1M')


    job.addChild(downloadJob)


    analysis = Job.wrapJobFn(analysisJob, fileStoreID=downloadJob.rv(0),


                             disk=PromisedRequirement(downloadJob.rv(1)))


    job.addFollowOn(analysis)
def stageFn(job, url, cores=1):


    importedFile = job.fileStore.importFile(url)


    return importedFile, importedFile.size
def analysisJob(job, fileStoreID, cores=2):


    # now do some analysis on the file


    pass
if __name__ == "__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    with Toil(options) as toil:


        toil.start(Job.wrapJobFn(parentJob))

Note that this also makes use of the size attribute of the FileID object. This promised requirements mechanism can also be used in combination with an aggregator for multiple jobs' output values:

def parentJob(job):


    aggregator = []


    for fileNum in range(0,10):


        downloadJob = Job.wrapJobFn(stageFn, "File://"+os.path.realpath(__file__), cores=0.1, memory='32M', disk='1M')


        job.addChild(downloadJob)


        aggregator.append(downloadJob)


    analysis = Job.wrapJobFn(analysisJob, fileStoreID=downloadJob.rv(0),


                             disk=PromisedRequirement(lambda xs: sum(xs), [j.rv(1) for j in aggregator]))


    job.addFollowOn(analysis)

FileID¶

The toil.fileStore.FileID class is a small wrapper around Python's builtin string class. It is used to represent a file's ID in the file store, and has a size attribute that is the file's size in bytes. This object is returned by importFile and writeGlobalFile.

Managing files within a workflow¶

It is frequently the case that a workflow will want to create files, both persistent and temporary, during its run. The toil.fileStores.abstractFileStore.AbstractFileStore class is used by jobs to manage these files in a manner that guarantees cleanup and resumption on failure.

The toil.job.Job.run() method has a file store instance as an argument. The following example shows how this can be used to create temporary files that persist for the length of the job, be placed in a specified local disk of the node and that will be cleaned up, regardless of failure, when the job finishes:

from toil.common import Toil
from toil.job import Job
class LocalFileStoreJob(Job):


    def run(self, fileStore):


        # self.TempDir will always contain the name of a directory within the allocated disk space reserved for the job


        scratchDir = self.tempDir


        # Similarly create a temporary file.


        scratchFile = fileStore.getLocalTempFile()
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    # Create an instance of FooJob which will have at least 2 gigabytes of storage space.


    j = LocalFileStoreJob(disk="2G")


    #Run the workflow


    with Toil(options) as toil:


        toil.start(j)

Job functions can also access the file store for the job. The equivalent of the LocalFileStoreJob class is

def localFileStoreJobFn(job):


    scratchDir = job.tempDir


    scratchFile = job.fileStore.getLocalTempFile()

Note that the fileStore attribute is accessed as an attribute of the job argument.

In addition to temporary files that exist for the duration of a job, the file store allows the creation of files in a global store, which persists during the workflow and are globally accessible (hence the name) between jobs. For example:

import os
from toil.common import Toil
from toil.job import Job
def globalFileStoreJobFn(job):


    job.log("The following example exercises all the methods provided"


            " by the toil.fileStores.abstractFileStore.AbstractFileStore class")


    # Create a local temporary file.


    scratchFile = job.fileStore.getLocalTempFile()


    # Write something in the scratch file.


    with open(scratchFile, 'w') as fH:


        fH.write("What a tangled web we weave")


    # Write a copy of the file into the file-store; fileID is the key that can be used to retrieve the file.


    # This write is asynchronous by default


    fileID = job.fileStore.writeGlobalFile(scratchFile)


    # Write another file using a stream; fileID2 is the


    # key for this second file.


    with job.fileStore.writeGlobalFileStream(cleanup=True) as (fH, fileID2):


        fH.write(b"Out brief candle")


    # Now read the first file; scratchFile2 is a local copy of the file that is read-only by default.


    scratchFile2 = job.fileStore.readGlobalFile(fileID)


    # Read the second file to a desired location: scratchFile3.


    scratchFile3 = os.path.join(job.tempDir, "foo.txt")


    job.fileStore.readGlobalFile(fileID2, userPath=scratchFile3)


    # Read the second file again using a stream.


    with job.fileStore.readGlobalFileStream(fileID2) as fH:


        print(fH.read()) #This prints "Out brief candle"


    # Delete the first file from the global file-store.


    job.fileStore.deleteGlobalFile(fileID)


    # It is unnecessary to delete the file keyed by fileID2 because we used the cleanup flag,


    # which removes the file after this job and all its successors have run (if the file still exists)
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    with Toil(options) as toil:


        toil.start(Job.wrapJobFn(globalFileStoreJobFn))

The example demonstrates the global read, write and delete functionality of the file-store, using both local copies of the files and streams to read and write the files. It covers all the methods provided by the file store interface.

What is obvious is that the file-store provides no functionality to update an existing "global" file, meaning that files are, barring deletion, immutable. Also worth noting is that there is no file system hierarchy for files in the global file store. These limitations allow us to fairly easily support different object stores and to use caching to limit the amount of network file transfer between jobs.

Staging of Files into the Job Store¶

External files can be imported into or exported out of the job store prior to running a workflow when the toil.common.Toil context manager is used on the leader. The context manager provides methods toil.common.Toil.importFile(), and toil.common.Toil.exportFile() for this purpose. The destination and source locations of such files are described with URLs passed to the two methods. A list of the currently supported URLs can be found at toil.jobStores.abstractJobStore.AbstractJobStore.importFile(). To import an external file into the job store as a shared file, pass the optional sharedFileName parameter to that method.

If a workflow fails for any reason an imported file acts as any other file in the job store. If the workflow was configured such that it not be cleaned up on a failed run, the file will persist in the job store and needs not be staged again when the workflow is resumed.

Example:

import os
from toil.common import Toil
from toil.job import Job
class HelloWorld(Job):


    def __init__(self, id):


        Job.__init__(self,  memory="2G", cores=2, disk="3G")


        self.inputFileID = id


    def run(self, fileStore):


        with self.fileStore.readGlobalFileStream(self.inputFileID) as fi:


            with self.fileStore.writeGlobalFileStream() as (fo, outputFileID):


                fo.write(fi.read() + 'World!')


        return outputFileID
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    with Toil(options) as toil:


        if not toil.options.restart:


            ioFileDirectory = os.path.join(os.path.dirname(os.path.abspath(__file__)), "stagingExampleFiles")


            inputFileID = toil.importFile("file://" + os.path.abspath(os.path.join(ioFileDirectory, "in.txt")))


            outputFileID = toil.start(HelloWorld(inputFileID))


        else:


            outputFileID = toil.restart()


        toil.exportFile(outputFileID, "file://" + os.path.abspath(os.path.join(ioFileDirectory, "out.txt")))

Using Docker Containers in Toil¶

Docker containers are commonly used with Toil. The combination of Toil and Docker allows for pipelines to be fully portable between any platform that has both Toil and Docker installed. Docker eliminates the need for the user to do any other tool installation or environment setup.

In order to use Docker containers with Toil, Docker must be installed on all workers of the cluster. Instructions for installing Docker can be found on the Docker website.

When using Toil-based autoscaling, Docker will be automatically set up on the cluster's worker nodes, so no additional installation steps are necessary. Further information on using Toil-based autoscaling can be found in the Autoscaling documentation.

In order to use docker containers in a Toil workflow, the container can be built locally or downloaded in real time from an online docker repository like Quay. If the container is not in a repository, the container's layers must be accessible on each node of the cluster.

When invoking docker containers from within a Toil workflow, it is strongly recommended that you use dockerCall(), a toil job function provided in toil.lib.docker. dockerCall leverages docker's own python API, and provides container cleanup on job failure. When docker containers are run without this feature, failed jobs can result in resource leaks. Docker's API can be found at docker-py.

In order to use dockerCall, your installation of Docker must be set up to run without sudo. Instructions for setting this up can be found here.

An example of a basic dockerCall is below:

dockerCall(job=job,


            tool='quay.io/ucsc_cgl/bwa',


            workDir=job.tempDir,


            parameters=['index', '/data/reference.fa'])

Note the assumption that reference.fa file is located in /data. This is Toil's standard convention as a mount location to reduce boilerplate when calling dockerCall. Users can choose their own mount locations by supplying a volumes kwarg to dockerCall, such as: volumes={working_dir: {'bind': '/data', 'mode': 'rw'}}, where working_dir is an absolute path on the user's filesystem.

dockerCall can also be added to workflows like any other job function:

import os
from toil.common import Toil
from toil.job import Job
from toil.lib.docker import apiDockerCall
align = Job.wrapJobFn(apiDockerCall,


                      image='ubuntu',


                      working_dir=os.getcwd(),


                      parameters=['ls', '-lha'])
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    with Toil(options) as toil:


       toil.start(align)

cgl-docker-lib contains dockerCall-compatible Dockerized tools that are commonly used in bioinformatics analysis.

The documentation provides guidelines for developing your own Docker containers that can be used with Toil and dockerCall. In order for a container to be compatible with dockerCall, it must have an ENTRYPOINT set to a wrapper script, as described in cgl-docker-lib containerization standards. This can be set by passing in the optional keyword argument, 'entrypoint'. Example:

dockerCall supports currently the 75 keyword arguments found in the python Docker API, under the 'run' command.

Services¶

It is sometimes desirable to run services, such as a database or server, concurrently with a workflow. The toil.job.Job.Service class provides a simple mechanism for spawning such a service within a Toil workflow, allowing precise specification of the start and end time of the service, and providing start and end methods to use for initialization and cleanup. The following simple, conceptual example illustrates how services work:

from toil.common import Toil
from toil.job import Job
class DemoService(Job.Service):


    def start(self, fileStore):


        # Start up a database/service here


        # Return a value that enables another process to connect to the database


        return "loginCredentials"


    def check(self):


        # A function that if it returns False causes the service to quit


        # If it raises an exception the service is killed and an error is reported


        return True


    def stop(self, fileStore):


        # Cleanup the database here


        pass
j = Job()
s = DemoService()
loginCredentialsPromise = j.addService(s)
def dbFn(loginCredentials):


    # Use the login credentials returned from the service's start method to connect to the service


    pass
j.addChildFn(dbFn, loginCredentialsPromise)
if __name__=="__main__":


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    with Toil(options) as toil:


        toil.start(j)

In this example the DemoService starts a database in the start method, returning an object from the start method indicating how a client job would access the database. The service's stop method cleans up the database, while the service's check method is polled periodically to check the service is alive.

A DemoService instance is added as a service of the root job j, with resource requirements specified. The return value from toil.job.Job.addService() is a promise to the return value of the service's start method. When the promised is fulfilled it will represent how to connect to the database. The promise is passed to a child job of j, which uses it to make a database connection. The services of a job are started before any of its successors have been run and stopped after all the successors of the job have completed successfully.

Multiple services can be created per job, all run in parallel. Additionally, services can define sub-services using toil.job.Job.Service.addChild(). This allows complex networks of services to be created, e.g. Apache Spark clusters, within a workflow.

Checkpoints¶

Services complicate resuming a workflow after failure, because they can create complex dependencies between jobs. For example, consider a service that provides a database that multiple jobs update. If the database service fails and loses state, it is not clear that just restarting the service will allow the workflow to be resumed, because jobs that created that state may have already finished. To get around this problem Toil supports checkpoint jobs, specified as the boolean keyword argument checkpoint to a job or wrapped function, e.g.:

j = Job(checkpoint=True)

A checkpoint job is rerun if one or more of its successors fails its retry attempts, until it itself has exhausted its retry attempts. Upon restarting a checkpoint job all its existing successors are first deleted, and then the job is rerun to define new successors. By checkpointing a job that defines a service, upon failure of the service the database and the jobs that access the service can be redefined and rerun.

To make the implementation of checkpoint jobs simple, a job can only be a checkpoint if when first defined it has no successors, i.e. it can only define successors within its run method.

Encapsulation¶

Let A be a root job potentially with children and follow-ons. Without an encapsulated job the simplest way to specify a job B which runs after A and all its successors is to create a parent of A, call it Ap, and then make B a follow-on of Ap. e.g.:

from toil.common import Toil
from toil.job import Job
if __name__=="__main__":


    # A is a job with children and follow-ons, for example:


    A = Job()


    A.addChild(Job())


    A.addFollowOn(Job())


    # B is a job which needs to run after A and its successors


    B = Job()


    # The way to do this without encapsulation is to make a parent of A, Ap, and make B a follow-on of Ap.


    Ap = Job()


    Ap.addChild(A)


    Ap.addFollowOn(B)


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    with Toil(options) as toil:


        print(toil.start(Ap))

An encapsulated job E(A) of A saves making Ap, instead we can write:

from toil.common import Toil
from toil.job import Job
if __name__=="__main__":


    # A


    A = Job()


    A.addChild(Job())


    A.addFollowOn(Job())


    # Encapsulate A


    A = A.encapsulate()


    # B is a job which needs to run after A and its successors


    B = Job()


    # With encapsulation A and its successor subgraph appear to be a single job, hence:


    A.addChild(B)


    options = Job.Runner.getDefaultOptions("./toilWorkflowRun")


    options.logLevel = "INFO"


    options.clean = "always"


    with Toil(options) as toil:


        print(toil.start(A))

Note the call to toil.job.Job.encapsulate() creates the toil.job.Job.EncapsulatedJob.

Depending on Toil¶

If you are packing your workflow(s) as a pip-installable distribution on PyPI, you might be tempted to declare Toil as a dependency in your setup.py, via the install_requires keyword argument to setup(). Unfortunately, this does not work, for two reasons: For one, Toil uses Setuptools' extra mechanism to manage its own optional dependencies. If you explicitly declared a dependency on Toil, you would have to hard-code a particular combination of extras (or no extras at all), robbing the user of the choice what Toil extras to install. Secondly, and more importantly, declaring a dependency on Toil would only lead to Toil being installed on the leader node of a cluster, but not the worker nodes. Auto-deployment does not work here because Toil cannot auto-deploy itself, the classic "Which came first, chicken or egg?" problem.

In other words, you shouldn't explicitly depend on Toil. Document the dependency instead (as in "This workflow needs Toil version X.Y.Z to be installed") and optionally add a version check to your setup.py. Refer to the check_version() function in the toil-lib project's setup.py for an example. Alternatively, you can also just depend on toil-lib and you'll get that check for free.

If your workflow depends on a dependency of Toil, consider not making that dependency explicit either. If you do, you risk a version conflict between your project and Toil. The pip utility may silently ignore that conflict, breaking either Toil or your workflow. It is safest to simply assume that Toil installs that dependency for you. The only downside is that you are locked into the exact version of that dependency that Toil declares. But such is life with Python, which, unlike Java, has no means of dependencies belonging to different software components within the same process, and whose favored software distribution utility is incapable of properly resolving overlapping dependencies and detecting conflicts.

Best Practices for Dockerizing Toil Workflows¶

Computational Genomics Lab's Dockstore based production system provides workflow authors a way to run Dockerized versions of their pipeline in an automated, scalable fashion. To be compatible with this system of a workflow should meet the following requirements. In addition to the Docker container, a common workflow language descriptor file is needed. For inputs:

For outputs:

FunctionWrappingJob¶

The subclass of Job for wrapping user functions.

JobFunctionWrappingJob¶

The subclass of FunctionWrappingJob for wrapping user job functions.

Job.wrapJobFn(myJob, memory='100k', disk='1M', cores=0.1)

EncapsulatedJob¶

The subclass of Job for encapsulating a job, allowing a subgraph of jobs to be treated as a single job.

#  Job A and subgraph, Job B
A, B = A(), B()
Aprime = A.encapsulate()
Aprime.addChild(B)
#  B will run after A and all its successors have completed, A and its subgraph of
# successors in effect appear to be just one job.

Promise¶

The class used to reference return values of jobs/services not yet run/started.

Batch System Enivronmental Variables¶

Environmental variables allow passing of scheduler specific parameters.

For SLURM:

export TOIL_SLURM_ARGS="-t 1:00:00 -q fatq"

For TORQUE there are two environment variables - one for everything but the resource requirements, and another - for resources requirements (without the -l prefix):

export TOIL_TORQUE_ARGS="-q fatq"
export TOIL_TORQUE_REQS="walltime=1:00:00"

For GridEngine (SGE, UGE), there is an additional environmental variable to define the parallel environment for running multicore jobs:

export TOIL_GRIDENGINE_PE='smp'
export TOIL_GRIDENGINE_ARGS='-q batch.q'

For HTCondor, additional parameters can be included in the submit file passed to condor_submit:

export TOIL_HTCONDOR_PARAMS='requirements = TARGET.has_sse4_2 == true; accounting_group = test'

The environment variable is parsed as a semicolon-separated string of parameter = value pairs.

Batch System API¶

Running Tests with pytest¶

Often it is simpler to use pytest directly, instead of calling the make wrapper. This usually works as expected, but some tests need some manual preparation. To run a specific test with pytest, use the following:

python -m pytest src/toil/test/sort/sortTest.py::SortTest::testSort

For more information, see the pytest documentation.

Running Integration Tests¶

These tests are generally only run using in our CI workflow due to their resource requirements and cost. However, they can be made available for local testing:

$ make push_docker

$ export TOIL_TEST_INTEGRATIVE=True

$ export TOIL_X_KEYNAME=[Your Keyname]
$ export TOIL_X_ZONE=[Desired Zone]

Test Environment Variables¶

Using Docker with Quay¶

Docker is needed for some of the tests. Follow the appropriate installation instructions for your system on their website to get started.

When running make test you might still get the following error:

$ make test
Please set TOIL_DOCKER_REGISTRY, e.g. to quay.io/USER.

To solve, make an account with Quay and specify it like so:

$ TOIL_DOCKER_REGISTRY=quay.io/USER make test

where USER is your Quay username.

For convenience you may want to add this variable to your bashrc by running

$ echo 'export TOIL_DOCKER_REGISTRY=quay.io/USER' >> $HOME/.bashrc

Running Mesos Tests¶

If you're running Toil's Mesos tests, be sure to create the virtualenv with --system-site-packages to include the Mesos Python bindings. Verify this by activating the virtualenv and running pip list | grep mesos. On macOS, this may come up empty. To fix it, run the following:

for i in /usr/local/lib/python2.7/site-packages/*mesos*; do ln -snf $i venv/lib/python2.7/site-packages/; done

Making Your Own Toil Docker Image¶

Note! Toil checks if the docker image specified by TOIL_APPLIANCE_SELF exists prior to launching by using the docker v2 schema. This should be valid for any major docker repository, but there is an option to override this if desired using the option: -\-forceDockerAppliance.

Here is a general workflow (similar instructions apply when using Docker Hub):

$ make docker

export TOIL_DOCKER_REGISTRY=quay.io/<MY_QUAY_USERNAME>

$ make push_docker

Running a Cluster Locally¶

The Toil Appliance container can also be useful as a test environment since it can simulate a Toil cluster locally. An important caveat for this is autoscaling, since autoscaling will only work on an EC2 instance and cannot (at this time) be run on a local machine.

To spin up a local cluster, start by using the following Docker run command to launch a Toil leader container:

docker run \


    --entrypoint=mesos-master \


    --net=host \


    -d \


    --name=leader \


    --volume=/home/jobStoreParentDir:/jobStoreParentDir \


    quay.io/ucsc_cgl/toil:3.6.0 \


    --registry=in_memory \


    --ip=127.0.0.1 \


    --port=5050 \


    --allocation_interval=500ms

A couple notes on this command: the -d flag tells Docker to run in daemon mode so the container will run in the background. To verify that the container is running you can run docker ps to see all containers. If you want to run your own container rather than the official UCSC container you can simply replace the quay.io/ucsc_cgl/toil:3.6.0 parameter with your own container name.

Also note that we are not mounting the job store directory itself, but rather the location where the job store will be written. Due to complications with running Docker on MacOS, I recommend only mounting directories within your home directory. The next command will launch the Toil worker container with similar parameters:

docker run \


    --entrypoint=mesos-slave \


    --net=host \


    -d \


    --name=worker \


    --volume=/home/jobStoreParentDir:/jobStoreParentDir \


    quay.io/ucsc_cgl/toil:3.6.0 \


    --work_dir=/var/lib/mesos \


    --master=127.0.0.1:5050 \


    --ip=127.0.0.1 \


    —-attributes=preemptable:False \


    --resources=cpus:2

Note here that we are specifying 2 CPUs and a non-preemptable worker. We can easily change either or both of these in a logical way. To change the number of cores we can change the 2 to whatever number you like, and to change the worker to be preemptable we change preemptable:False to preemptable:True. Also note that the same volume is mounted into the worker. This is needed since both the leader and worker write and read from the job store. Now that your cluster is running, you can run

docker exec -it leader bash

to get a shell in your leader 'node'. You can also replace the leader parameter with worker to get shell access in your worker.

Naming Conventions¶