Refine.bio harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists.

This README file is about building and running the refine.bio project source code.

If you're interested in simply using the service, you should go to the website or read the documentation.

Refine.bio currently has four sub-projects contained within this repo:

• common Contains code needed by both foreman and workers.
• foreman Discovers data to download/process and manages jobs.
• workers Runs Downloader and Processor jobs.
• infrasctructure Manages infrastructure for Refine.bio.

• Development
  • Git Workflow
  • Installation
    • Linux
    • Mac
    • Virtual Environment
    • Services
      • Postgres
      • Nomad
      • ElasticSearch
    • Common Dependecies
  • Testing
    • API
    • Common
    • Foreman
    • Workers
  • Style
  • Gotchas
    • R
• Running Locally
  • Surveyor Jobs
    • Sequence Read Archive
    • Ensembl Transcriptome Indices
  • Downloader Jobs
  • Processor Jobs
  • Creating Quantile Normalization Reference Targets
  • Creating Compendia
  • Running Tximport Early
  • Checking on Local Jobs
  • Development Helpers
• Cloud Deployment
  • Docker Images
  • Autoscaling and Setting Spot Prices
  • Terraform
  • Running Jobs
  • Log Consumption
  • Dumping and Restoring Database Backups
  • Tearing Down
• Support
• Meta-README
• License

refinebio uses a feature branch based workflow. New features should be developed on new feature branches, and pull requests should be sent to the dev branch for code review. Merges into master happen at the end of sprints, and tags in master correspond to production releases.

To run Refine.bio locally, you will need to have the prerequisites installed onto your local machine. This will vary depending on whether you are developing on a Mac or a Linux machine. Linux instructions have been tested on Ubuntu 16.04 or later, but other Linux distributions should be able to run the necessary services. Microsoft Windows is currently unsupported by this project.

The following services will need to be installed:

• Python3 and Pip: sudo apt-get -y install python3-pip
• Docker: Be sure to follow the [post installation steps] (https://docs.docker.com/install/linux/linux-postinstall/#manage-docker-as-a-non-root-user) so Docker does not need sudo permissions.
• Terraform
• Nomad can be installed on Linux clients with sudo ./install_nomad.sh.
• pip3 can be installed on Linux clients with sudo apt-get install python3-pip
• git-crypt
• jq
• iproute2

Instructions for installing Docker, Terraform, and Nomad can be found by following the link for each service. git-crypt, jq, and iproute2 can be installed via sudo apt-get install git-crypt jq iproute2.

When installing pip packages later in the install, you might get an error saying you need sudo permissions. In order to fix this you have to edit your ~/.config/pip/pip.conf to add this:

[install]
user = yes
no-binary = :all:

This sets pip to install all packages in your user directory so sudo is not required for pip intalls.

The following services will need to be installed:

• Homebrew
• Docker for Mac
• Terraform
• Nomad
• git-crypt
• iproute2mac
• jq

Instructions for installing Docker and Homebrew can be found by on their respective homepages.

Once Homebrew is installed, the other required applications can be installed by running: brew install iproute2mac git-crypt nomad terraform jq.

Many of the computational processes running are very memory intensive. You will need to raise the amount of virtual memory available to Docker from the default of 2GB to 12GB or 24GB, if possible.

Run ./create_virtualenv.sh to set up the virtualenv. It will activate the dr_env for you the first time. This virtualenv is valid for the entire refinebio repo. Sub-projects each have their own environments managed by their containers. When returning to this project you should run source dr_env/bin/activate to reactivate the virtualenv.

refinebio also depends on Postgres and Nomad. Postgres can be run in a local Docker container, but Nomad must be run on your development machine.

To start a local Postgres server in a Docker container, use:

./run_postgres.sh

Then, to initialize the database, run:

./common/install_db_docker.sh

If you need to access a psql shell for inspecting the database, you can use:

./run_psql_shell.sh

or if you have psql installed this command will give you a better shell experience:

source common.sh && PGPASSWORD=mysecretpassword psql -h $(get_docker_db_ip_address) -U postgres -d data_refinery

Similarly, you will need to run a local Nomad service in development mode.

However if you run Linux and you have followed the installation instructions, you can run Nomad with:

sudo -E ./run_nomad.sh

(Note: This step may take some time because it downloads lots of files.)

Nomad is an orchestration tool which Refine.bio uses to run Surveyor, Downloader, Processor jobs. Jobs are queued by sending a message to the Nomad agent, which will then launch a Docker container which runs the job. If address conflicts emerge, old Docker containers can be purged with docker container prune -f.

One of the API endpoints is powered by ElasticSearch. ElasticSearch must be running for this functionality to work. A local ElasticSearch instance in a Docker container can be executed with:

./run_es.sh

And then the ES Indexes (akin to Postgres 'databases') can be created with:

./run_manage.sh search_index --rebuild -f;

The common sub-project contains common code which is depended upon by the other sub-projects. So before anything else you should prepare the distribution directory common/dist with this script:

./update_models.sh

(Note: This step requires the postgres container to be running and initialized.)

Note: there is a small chance this might fail with a can't stat, error. If this happens, you have to manually change permissions on the volumes directory with sudo chmod -R 740 volumes_postgres then re-run the migrations.

The end to end tests require a separate Nomad client to be running so that the tests can be run without interfering with local development. The second Nomad client can be started with:

sudo -E ./run_nomad.sh -e test

To run the entire test suite:

./run_all_tests.sh

(Note: Running all the tests can take some time, especially the first time because it downloads a lot of files.)

These tests will also be run continuosly for each commit via CircleCI.

For more granular testing, you can just run the tests for specific parts of the system.

To just run the API tests:

./api/run_tests.sh

To just run the common tests:

./common/run_tests.sh

To just run the foreman tests:

./foreman/run_tests.sh

To just run the workers tests:

./workers/run_tests.sh

If you only want to run tests with a specific tag, you can do that too. For example, to run just the salmon tests:

./workers/run_tests.sh -t salmon

All of our worker tests are tagged, generally based on the Docker image required to run them. Possible values for worker test tags are:

• affymetrix
• agilent
• downloaders
• illumina
• no_op
• qn (short for quantile normalization)
• salmon
• smasher
• transcriptome

R files in this repo follow Google's R Style Guide. Python Files in this repo follow PEP 8. All files (including Python and R) have a line length limit of 100 characters.

A setup.cfg file has been included in the root of this repo which specifies the line length limit for the autopep8 and flake8 linters. If you run either linter within the project's directory tree, it will enforce a line length limit of 100 instead of 80. This will also be true for editors which rely on either linter.

During development, you make encounter some occasional strangeness. Here's some things to watch out for:

• Since we use multiple Docker instances, don't forget to ./update_models
• If builds are failing, increase the size of Docker's memory allocation. (Mac only.)
• If Docker images are failing mysteriously during creation, it may be the result of Docker's Docker.qcow2 or Docker.raw file filling. You can prune old images with docker system prune -a.
• If it's killed abruptly, the containerized Postgres images can be left in an unrecoverable state. Annoying.

We have created some utilities to help us keep R stable, reliable, and from periodically causing build errors related to version incompatibilites. The primary goal of these is to pin the version for every R package that we have. The R package devtools is useful for this, but in order to be able to install a specific version of it, we've created the R script common/install_devtools.R.

There is annother gotcha to be aware of should you ever need to modify versions of R or its packages. In Dockerfiles for images that need the R language, we install apt packages that look like r-base-core=3.4.2-1xenial1. It's unclear why the version for these is so weird, but it was determined by visiting the package list here: https://cran.revolutionanalytics.com/bin/linux/ubuntu/xenial/ If it needs to be updated then a version should be selected from that list.

Additionally there are two apt packages, r-base and r-base-core, which seem to be very similar except that r-base-core is slimmed down some by not including some additional packages. For a while we were using r-base, but we switched to r-base-core when we pinned the version of the R language because the r-base package caused an apt error.

Once you've built the common/dist directory and have the Nomad and Postgres services running, you're ready to run jobs. There are three kinds of jobs within Refine.bio.

Surveyor Jobs discover samples to download/process along with recording metadata about the samples. A Surveyor Job should queue Downloader Jobs to download the data it discovers.

The Surveyor can be run with the ./foreman/run_surveyor.sh script. The first argument to this script is the type of Surveyor Job to run, which will always be survey_all.

Details on these expected arguments can be viewed by running:

./foreman/run_surveyor.sh survey_all -h

The Surveyor can accept a single accession code from any of the source data repositories (e.g., Sequencing Read Archive, ArrayExpress, Gene Expression Omnibus):

./foreman/run_surveyor.sh survey_all --accession <ACCESSION_CODE>

Example for a GEO experiment:

./foreman/run_surveyor.sh survey_all --accession GSE85217

Example for an ArrayExpress experiment:

./foreman/run_surveyor.sh survey_all --accession E-MTAB-3050 # AFFY
./foreman/run_surveyor.sh survey_all --accession E-GEOD-3303 # NO_OP

Transcriptome indices are a bit special. For species within the "main" Ensembl division, the species name can be provided like so:

./foreman/run_surveyor.sh survey_all --accession "Homo sapiens"

However for species that are in other divisions, the division must follow the species name after a comma like so:

./foreman/run_surveyor.sh survey_all --accession "Caenorhabditis elegans, EnsemblMetazoa"

The possible divisions that can be specified are:

• Ensembl (this is the "main" division and is the default)
• EnsemblPlants
• EnsemblFungi
• EnsemblBacteria
• EnsemblProtists
• EnsemblMetazoa

If you are unsure what division a species falls into, unfortunately the only way to tell is go to check ensembl.com. (Although googling the species name + "ensembl" may work pretty well.)

You can also supply a newline-deliminated file to survey_all which will dispatch survey jobs based on accession codes like so:

./foreman/run_surveyor.sh survey_all --file MY_BIG_LIST_OF_CODES.txt

The main foreman job loop can be started with:

./foreman/run_surveyor.sh retry_jobs

This must actually be running for jobs to move forward through the pipeline.

When surveying SRA, you can supply either run accession codes (e.g., codes beginning in SRR, DRR, or ERR) or study accession codes (SRP, DRP, ERP).

Run example (single read):

./foreman/run_surveyor.sh survey_all --accession DRR002116

Run example (paired read):

./foreman/run_surveyor.sh survey_all --accession SRR6718414

Study example:

./foreman/run_surveyor.sh survey_all --accession ERP006872

Building transcriptome indices used for quantifying RNA-seq data requires us to retrieve genome information from Ensembl. The Surveyor expects a species' scientific name in the main Ensembl division as the accession:

./foreman/run_surveyor.sh survey_all --accession "Homo Sapiens"

TODO: Update once this supports organisms from multiple Ensembl divisions

Downloader Jobs will be queued automatically when Surveyor Jobs discover new samples. However, if you just want to queue a Downloader Job yourself rather than having the Surveyor do it for you, you can use the ./workers/tester.sh script:

./workers/tester.sh run_downloader_job --job-name=<EXTERNAL_SOURCE> --job-id=<JOB_ID>

For example:

./workers/tester.sh run_downloader_job --job-name=SRA --job-id=12345

or

./workers/tester.sh run_downloader_job --job-name=ARRAY_EXPRESS --job-id=1

Or for more information run:

./workers/tester.sh -h

Processor Jobs will be queued automatically by successful Downloader Jobs. However, if you just want to run a Processor Job without yourself without having a Downloader Job do it for you, the following command will do so:

./workers/tester.sh -i <IMAGE_NAME> run_processor_job --job-name=<JOB_NAME> --job-id=<JOB_ID>

For example

./workers/tester.sh -i affymetrix run_processor_job --job-name=AFFY_TO_PCL --job-id=54321

or

./workers/tester.sh -i no_op run_processor_job --job-name=NO_OP --job-id=1

or

./workers/tester.sh -i salmon run_processor_job --job-name=SALMON --job-id=1

or

./workers/tester.sh -i transcriptome run_processor_job --job-name=TRANSCRIPTOME_INDEX_LONG --job-id=1

Or for more information run:

./workers/tester.sh -h

If you want to quantile normalize combined outputs, you'll first need to create a reference target for a given organism. This can be done in a production environment with the following:

nomad job dispatch -meta ORGANISM=DANIO_RERIO CREATE_QN_TARGET

Creating species-wide compendia for a given species can be done in a production environment with the following:

nomad job dispatch -meta ORGANISM=DANIO_RERIO CREATE_COMPENDIA

or for all organisms with sufficient data:

nomad job dispatch -meta ORGANISM= CREATE_COMPENDIA

Normally we wait until ever sample in an experiment has had Salmon run on it before we run Tximport. However Salmon won't work on every sample, so some experiments are doomed to never make it to 100% completion. Tximport can be run on such an experiment with:

nomad job dispatch -meta EXPERIMENT_ACCESSION=SRP009841 TXIMPORT

Note that if the experiment does not have at least 25 samples with at least 80% of them processed, this will do nothing.

Note: The following instructions assume you have set the environment variable NOMAD_ADDR to include the IP address of your development machine. This can be done with:

source common.sh && export NOMAD_ADDR=http://$(get_ip_address):4646

To check on the status of a job, run:

nomad status

It should output something like:

ID                                       Type                 Priority  Status   Submit Date
DOWNLOADER                               batch/parameterized  50        running  01/31/18 18:34:05 EST
DOWNLOADER/dispatch-1517441663-4b02e7a3  batch                50        dead     01/31/18 18:34:23 EST
PROCESSOR                                batch/parameterized  50        running  01/31/18 18:34:05 EST

The rows whose IDs are DOWNLOADER or PROCESSOR are the parameterized jobs which are waiting to dispatch Refine.bio jobs. If you don't understand what that means, don't worry about it. All you really need to do is select one of the jobs whose ID contains dispatch and whose Submit Date matches the time when the job you want to check on was run, copy that full ID (in this case DOWNLOADER/dispatch-1517437920-ae8b77a4), and paste it after the previous command, like so:

nomad status DOWNLOADER/dispatch-1517441663-4b02e7a3

This will output a lot of information about that Nomad Dispatch Job, of which we're mostly interested in the section titled Allocations. Here is an example:

Allocations
ID        Node ID   Task Group  Version  Desired  Status    Created At
b30e4edd  fda75a5a  jobs        0        run      complete  01/31/18 18:34:23 EST

If you paste that after the original nomad status command, like so:

nomad status b30e4edd

you'll see a lot of information about allocation, which probably isn't what you're interested in. Instead, you should run:

nomad logs -verbose b30e4edd

This command will output both the stderr and stdout logs from the container which ran that allocation. The allocation is really a Refine.bio job.

It can be useful to have an interactive Python interpreter running within the context of the Docker container. The run_shell.sh script has been provided for this purpose. It is in the top level directory so that if you wish to reference it in any integrations its location will be constant. However, it is configured by default for the Foreman project. The interpreter will have all the environment variables, dependencies, and Django configurations for the Foreman project. There are instructions within the script describing how to change this to another project.

Refine.bio requires an active, credentialed AWS account with appropriate permissions to create network infrastructure, users, compute instances and databases.

Deploys are automated to run via CirlceCI whenever a signed tag starting with a v is pushed to either the dev or master branches (v as in version, i.e. v1.0.0). Tags intended to trigger a staging deploy MUST end with -dev, i.e. v1.0.0-dev. CircleCI runs a deploy on a dedicated AWS instance so that the Docker cache can be preserved between runs. Instructions for setting up that instance can be found in the infrastructure/deploy_box_instance_data.sh script.

To trigger a new deploy, first see what tags already exist with git tag --list | sort --version-sort We have two different version counters, one for dev and one for master so a list including things like:

• v1.1.2
• v1.1.2-dev
• v1.1.3
• v1.1.3-dev

However you may see that the dev counter is way ahead, because we often need more than one staging deploy to be ready for a production deploy. This is okay, just find the latest version of the type you want to deploy and increment that to get your version. For example, if you wanted to deploy to staging and the above versions were the largest that git tag --list output, you would increment v1.1.3-dev to get v1.1.4-dev.

Once you know which version you want to deploy, say v1.1.4-dev, you can trigger the deploy with these commands:

git checkout dev
git pull origin dev
git tag -s v1.1.4-dev
git push origin v1.1.4-dev

git tag -s v1.1.4-dev will prompt you to write a tag message; please try to make it descriptive.

We use semantic versioning for this project so the last number should correspond to bug fixes and patches, the second middle number should correspond to minor changes that don't break backwards compatibility, and the first number should correspond to major changes that break backwards compatibility. Please try to keep the dev and master versions in sync for major and minor versions so only the patch version gets out of sync between the two.

Refine.bio uses a number of different Docker images to run different pieces of the system. By default, refine.bio will pull images from the Dockerhub repo ccdlstaging. If you would like to use images you have built and pushed to Dockerhub yourself you can pass the -d option to the deploy.sh script.

To make building and pushing your own images easier, the update_my_docker_images.sh has been provided. The -d option will allow you to specify which repo you'd like to push to. If the Dockerhub repo requires you to be logged in, you should do so before running the script using docker login. The -v option allows you to specify the version, which will both end up on the Docker images you're building as the SYSTEM_VERSION environment variable and also will be the docker tag for the image.

update_my_docker_images.sh will not build the dr_affymetrix image, because this image requires a lot of resources and time to build. It can instead be built with ./prepare_image.sh -i affymetrix -d <YOUR_DOCKERHUB_REPO. WARNING: The affymetrix image installs a lot of data-as-R-packages and needs a lot of disk space to build the image. It's not recommended to build the image with less than 60GB of free space on the disk that Docker runs on.

refinebio uses AWS Auto Scaling Groups to provide elastic capacity for large work loads. To do this, we use "Spot Requests". To find a good bid price for your instance type, use the spot request page and then click on the view pricing history chart. Choose your instance type and then choose a bid price that is slightly higher than the current price for your availability zone (AZ). This graph is useful for understanding instance types.

Then set your TF_VAR_client_instance_type, TF_VAR_spot_price and TF_VAR_max_clients to configure your scaling instance types, cost and size. TF_VAR_scale_up_threshold and TF_VAR_scale_down_threshold define the queue lengths which trigger the scaling alarms, though you probably won't need to tweak these as much.

Once you have Terraform installed and your AWS account credentials installed, you're ready to deploy. The correct way to deploy to the cloud is by running the deploy.sh script. This script will perform additional configuration steps, such as setting environment variables, setting up Nomad job specifications, and performing database migrations. It can be used from the infrastructure directory like so:

./deploy.sh -u myusername -e dev -r us-east-1 -v v1.0.0 -d my-dockerhub-repo

This will spin up the whole system. It will usually take about 15 minutes, most of which is spent waiting for the Postgres instance to start. The command above would spin up a development stack in the us-east-1 region where all the resources' names would end with -myusername-dev. All of the images used in that stack would come from my-dockerhub-repo and would be tagged with v1.0.0.

The -e specifies the environment you would like to spin up. You may specify, dev, staging, or prod. dev is meant for individuals to test infrastructure changes or to run large tests. staging is to test the overall system before re-deploying to prod.

To see what's been created at any time, you can:

terraform state list

If you want to change a single entity in the state, you can use

terraform taint <your-entity-from-state-list>

And then rerun deploy.sh with the same parameters you originally ran it with.

Jobs can be submitted via Nomad, either from a server/client or a local machine if you supply a server address and have an open network ingress.

To start a job with a file located on the foreman docker image:

nomad job dispatch -meta FILE=NEUROBLASTOMA.txt SURVEYOR_DISPATCHER

or to start a job with a file located in S3:

nomad job dispatch -meta FILE=s3://data-refinery-test-assets/NEUROBLASTOMA.txt SURVEYOR_DISPATCHER

All of the different Refine.bio subservices log to the same AWS CloudWatch Log Group. If you want to consume these logs, you can use the awslogs tool, which can be installed from pip like so:

pip install awslogs

or, for OSX El Capitan:

pip install awslogs --ignore-installed six

Once awslogs is installed, you can find your log group with:

awslogs groups

Then, to see all of the logs in that group for the past day, watching as they come in:

awslogs get <your-log-group> ALL --start='1 days' --watch

You can also apply a filter on these logs like so:

awslogs get <your-log-group> ALL --start='1 days' --watch --filter-pattern="DEBUG"

Or, look at a named log stream (with or without a wildcard.) For instance: (Unfortunately this feature seems to be broken at the moment: jorgebastida/awslogs#158)

awslogs get data-refinery-log-group-myusername-dev log-stream-api-nginx-access-* --watch

will show all of the API access logs made by Nginx.

Automatic snapshots are created automatically by RDS. Manual database dumps can be created by priveledged users with these instructions. Postgres versions on the host (I suggest the PGBouncer instance) must match the RDS instance version:

sudo add-apt-repository "deb http://apt.postgresql.org/pub/repos/apt/ $(lsb_release -sc)-pgdg main"
wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | sudo apt-key add -
sudo apt-get update
sudo apt-get install postgresql-9.6

Archival dumps can also be provided upon request.

Dumps can be restored locally by copying the backup.sql file to the volumes_postgres directory, then executing:

docker exec -it drdb /bin/bash
psql --user postgres -d data_refinery -f /var/lib/postgresql/data/backup.sql

This can take a long time (>30 minutes)!

A stack that has been spun up via deploy.sh -u myusername -e dev can be taken down with destroy_terraform.sh -u myusername -e dev. The same username and environment must be passed into destroy_terraform.sh as were used to run deploy.sh either via the -e and -u options or by specifying TF_VAR_stage or TF_VAR_user so that the script knows which to take down. Note that this will prompt you for confirmation before actually destroying all of your cloud resources.

Refine.bio is supported by Alex's Lemonade Stand Foundation, with some initial development supported by the Gordon and Betty Moore Foundation via GBMF 4552 to Casey Greene.

The table of contents for this README is generated using doctoc. doctoc can be installed with: sudo npm install -g doctoc Once doctoc is installed the table of contents can be re-generated with: doctoc README.md

BSD 3-Clause License.