Notes, Galaxy Community Conference 2014 day 1 afternoon: State of the Galaxy, IonTorrent, Lightning Talks

I’m at the 2014 Galaxy Community Conference in Baltimore. These are my notes from the day 1 afternoon session, following up on notes from the morning session.

State of the Galaxy

Anton Nekrutenko and James Taylor, Galaxy Project

Anton and James talk about the history and current status of Galaxy. Start off by recapping previous GCCs: went from 75 to 250 attendees. Nice numbers about growth in contributors over the past year. For Galaxy main, job usage became a crisis: more jobs than hardware could handle. Galaxy main switched over to TACC last October. Biggest issue is that with more data, jobs are now longer.

Summarization of new features: new visualizations and full visualization framework, dataset collections, Galaxy BioStar community, Toolshed with automated installation, data managers.

New stuff that is coming: organization of the toolshed, want to make the toolshed process more straightforward. New workflow scheduling engine and streaming to improve scaling on large datasets. Visualization a planned focus for the next year. Goal is to think about a distributed Galaxy ecosystem that includes federation and data localization. This is hard, but would be so awesome. Also want to figure out use of Docker integration with Galaxy. A nice discussion by Anton about scalable training, to better coordinate how training works across institutions.

Update on Ion Torrent Sequencing – Accurate, Long Reads

Mike Lelivelt – Ion Torrent

Mike talks about the role of Ion Torrent sequencing in world where Illumina dominates: challenging and driving cost and accuracy. Mike talks about work to improve indels with inherent chemistry limitations in homopolymers. New chemistry: Hi-Q that provides improved resolution of SNPs and indels. Shows a nice IGV plot and errors are now random instead of systematic. Advantage is that depth and consensus can now resolve issues.

Mike talks through great work re-evaluating the Genome in a Bottle paper. Biggest issue was using bwa + GATK, which are not good with Ion Torrent inputs. Recommended workflow is TMAP + TVC. We need a place to find these best practices and tools. TMAP and Torrent Suite are available on GitHub but not clear externally where to get and compile. After registration on IonCommunity site, can find recommended approaches: RNA-seq recommendations. Need similar summaries of recommendations for variant calling. They are releasing new versions of Torrent Caller and TMAP soon as easy to use separate command line programs, so a great time to work on integrating it.

The Galaxy Tool Shed: A Framework for Building Galaxy Tools

Greg von Kuster, Penn State University

Greg talks about recent work on the Galaxy toolshed to enable building tool dependencies automatically. Shows a demo with HVIS tool that makes Hilbert curves. He walks through the process of bootstrapping a toolshed installation on the local machine. This allows you to test and evaluate the tool locally in entirely isolated environment. Once validated, this can get exported to Galaxy toolshed, where it is run through a similar isolated framework for testing every 48 hours.

Integrating the NCBI BLAST+ suite into Galaxy

Peter Cock, The James Hutton Institute

Peter talks about his work integrating BLAST+ into Galaxy. He emphasizes the importance of making tools freely distributable so we can automated installation and distribution. They have done awesome work creating a community around developing these tools on GitHub, with functional tests automatically run via TravisCI. Good example of tricky tool because they needed to add new Galaxy datatypes to support potential output formats. BLAST tools had a lot of repeated XML and used macros to reduce this. Downside is the added complexity to the tool definitions.

On their local instance, they have Galaxy job splitting enabled which batches files into groups of 1000 query sequences. Peter also has a wrapper script which caches BLAST databases on individual nodes. Current work in progress is to create data managers for BLAST databases.

deepTools: a flexible platform for exploring deep-sequencing data

Björn Grüning, University of Freiburg

deepTools aims to standardize work to do quality control and conversion to bigWig format. Some tools available: bamCorrelate compares similarity between multiple BAM files. bamCoverage does the conversion of BAM to bigWig. bamCompare shows the differences between two BAM files. heatmapper: beautiful visualization of BAM coverage across all genes. Really need to integrate this work into bcbio-nextgen. They also have an awesome Galaxy instance for exploring usage. Finally to add they’ve got a docker instance with everything pre-installed.

Lightning talks

Lots of 5 minute talks. Will try to keep up.

David van Enckevort talks about work building a scalable Galaxy cluster in the Netherlands. Using Galaxy in a clinical setting for NGS and proteomics work. Main bottleneck is I/O performance of file intermediates.

Marius talks about Mississippi, a tool suite to work on short RNA work. Main components: trimming of small RNAs, uploaded bowtie to handle short regions, cascade tool provides a quick overview of small RNA targets. Have nice visualizations to look at the size distribution of reads and small RNA properties with good look faceted plots.

Next talk is on handling online streaming analytics for heart rate variability. Used BioBlend to retrieve and execute workflows, and provided a custom Django GUI for users to select workflows. Future work includes adding an intermediate distribute queue via Celery for streaming.

Yvan talks about a use case for the structuration of the biologist community, where they did a project in France to bring together scientists working in multiple areas. Found that with more automation, need additional human expertise to train and improve.

Ira talks about visualization of proteomics data in Galaxy. Protviz was an initial visualization tool build within Galaxy by communicating with an outside server. Unfortunately leads to confusing error messages and issues during communication. Issues is that data is in multiple places leading to long lead times for visualization. Results are not self-contained and difficult to install and maintain. Improved approaches does processing up front and gather results in a SQLite database, now integrated directly into Galaxy visualization based on prototype at Galaxy hackathon.

Nate talks about what the Galaxy team had to go through to move Galaxy main over to TACC thanks to collaboration with iPlant collaboration. Got a 10Gb/s connection to XSEDE via PSC. Tried using GlobusOnline, GridFTP and ended up with rsync. To transfer 600Tb, had to slow down because of saturating 10Gb line; ended up taking 2 months. Used Pulsar and hierarchical object store to help manage infrastructure


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