Pulsar

This project is a Python server application that allows a Galaxy server to run jobs on remote systems (including Windows) without requiring a shared mounted file systems. Unlike traditional Galaxy job runners - input files, scripts, and config files may be transferred to the remote system, the job is executed, and the result downloaded back to the Galaxy server.

Full documentation for the project can be found on Read The Docs.

Configuring Galaxy

Galaxy job runners are configured in Galaxy's job_conf.xml file. Some small examples of how to configure this can be found here, but be sure to checkout job_conf.xml.sample_advanced in your Galaxy code base or on Bitbucket for complete information.

Downloading Pulsar

Pulsar is distributed as a Python project and can be obtained from Github using the following command:

git clone https://github.com/galaxyproject/pulsar

Pulsar Dependencies

Several Python packages must be installed to run the Pulsar server. These can either be installed into a Python virtualenv or into your system wide Python environment using easy_install. Instructions for both are outlined below. Additionally, if DRMAA is going to be used to communicate with a cluster, this dependency must be installed as well - again see note below.

virtualenv

The script setup_venv.sh distributed with Pulsar is a short-cut for *nix machines to setup a Python environment (including the installation of virtualenv). Full details for installation suitable for *nix are as follows. These instructions can work for Windows as well but generally the easy_install instructions below are more robust for Window's environments.

1. Install virtualenv (if not available):

   pip install virtualenv

2. Create a new Python environment:

   virtualenv .venv

3. Activate environment (varies by OS).

From a Linux or MacOS terminal:

. .venv/bin/activate

From a Windows terminal:

.venv\Scripts\activate

4. Install required dependencies into this virtual environment:

   pip install -r requirements.txt

easy_install

Install python setuptools for your platform, more details on how to do this can be found here.

The easy_install command line application will be installed as part of setuptools. Use the following command to install the needed packages via easy_install:

easy_install paste wsgiutils PasteScript PasteDeploy webob six psutil

DRMAA

If your Pulsar instance is going to communicate with a cluster via DRMAA, in addition to the above dependencies, a DRMAA library will need to be installed and the python dependency drmaa will need to be installed as well.:

. .venv/bin/activate; pip install drmaa

or:

easy_install drmaa

Running Pulsar

*nix Instructions

Pulsar can be started and stopped via the run.sh script distributed with the project.:

./run.sh --daemon
./run.sh --stop-daemon

These commands will start and stop the WSGI web server in daemon mode. In this mode, logs are writtin to paster.log.

If uWSGI, circus and/or chassuette, are available, more sophisticated web servers can be launched via this run.sh command. See the script for more details.

Alternative Cross Platform Instructions (Windows and *nix)

The paster command line application will be installed as part of the previous dependency installation process. This application can be used to start and stop a paste web server running the Pulsar.

The server may be ran as a daemon via the command:

paster serve server.ini --daemon

When running as daemon, the server may be stopped with the following command:

paster serve server.ini --stop-daemon

If you setup a virtual environment for the Pulsar you will need to activate this before executing these commands.

Configuring Pulsar

Rename the server.ini.sample file distributed with Pulsar to server.ini, and edit the values therein to configure the server application. Default values are specified for all configuration options that will work if Pulsar is running on the same host as Galaxy. However, the parameter "host" must be specified for remote submissions to the Pulsar server to run properly. The server.ini file contains documentation for many configuration parameters you may want to modify.

Some advanced configuration topics are discussed below.

Security

Out of the box the Pulsar essentially allows anyone with network access to the Pulsar server to execute arbitrary code and read and write any files the web server can. Hence, in most settings steps should be taken to secure the Pulsar server.

Pulsar Web Server

The Pulsar web server can be configured to use SSL and to require the client (i.e. Galaxy) to pass along a private token authorizing use.

pyOpenSSL is required to configure a Pulsar web server to server content via HTTPS/SSL. This dependency can be difficult to install and seems to be getting more difficult. Under Linux you will want to ensure the needed dependencies to compile pyOpenSSL are available - for instance in a fresh Ubuntu image you will likely need:

sudo apt-get install libffi-dev python-dev libssl-dev

Then pyOpenSSL can be installed with the following command (be sure to source your virtualenv if setup above):

pip install pyOpenSSL

Under Windows only older versions for pyOpenSSL are installable via pre- compiled binaries (i.e. using easy_install) so it might be good to use non- standard sources such as eGenix.

Once installed, you will need to set the option ssl_pem in server.ini. This parameter should reference an OpenSSL certificate file for use by the Python paste server. This parameter can be set to * to automatically generate such a certificate. Such a certificate can manually be generated by the following method:

$ openssl genrsa 1024 > host.key
$ chmod 400 host.key
$ openssl req -new -x509 -nodes -sha1 -days 365  \
          -key host.key > host.cert
$ cat host.cert host.key > host.pem
$ chmod 400 host.pem

More information can be found in the paste httpserver documentation.

Finally, in order to force Galaxy to authorize itself, you will want to specify a private token - by simply setting private_token to some long random string in server.ini.

Once SSL has been enabled and a private token configured, Galaxy job destinations should include a private_token parameter to authenticate these jobs.

Pulsar Message Queue

If Pulsar is processing requests via a message queue instead of a web server the underlying security mechanisms of the message queue should be used to secure communication - deploying Pulsar with SSL and a private_token described above are not required.

This will likely consist of setting some combination of amqp_connect_ssl_ca_certs, amqp_connect_ssl_keyfile, amqp_connect_ssl_certfile, amqp_connect_ssl_cert_reqs, in Pulsar's server.ini file. See server.ini.sample for more details and the Kombu documentation for even more information.

Customizing the Pulsar Environment

In more sophisticated deployments, the Pulsar's environment will need to be tweaked - for instance to define a DRMAA_LIBRARY_PATH environment variable for the drmaa Python module or to define the location to a find a location of Galaxy (via GALAXY_HOME) if certain Galaxy tools require it or if Galaxy metadata is being set by the Pulsar. The recommend way to do this is to copy local_env.sh.sample to local_env.sh and customize it.

This file of deployment specific environment tweaks will be source by run.sh if it exists as well as by other Pulsar scripts in more advanced usage scenarios.

Job Managers (Queues)

By default the Pulsar will maintain its own queue of jobs. While ideal for simple deployments such as those targetting a single Windows instance, if the Pulsar is going to be used on more sophisticate clusters, it can be configured to maintain multiple such queues with different properties or to delegate to external job queues (via DRMAA, qsub/qstat CLI commands, or Condor).

For more information on configured external job managers, see the job managers documentation.

Warning: If you are using DRMAA, be sure to define DRMAA_LIBRARY_PATH in local_env.sh defined above.

Galaxy Tools

Some Galaxy tool wrappers require a copy of the Galaxy codebase itself to run. Such tools will not run under Windows, but on *nix hosts the Pulsar can be configured to add the required Galaxy code a jobs PYTHON_PATH by setting GALAXY_HOME environment variable in the Pulsar's local_env.sh file (described above).

Caching (Experimental)

Pulsar and its client can be configured to cache job input files. For some workflows this can result in a significant decrease in data transfer and greater throughput. On the Pulsar server side - the property file_cache_dir in server.ini must be set. See Galaxy's job_conf.xml for information on configuring the client.

More discussion on this can be found in this galaxy-dev mailing list thread and future plans and progress can be tracked on this Trello card.

Message Queue (Experimental)

Galaxy and the Pulsar can be configured to communicate via a message queue instead of an Pulsar web server. In this mode, the Pulsar will download files from and upload files to Galaxy instead of the inverse - this may be very advantageous if the Pulsar needs to be deployed behind a firewall or if the Galaxy server is already setup (via proxy web server) for large file transfers.

To bind the PUlsar server to a message queue, one needs to first ensure the kombu Python dependency is installed (pip install kombu). Once this available, simply set the message_queue_url property in server.ini to the correct URL of your configured AMQP endpoint.

Configuring your AMQP compatible message queue is beyond the scope of this document - see RabbitMQ for instance for more details (other MQs should work also).

Testing

A simple sanity test can be run against a running Pular server by executing the following command (replace the URL command with the URL of your running Pulsar application):

python run_client_tests.py --url=http://localhost:8913

Development

This project is distributed with unit and integration tests (many of which will not run under Windows), the following command will install the needed python components to run these tests.:

pip install -r dev-requirements.txt

The following command will then run these tests:

make tests

The following command will then produce a coverage report corresponding to this test and place it in the coverage_html_report subdirectory of this project.:

coverage html

Checkout the Contributing documentation for many more details on developing and contributing to Pulsar.