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GalaxyUpdates/2015_01

January 2015 Galaxy Update

Galaxy Updates

Welcome to the January Galaxy Update, a 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 Papers

63 papers referencing, using, extending, and implementing Galaxy were added to the Galaxy CiteULike Group in December, bringing the total to over 2000 papers. Some of those new papers are:

The new papers covered these topics:

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Tag

  

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Tag

  

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Tag

2

Cloud

-

Project

7

Tools

10

UsePublic

-

HowTo

2

RefPublic

-

UseCloud

-

Visualization

9

IsGalaxy

-

Reproducibility

5

UseLocal

22

Workbench

21

Methods

-

Shared

10

UseMain

Events

GCC2015: 6-8 July, Norwich UK

Training Day Topic Nominations Close 6 January


   Nominate a topic now!   


GCC2015 Training Day topics are nominated by you, the Galaxy Community. Please take a few minutes to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one topic. If you are looking for ideas, see what topics were nominated in 2013 and 2014, and the Events and the Events Archives.

Nominated topics will be published on the Training Day page as they come in. Nominations close 6 January. Topics will be compiled into a uniform list by the GCC2015 Organising Committee, and topics will be voted on by the Galaxy Community 12-23 January.

Topics will then be selected and scheduled based on topic interest, and the organisers' ability to confirm instructors for each session.  Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens.

GCC2015 Organising Committee

2015 Galaxy Community Conference (GCC2015)

Call for Sponsors

The 2015 Galaxy Community Conference (GCC2015) is now accepting Sponsorships. Your organisation can play a prominent part in the Galaxy community by sponsoring GCC2015. Sponsorship is an excellent way to raise your organization’s visibility.

Several sponsorship levels are available, including two levels of premier sponsorships that include presentations. Premium sponsorships are limited, however, so you are encouraged to act soon.

Please let the GCC2015 Organising Committee (<gcc2015-org AT lists DOT galaxyproject DOT org>) know if you are interested in helping make this event a success.

Other Events

Galaxy @ Plant and Animal Genome (PAG 2015) Galaxy Workshops @ San Diego State University   Revolutionizing Next-Generation Sequencing: Tools and Technologies   Analyse bioinformatique de séquences sous Galaxy

http://bit.ly/gxycal

There are upcoming events on two continents. See the Galaxy Events Google Calendar for details on other events of interest to the community.

Date

Topic/Event

Venue/Location

Contact

January 10-14

Galaxy for SNP and Variant Data Analysis

Plant and Animal Genome XXIII (PAG2014), San Diego, California, United States

Dave Clements

January 15

Galaxy Workshops

San Diego State University, San Diego, California, United States

Dave Clements

January 15-16

Accessible and Reproducible Genomics at Scale with Galaxy

Revolutionizing Next-Generation Sequencing: Tools and Technologies, Leuven, Belgium

James Taylor

January 19-20

NGS pipelines with Galaxy

e-Infrastructures for Massively Parallel Sequencing, SciLifeLab, Uppsala, Sweden

Luca Pireddu

February 9-13

Analyse bioinformatique de séquences sous Galaxy

Montpellier, France

J.F. Dufayard <jean-francois.dufayard@cirad.fr>

February 16-18

Accessible and Reproducible Large-Scale Analysis with Galaxy

Genome and Transcriptome Analysis, part of Molecular Medicine Tri-Conference, San Francisco, California, United States

James Taylor

Large-Scale NGS data Analysis on Amazon Web Services Using Globus Genomic

Genomics & Sequencing Data Integration, Analysis and Visualization, part of Molecular Medicine Tri-Conference, San Francisco, California, United States

Ravi Madduri

iReport: An Integrative “omics” Reporting and Visualisation Platform

Andrew Stubbs

May 25-29

MIPRO

Opatija, Croatia

Enis Afgan

July 6-8

2015 Galaxy Community Conference (GCC2015)

The Sainsbury Lab, Norwich, United Kingdom

Galaxy Outreach <outreach@galaxyproject.org>

GalaxyAdmins is back!

GalaxyAdmins is back!

We just don't know exactly when, yet ...

Except for a meetup at GCC2014, the GalaxyAdmins group has been hiatus for a while. Well, thanks to the efforts of Hans-Rudolf Hotz the GalaxyAdmins group is back. Starting this month, we will resume our bi-monthly conference calls.

Galaxy-Admins is a discussion group for Galaxy community members who are responsible for large Galaxy installations.

In an effort to better serve the global community we will rotate the time of the call in different months to be convenient for different parts of the world. To help us pick the best set of times for the calls, please take a few minutes and fill out this Doodle poll. It covers every hour in a 72 hour period. Please don't forget to select the timezone before you start filling it out.

The likely presentation for the January meetup will be a summary of the Galaxy Community Survey last fall, presented by Dave Clements. The survey covered both Galaxy usage and deployment. The survey results will be published online before the call.

   Take the Doodle poll   

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.


New Public Servers

2 new public Galaxy servers were added in December

MetaNET

MetaNET

VectorBase Galaxy

VectorBase Galaxy

Galaxy Community Hubs

New Galaxy Training Resources

Several new Training Resources were added in December:

New Releases

BioBlend v0.5.2 was released in October. BioBlend is a python library for interacting with CloudMan and the Galaxy API.

New versions of Galaxy, CloudMan, and blend4j were all released in August.


Galaxy ToolShed

ToolShed Contributions

Galaxy Project ToolShed Repos

Here are new contributions for the past month.

In no particular order:

Tools

  • From rnateam:

    • rnabob: Fast pattern searching for RNA structural motifs RNABOB is an implementation of D. Gautheret's RNAMOT, but with a different underlying algorithm using a nondeterministic finite state machine with node rewriting rules.

  • From schang:

    • frp_tool: Scripts to create a fragment recruitment plot Python scripts using matlibplot to create scatter plots of metagenomic reads aligned against a reference genome.

  • From subazini:

    • ngsaligners: NGS aligners Aligners for NGS sequence analysis

  • From mrvollger:

    • trtr: Version 1.0. TRTR Trim Reads of Tandem Repeats. Recommended before calling SNPs. This tool removes tandem repeats from ends of unaligned sequencing reads (leaving one copy). This prevents reads that don't span the repeated region from overlapping, leading to innaccurate SNPs calls.

      • The maximum repeat length is adjustable (use 1 to trim only homopolymers). The "aggressive" option should not be touched in general. Setting to 0 will prevent the program from trimming to exactly 1 copy of the repeat, instead leaving between 1 and 2 copies. This could also be a useful first step before assembly. More testing needs to be done.
  • From wolma:

    • mimodd_fileinfo: use MiModD to explore metadata in various NGS file formats install this tool from the suite_mimodd_0_1_5 repository

    • mimodd_bamsort: use MiModD to sort a BAM file by coordinates (or names) of the mapped reads install this tool from the suite_mimodd_0_1_5 repository

    • mimodd_deletion_prediction: use MiModD to predict deletions in one or more samples of aligned paired-end reads install this tool from the suite_mimodd_0_1_3 repository

    • mimodd_convert: use MiModD to convert between NGS reads sequence formats install this tool from the suite_mimodd_0_1_5 repository

    • mimodd_reheader: use MiModD to reheader a BAM file install this tool from the suite_mimodd_0_1_5 repository

    • mimodd_vcf_filter: use MiModD to extract lines from a vcf variant file based on sample- and field-specific filters install this tool from the suite_mimodd_0_1_5 repository

    • mimodd_snpeff_genomes: use MiModD to list installed SnpEff genomes install this tool from the suite_mimodd_0_1_5 repository

    • mimodd_extract_variants: use MiModD to extract variant sites from BCF input generated with mimodd_variant_calling and report them in VCF install this tool from the suite_mimodd_0_1_5 repository

    • mimodd_ngs_run_annotation: use MiModD to generate a SAM format header from an NGS run description install this tool from the suite_mimodd_0_1_5 repository

    • mimodd_variant_calling: use MiModD to call variants from an aligned reads BAM file install this tool from the suite_mimodd_0_1_5 repository

    • mimodd_coverage_stats: use MiModD to obtain a coverage report for a bcf file generated with mimodd_variant_calling install this tool from the suite_mimodd_0_1_5 repository

    • mimodd_cloudmap_prepare: use MiModD to generate CloudMap-compatible output from a vcf file install this tool from the suite_mimodd_0_1_5 repository

    • mimodd_read_alignment: use MiModD to align NGS reads to a reference genome install this tool from the suite_mimodd_0_1_5 repository

    • mimodd_annotate_variants: use MiModD to annotate a vcf variant file with information about the affected genes install this tool from the suite_mimodd_0_1_5 repository

  • From devteam:

    • cuffquant: Cuffquant is part of Cufflinks. Cuffquant allows precalculation of gene expression levels. Output can be used in cuffdiff and cuffnorm.

    • bwa: Uploaded Wrapper for bwa mem. aln, sampe, and samse Al collection of Galaxy bwa wrapper based on version 0.7.10 (039ea206392ada2542bc41ff2581c53fa2fe2bf2).

    • cuffnorm: Cuffnorm is part of Cufflinks. Cuffnorm is similar to cuffdiff, but does not perform differential expression testing. It provides normalized gene expression tables for use in downstream tools (R/matlab/...).

      • Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621
    • cummerbund: Initial commit with version 1.0.0 of the cummeRbund wrapper. Wrapper for the Bioconductor cummeRbund library Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.

    • cummerbund_to_tabular: Initial commit with version 1.0.0 of the tool. Regenerate the tabular files generated by cuffdiff from a cummeRbund SQLite database. This tool extracts one or more of the original tabular data files from a cummeRbund SQLite database.

  • From pjbriggs:

    • pal_finder: Find microsatellite repeat elements sequencing reads and design PCR primers to amplif y them Runs the pal_finder Perl script and PRIMER3 to find microsatellite repeat elements sequencing reads and design PCR primers to amplify them

    • trimmomatic: A flexible read trimming tool for Illumina NGS data Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.

  • From eric-rasche:

    • gsaf_downloader: Download data from GSAF Easy download utility for fastq.gz files provided by GSAF (Genomic Sequencing and Analysis Facility)

  • From nikhil-joshi:

    • ceas: CEAS - Cis-regulatory Element Annotation System A tool designed to characterize genome-wide protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad binding factors.

  • From shian_su:

    • voom_rnaseq: Perform RNA-Seq analysis using limma voom pipeline

Tool Suites

  • From wolma:

    • suite_mimodd_0_1_5: This metapackage should be used to install the MiModD suite of tools for the analysis of genome-wide sequencing data from model organisms along with its Galaxy tool wrappers.

Packages / Tool Dependency Definitions

  • From wolma:

    • package_mimodd_0_1_5: dependency package for the MiModD suite of tools

    • package_python3_zlib_dependent_1_0: a lean build of Python3.4.1 including the zlib module - based on package_python_3_4 by jankanis Several modules of the Python standard library depend on external libraries being installed. Of these modules, this package forces only the installation of the zlib module, so the zlib library version 1.2.8 is its only requirement.

    • package_zlib_1_2_8: zlib library dependency definition

  • From iuc:

    • package_cummerbund_2_8_2: Contains a tool dependency definition that downloads and installs version 2.8.2 of the cummeRbund R library. Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.

    • package_r_3_1_2: Contains a tool dependency definition that downloads and compiles version 3.0.3 of the the R package.

  • From devteam:

  • From mrvollger:

    • package_trtr_0_1: Trim Reads of Tandem Repeat in a fastq file. This tool removes tandem repeats from ends of unaligned sequencing reads (leaving one copy). This prevents reads that don't span the repeated region from overlapping and leading to inaccurate SNPs calls.

Select Updates

  • From peterjc:

    • ncbi_blast_plus: Uploaded v0.1.01 - Requires blastdbd datatype (blast_datatypes v0.0.19). Support for makeprofiledb to create protein domain databases and use them in RPS-BLAST and RPS-TBLASTN. Tools now support GI and SeqID filters, and embed the citations.

Other News