Building from Source¶
For developers, tinkerers, and people otherwise interested in Toil’s internals, this section explains how to build Toil from source and run its test suite.
Building from master¶
First, clone the source:
$ git clone https://github.com/BD2KGenomics/toil $ cd toil
Then, create and activate a virtualenv:
$ virtualenv venv $ . venv/bin/activate
From there, you can list all available Make targets by running
First and foremost, we want to install Toil’s build requirements. (These are
additional packages that Toil needs to be tested and built but not to be run.)
$ make prepare
Now, we can install Toil in development mode (such that changes to the source code will immediately affect the virtualenv):
$ make develop
Or, to install with support for all optional Extras:
$ make develop extras=[aws,mesos,azure,google,encryption,cwl]
To build the docs, run
make develop with all extras followed by
$ make docs
To invoke all tests (unit and integration) use
$ make test
Installing Docker with Quay
Docker is needed for some of the tests. Follow the appopriate installation instructions for your system on their website to get started.
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
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
Run an individual test with
$ make test tests=src/toil/test/sort/sortTest.py::SortTest::testSort
The default value for
"src" which includes all tests in the
src/ subdirectory of the project root. Tests that require a particular
feature will be skipped implicitly. If you want to explicitly skip tests that
depend on a currently installed feature, use
$ make test tests="-m 'not azure' src"
This will run only the tests that don’t depend on the
azure extra, even if
that extra is currently installed. Note the distinction between the terms
feature and extra. Every extra is a feature but there are features that are
not extras, such as the
parasol features. To skip tests
involving both the Parasol feature and the Azure extra, use the following:
$ make test tests="-m 'not azure and not parasol' src"
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
Developing with the Toil Appliance¶
To develop on features reliant on the Toil Appliance (i.e. autoscaling), you should consider setting up a personal registry on Quay or Docker Hub. Because the Toil Appliance images are tagged with the Git commit they are based on and because only commits on our master branch trigger an appliance build on Quay, as soon as a developer makes a commit or dirties the working copy they will no longer be able to rely on Toil to automatically detect the proper Toil Appliance image. Instead, developers wishing to test any appliance changes in autoscaling should build and push their own appliance image to a personal Docker registry.
Here is a general workflow: (similar instructions apply when using Docker Hub)
Make some changes to the provisioner of your local version of Toil.
Go to the location where you installed the Toil source code and run:
$ make docker
If it’s not already you will need Docker installed and need to log into Quay. Also you will want to make sure that your Quay account is public.
Set the environment variable
TOIL_DOCKER_REGISTRYto your Quay account. If you find yourself doing this often you may want to add:
Now you can run:
$ make push_docker
which will upload the docker image to your Quay account. Take note of the image’s tag for the next step.
Finally you will need to tell Toil from where to pull the Appliance image you’ve created (it uses the Toil release you have installed by default). To do this set the environment variable
TOIL_APPLIANCE_SELFto the url of your image. For more info see Environment variable options.
Now you can launch your cluster! For more information see Toil Provisioner.
Running 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
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: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
worker to get shell access in your worker.
If you want to run Docker inside this Docker cluster (Dockerized tools, perhaps),
you should also mount in the Docker socket via
This will give the Docker client inside the Toil Appliance access to the Docker engine
on the host. Client/engine version mismatches have been known to cause issues, so we
recommend using Docker version 1.12.3 on the host to be compatible with the Docker
client installed in the Appliance. Finally, be careful where you write files inside
the Toil Appliance - ‘child’ Docker containers launched in the Appliance will actually
be siblings to the Appliance since the Docker engine is located on the host. This
means that the ‘child’ container can only mount in files from the Appliance if
the files are located in a directory that was originally mounted into the Appliance
from the host - that way the files are accessible to the sibling container. Note:
if Docker can’t find the file/directory on the host it will silently fail and mount
in an empty directory.
- We strive to never break the build on master.
- Pull requests should be used for any and all changes (except truly trivial ones).
- The commit message of direct commits to master must end in
(resolves #followed by the issue number followed by
- The branch name for a pull request starts with
issues/followed by the issue number (or numbers, separated by a dash), followed by a short snake-case description of the change. (There can be many open pull requests with their associated branches at any given point in time and this convention ensures that we can easily identify branches.)
- The commit message of the first commit in a pull request needs to end in
(resolves #followed by the issue number, followed by
). See here for details about writing properly-formatted and informative commit messages.
- The title of the pull request needs to have the same
(resolves #...)suffix as the commit message. This lets Waffle stack the pull request and the associated issue. (Fortunately, Github automatically prepopulates the title of the PR with the message of the first commit in the PR, so this isn’t any additional work.)
Say there is an issue numbered #123 titled Foo does not work. The branch name
issues/123-fix-foo and the title of the commit would be Fix foo in
case of bar (resolves #123).
- Pull requests that address multiple issues use the
(resolves #602, resolves #214)suffix in the request’s title. These pull requests can and should contain multiple commits, with each commit message referencing the specific issue(s) it addresses. We may or may not squash the commits in those PRs.
- All pull requests must be reviewed by a person other than the request’s author.
- Only the reviewer of a pull request can merge it.
- Until the pull request is merged, it should be continually rebased by the author on top of master.
- Pull requests are built automatically by Jenkins and won’t be merged unless all tests pass.
- Ideally, a pull request should contain a single commit that addresses a single, specific issue. Rebasing and squashing can be used to achieve that goal (see Multi-author pull requests).