Update to Ubuntu 14.04

Ubuntu 12.04 has reached end-of-life, and the DNAnexus team is taking  steps to ensure that customer applications and DNAnexus backend systems migrate away from this version of the software. We recommend any customers who develop and maintain DNAnexus applications update your applications and applets to Ubuntu 14.04 as soon as possible to identify any issues that may arise. We are currently using Canonical’s Extended Security Maintenance feature to help ensure the ongoing security and integrity of Ubuntu 12.04 systems, however, support for 12.04 DNAnexus applications and applets on all instance types will officially end on April 28th, 2018.

Tips for Updating to Ubuntu 14.04: 

  • If your application uses assets, ‘execDepends’, or installs from ‘apt’ directly within the application, it is recommended that you ensure any version changes in these packages when using Ubuntu 14.04 are compatible with your application. It may be helpful to use a Cloud Workstation to test out these differences.
  • Instead of using ‘execDepends’ for installing packages, consider using DNAnexus assets or Docker images. Your application will incur less runtime dependency on the network availability of Canonical packages, and by using Docker, you can choose different runtime environments, including Ubuntu 16.04, to encapsulate the core functionality of the application.

Beginning October 15th, 2017, the DNAnexus Platform will also require the ‘distribution’ and ‘release’ fields to be specified within the application’s ‘runSpec’ when building an applet. Please ensure that any applications you build from source contain those fields. Note that if you use ‘dx-app-wizard’ to generate an application template, these fields are populated for you. Please ensure you are using a recent version of the dx-toolkit when using ‘dx-app-wizard’ or performing a build. You can obtain the latest version of the toolkit from our wiki or by using the ‘dx upgrade‘ command.

Please do not hesitate to contact support@dnanexus.com with any questions or concerns regarding this software update.

The New UI: Sleeker. Modern. Intuitive.

We are pleased to announce a design refresh of the DNAnexus web user interface! The new, modern interface incorporates visual enhancements that make the most common tasks and interactions intuitive and delightful, without changing the underlying functions that power your biomedical research. Explore some of the updates below, highlighted in yellow.

Project List

Your list of projects and files has a sleeker layout and more intuitive filtering system. Looking for your Bookmarks? The Bookmarks tab has been renamed to Saved Filters so you can quickly find and access the projects you’re looking for.

Project Page

Managing workflows has never been easier. The main actions are listed using clear, modernized icons to help you know exactly which steps to take next. Each file also has a context menu. Clicking on these three dots will help you accomplish actions such as view, copy, delete, and download one item at a time. You can still apply bulk action to all the files by clicking the icons at the top of the page.

App Library

The available apps are displayed in a simplified and visually appealing manner. The inputs and outputs of each tool are clearly shown, and finding the appropriate app for your analysis is now easier than ever. 

Billing Information

Your user settings have been reorganized to show your billing information in one distinct location. This will help you easily review your budget, spend, and remaining funds.

We hope these changes make using the DNAnexus web interface an intuitive and seamless experience. If you have any questions about the updates, let us know at support@dnanexus.com.

DNAnexus Introduces Faster Cloud Options

Spring has arrived at DNAnexus, ushering in important updates! Starting May 1, 2014, we are excited to announce your analyses on DNAnexus will be faster, thanks to new instance types .

What does that really mean? Here’s an example before we dive into all the details…  A specific exome pipeline (e.g., BWA-MEM, GATK-Lite) now runs in less than 4 hours! Previously, the run would have taken nearly 6 hours.

New instance types

We believe, and hope you do too, that DNAnexus is the best choice for expanding your genomic analysis infrastructure. Because, unlike local equipment, which from day one starts collecting dust in your server room while technological advances pile up, the cloud is always on the forefront of computing technology as newer, faster hardware is made available.

These new hardware options are in the form of new instance types (virtual computer configurations) on which your cloud analyses can run. And thanks to the flexibility and reproducibility aspects of the DNAnexus platform, you can start using these new instance types right away—simply launch your existing analyses on one of those new instance types (e.g., using the “–instance-type <…>” option of our “dx run” command-line tool) and enjoy a completely effortless hardware upgrade!

The new instance types are built on high-frequency Intel® processors of the Sandy Bridge and Ivy Bridge microarchitectures, support the Intel® Advanced Vector Extensions (Intel® AVX), and have solid-state drive (SSD) local storage technology for fast I/O performance.

The following table summarizes these new instance types. For a given column (which represents a certain number of cores and local storage capacity), there are up to three different instance types to choose from (with different amounts of memory). Overall these new instance types span a large spectrum, starting at 2 cores, 32 GB SSD, and 3.8 GB RAM, all the way to 32 cores, 640 GB SSD, and 244 GB RAM:

summary new instance types
In an effort to be more informative and transparent, we have also come up with a new, easy to remember, and consistent naming scheme:

  • The prefix (mem1, mem2, or mem3) denotes the memory capacity per core;
  • the infix (ssd1) denotes that these instances have solid-state drive technology;
  • the suffix (x2 through x32) denotes the number of cores.

New names for existing instance types

We liked the convenient new naming scheme so much that we have applied it to existing instance types as well, as shown in the following table.

Compared to the new instance types mentioned earlier, the existing instance types are distinguished by a different storage infix (hdd2), given their regular hard disk drive technology. More information is available on our wiki page, which explains the new naming conventions and includes a detailed list of all instance types.

new instance names
To ease the transition, existing instances can currently be called by either their original name or the new name; the DNAnexus system understands both. However, we encourage you to adopt the new names in a timely manner to avoid any future interruption.

We are very excited to announce these important updates, and we cannot wait to hear your success stories out of them. Drop us a note at support@dnanexus.com if you’d like to get in touch with us.