July 2013 Galaxy Update

Galaxy Updates

Welcome to the July 2013 Galaxy Update, a monthly summary of what is going on in the Galaxy community. Galaxy Updates complement the Galaxy Development News Briefs which accompany new Galaxy releases and focus on Galaxy code updates.

New Public Servers

Four new servers joined the list of over 30 publicly accessible Galaxy servers in June.



P-Galaxy is part of the DDBJ Read Annotation Pipeline and is described in "DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data" by Nagasaki, et al. in DNA Research. Support is available at [P-Galaxy Team](mailto:p-galaxy AT g DOT nig DOT ac DOT jp), and P-Galaxy is developed by the Genome Informatics Laboratory and the DNA Data Bank of Japan (DDBJ) of the National Institute of Genetics (NIG).

In Silico Galaxy

In Silico Galaxy
From "[Encore: Genetic Association Interaction Network Centrality Pipeline and Application to SLE Exome Data](http://onlinelibrary.wiley.com/doi/10.1002/gepi.21739/abstract)," by Davis *et al.,* [In Silico Galaxy](http://insilico.utulsa.edu/galaxy/) implements [Encore](http://onlinelibrary.wiley.com/doi/10.1002/gepi.21739/abstract)
an open source network analysis pipeline for genome-wide association studies and rare variant data. Encore constructs Genetic Association Interaction Networks or epistasis networks using two optional approaches: our previous information-theory method or a generalized linear model approach. Additionally, Encore includes multiple data filtering options, including Random Forest/Random Jungle for main effect enrichment and Evaporative Cooling and Relief-F filters for enrichment of interaction effects. Encore implements SNPrank network centrality for identifying susceptibility hubs (nodes containing a large amount of disease susceptibility information through the combination of multivariate main effects and multiple gene-gene interactions in the network)
[In Silico Galaxy](http://insilico.utulsa.edu/galaxy/) is developed and supported by the [In Silico Bioinformatics Lab](http://insilico.utulsa.edu/) at the [University of Tulsa](http://utulsa.edu/).



LiSIs is a platform for virtual screening. The !LiSIs platform has been developed in the context of the cross-disciplinary GRANATUM project aiming to bridge the gap between biomedical researchers by ensuring their seamless access to the globally available information needed to perform complex experiments and to conduct studies on large-scale datasets. LiSIs is developed and maintained by the e-Health Laboratory at the Department of Computer Science, University of Cyprus. LiSIs is an EU-funded project under FP7-(ICT-2009.5.3) and has its own LiSIS Support Google Group for questions.



Orione is a Galaxy based web server for microbiology. Orione includes all post mapping or assembling steps from scaffolding to complete annotation pipelines. From the GCC2013 poster abstract "Engaging Galaxy in Microbiology" We started on selecting the relevant software in the microbiology area, developing then all the necessary tools to integrate them into the Galaxy ecosystem. In addition to that, we made available several specialized workflows covering major applications such as bacterial resequencing, de novo assembly, scaffolding, bacterial RNA-seq, gene annotation and metagenomics. Orione provides additional capabilities to perform integrative, reproducible and transparent bioinformatic data analysis in microbiology thus expanding the constellation of specialized Galaxy based web servers as Nebula, Cistrome and several others.

This installation of Galaxy has been configured such that anonymous users can operate in a limited way. If you need to store data on this website and/or use advanced Galaxy features such as sharing and workflows, please send us an [email](mailto:galaxyadmin AT crs4 DOT it) with a short request.

New Papers

A record 53 new papers were added to the Galaxy CiteULike Group in June. These papers may be particularly interesting to the Galaxy community

The 1,000th Galaxy related paper was added to the Galaxy CiteULike Group in June. Those first thousand papers are tagged as

# Tag # Tag # Tag
502 methods 33 unknown 15 reproducibility
325 workbench 29 shared 9 uselocal*
49 isgalaxy 24 project 7 other
46 tools 23 howto 6 usepublic*
38 usemain* 18 cloud* 1 usecloud*
* These tags were added in 2013 and very few papers before 2013 have been back-curated with them. All the tags are explained on the CiteULike page.

Who's Hiring

Please Help! Yes you!

The Galaxy is expanding! Please help it grow.

Got a Galaxy-related opening? Send it to outreach@galaxyproject.org and we'll put it in the Galaxy News feed and include it in next month's update.


BOSC 2013
MS SIG 2013: Beyond the Proteomics


ISMB / ECCB 2013 (along with http://www.open-bio.org/wiki/BOSC\_2013|BOSC]], MS SIG and many other events) will be held in Berlin July 19-23. As of this writing there are 10 talks, 9 posters, and 2 workshops related to Galaxy at the events.


2013 Galaxy Community Conference (GCC2013)

The 2013 Galaxy Community Conference (GCC2013) starts today in Oslo Norway, at the University of Oslo.

2013 Galaxy Community Conference (GCC2013) Training Day

GCC2013 is an opportunity to participate in two full days of presentations, discussions, poster sessions, lightning talks and Birds of a Feather sessions, all about high-throughput biology and the tools that support it. The conference also includes a Training Day for the second year in a row, this year with more in-depth topic coverage, more concurrent sessions, and more topics. The conference ends with a closing dinner (sponsored by Ion Torrent) at the historic venue Sporten high above Oslo. (And for the two evenings before that, we have reserved a pub...)

Birds of a Feather Sessions

Past Galaxy Community Conferences have been the event for networking in the Galaxy: There is no better place to meet and learn from others doing high-throughput biology. GCC2013 extends this tradition by including Birds of a Feather (BoF) meetups at the event. Birds of a Feather meetups are informal gatherings where participants group together based on common interests. If you have something in the list at right you want to meet about, or you have a whole new topic, then please join or start a GCC2013 BoF.

Software Carpentry Boot Camp

Directly following GCC2013, there is a unique possibility to attend a two-day Software Carpentry Boot Camp at the University of Oslo (in a building close to where the GCC is held). Software Carpentry Boot Camps aim to to help scientists and engineers become more productive by teaching them basic computing skills like program design, version control, testing, and task automation. In this two-day boot camp, short tutorials will alternate with hands-on practical exercises.

The course is aimed at postgraduate students and other scientists who are familiar with basic programming concepts (like loops, conditionals, arrays, and functions) but need help to translate this knowledge into practical tools to help them work more productively.

Content: The syllabus for this boot camp will include:

Software Carpentry Boot Camp, 3-4 July, University of Oslo
  • using the shell to do more in less time
  • using version control to manage and share information
  • basic Python programming
  • how (and how much) to test programs

Visit the Boot Camp Page for more information, and registration.

Other Upcoming Events

2013 Galaxy Community Conference (GCC2013)QFAB WorkshopsBOSC 2013   ISMB/ECCB 2013
See the [Galaxy Events Google Calendar](http://bit.ly/gxycal) for details on these and other events.

Date Topic/Event Venue/Location Contact
June 30 - July 2 2013 Galaxy Community Conference (GCC2013) University of Oslo, Oslo, Norway Organizers
July 4 RNA-Seq analysis using GalaxyQUT Kelvin Grove Campus, Kelvin Grove, Australia Mark Crowe
July 18-23 Introduction to Galaxy Workshop
National Institute of Environmental Health Sciences (NIEHS)
2013 Research Triangle Workshop Tour, North Carolina, United States Dave Clements
Introduction to Galaxy Workshop
University of North Carolina, Chapel Hill
Galaxy Installation Tutorial
Introduction to Galaxy Workshop
North Carolina State University
July 19-23 ISMB/ECCB, BOSC and MS SIG 2013
Talks, posters and workshops. Lots of them.
Berlin, Germany Galaxy Outreach
July 21-25 Experiences in building a Next-Generation Sequencing Analysis Service using Galaxy, Globus Online, and Amazon Web ServicesXSEDE13, San Diego, California, United States Ravi Madduri
A Sustainable National Gateway for Biological Computation Josephine Palencia
Supporting Genomics and other Biological Research Richard LeDuc
September 28 - October 1 Galaxy WorkshopThe Genomic Bioinformatics Workshop, Sydney, Australia Jennifer Jackson, Ross Lazarus
October 1-3 Beyond the Genome 2013 San Francisco, California, United States James Taylor
October 22-26 High Throughput Data Analysis and Visualization with GalaxyASHG 2013, Boston, Massachusetts, United States James Taylor, Jennifer Jackson

Galaxy Distributions


The most recent official distribution was on June 3, 2013. There was minor security patch released on June 12.

June 3, 2013 Distribution





new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable

upgrade: $ hg pull 
$ hg update release_2013.06.03

June 12, 2013 Security Fix

A security vulnerability was recently discovered by Björn Grüning with Galaxy's "user impersonation" feature that can expose an administrator's active history to users whom they impersonate. Only Galaxy instances with

allow_user_impersonation = True

set in their configurations are affected, and only if an administrator makes use of the impersonation feature. By default, user impersonation is disabled.

A fix (id: 9d42f1e32efb) has been provided in the stable branch of Galaxy. To apply the fix, ensure you are on the stable branch and upgrade to the latest changeset:

% hg branch

% hg pull -u

For Galaxy installations on relatively old versions that administrators are not yet ready to upgrade, there are three workarounds. First, the patch can be downloaded and applied manually:

% wget -o security.patch https://bitbucket.org/galaxy/galaxy-central/commits/9d42f1e32efb654fda1e011dc66a4aa5888717f1/raw/

and then:

% hg patch security.patch


% patch -p1 < security.patch

Second, the impersonation feature can be disabled by setting the following option in Galaxy's configuration file:

allow_user_impersonation = False

In all of the above cases, the Galaxy server process(es) must be restarted for the change to take effect.

Third, the feature can be left enabled and unpatched, and the vulnerability can be worked around by educating administrators who use the feature. As long as a new history is created by the administrator prior to switching to the impersonated user, no data will be exposed to the impersonated user.

Tool Shed Contributions

Galaxy Tool Shed
  • MMuFLR: Missense Mutation and Frameshift Location Reporter Workflows.
  • ensembl_vep: Annotation tool using Ensembl Variant Effect Predictor for GVL
  • eqtl_tools: eQTL Analysis using PANAMA
  • fasta_extract: Extract a single sequence or set of sequences from a multifasta file
  • fasta_stats: Produce basic statistics on a fasta/multifasta file
  • repeat_masker: RepeatMasker
  • interproscan: Interproscan functional predictions of ORFs
  • fastq_validator: Validate your FastQ Files.
  • peptide_to_gff: Outputs GFF3 with the peptide position in a reference genome
  • cmpfastq: Compare two fastq files
  • samifier: integrate genomic & transcriptomic NGS data with proteomic MS data.
  • somatic_sniper: identify single nucleotide positions differences between tumor and normal

Other News