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[[Events/ISMB2014|{{attachment:Images/Logos/BOSC_logo.png|BOSC 2013|height="75"}}]]    [[Events/ISMB2014|{{attachment:Images/Logos/BOSC_logo.png|BOSC 2013|height="65"}}]]   
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 * ''[[http://www.iscb.org/uploaded/css/166/29988.pdf|TT03: Interactive Visual Analysis with Galaxy Charts]]'', [[SamGuerler|Sam Guerler]]  * ''[[http://www.iscb.org/uploaded/css/166/29988.pdf|TT03: Interactive Visual Analysis with Galaxy Charts]]'', [[AysamGuerler|Sam Guerler]]
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''xx papers'' were added to the [[http://www.citeulike.org/group/16008/|Galaxy CiteULike Group]] in June. Some papers that may be particularly interesting to the Galaxy community: ''48 papers'' were added to the [[http://www.citeulike.org/group/16008/|Galaxy CiteULike Group]] in June. Some papers that may be particularly interesting to the Galaxy community:

 * "[[http://dx.doi.org/10.1093/bioinformatics/btu386|BioBlend.objects: metacomputing with Galaxy]]", by S. Leo, L. Pireddu, G. Cuccuru, ''et al.'' ''Bioinformatics'' (12 June 2014), doi:10.1093/bioinformatics/btu386

 * "[[http://dx.doi.org/j.biosystems.2014.06.009|RPPApipe: A pipeline for the analysis of reverse-phase protein array data]]" by Johannes Eichner, Yvonne Heubach, Manuel Ruff, ''et al.'' ''Biosystems'' (June 2014), doi:10.1016/j.biosystems.2014.06.009

 * "[[http://dx.doi.org/10.1007/978-1-4939-0847-9_7|Using Bioinformatics Tools to Study the Role of microRNA in Cancer]]", by Fabio Passetti, Natasha Andressa Nogueira Jorge, Alan Durham; In ''Clinical Bioinformatics'', Vol. 1168 (2014), pp. 99-116, doi:10.1007/978-1-4939-0847-9_7

 * "[[http://dx.doi.org/10.1371/journal.pone.0098870|Ocular and Extraocular Expression of Opsins in the Rhopalium of Tripedalia cystophora (Cnidaria: Cubozoa)]]" by Jan Bielecki, Alexander K. Zaharoff, Nicole Y. Leung, Anders Garm, Todd H. Oakley, ''PLoS ONE'', Vol. 9, No. 6. (5 June 2014), e98870, doi:10.1371/journal.pone.0098870
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||<)> - || [[http://www.citeulike.org/group/16008/tag/cloud|Cloud]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/project|Project]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/tools|Tools]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/usepublic|UsePublic]] ||
||<)> - || [[http://www.citeulike.org/group/16008/tag/howto|HowTo]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/refpublic|RefPublic]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/usecloud|UseCloud]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/visualization|Visualization]] ||
||<)> - || [[http://www.citeulike.org/group/16008/tag/isgalaxy|IsGalaxy]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/reproducibility|Reproducibility]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/uselocal|UseLocal]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/workbench|Workbench]] ||
||<)> - || [[http://www.citeulike.org/group/16008/tag/methods|Methods]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/shared|Shared]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/usemain|UseMain]] ||
||<)> 2 || [[http://www.citeulike.org/group/16008/tag/cloud|Cloud]] ||<)> 1 || [[http://www.citeulike.org/group/16008/tag/project|Project]] ||<)> 3 || [[http://www.citeulike.org/group/16008/tag/tools|Tools]] ||<)> 4 || [[http://www.citeulike.org/group/16008/tag/usepublic|UsePublic]] ||
||<)> 2 || [[http://www.citeulike.org/group/16008/tag/howto|HowTo]] ||<)> 3 || [[http://www.citeulike.org/group/16008/tag/refpublic|RefPublic]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/usecloud|UseCloud]] ||<)> - || [[http://www.citeulike.org/group/16008/tag/visualization|Visualization]] ||
||<)> 1 || [[http://www.citeulike.org/group/16008/tag/isgalaxy|IsGalaxy]] ||<)> 1 || [[http://www.citeulike.org/group/16008/tag/reproducibility|Reproducibility]] ||<)> 2 || [[http://www.citeulike.org/group/16008/tag/uselocal|UseLocal]] ||<)> 17 || [[http://www.citeulike.org/group/16008/tag/workbench|Workbench]] ||
||<)> 16 || [[http://www.citeulike.org/group/16008/tag/methods|Methods]] ||<)> 1 || [[http://www.citeulike.org/group/16008/tag/shared|Shared]] ||<)> 7 || [[http://www.citeulike.org/group/16008/tag/usemain|UseMain]] ||
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== GVL-QLD ==

<<div(right solid)>>[[http://galaxy-qld.genome.edu.au/|{{attachment:GenomicsVirtualLab300.png|Genomics Virtual Lab|height="220"}}]]<<div>>
== GVL QLD ==

<<div(right solid)>>[[http://galaxy-qld.genome.edu.au/|{{attachment:PublicGalaxyServers/GenomicsVirtualLab300.png|Genomics Virtual Lab|height="220"}}]]<<div>>
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  [[http://galaxy-qld.genome.edu.au/|GVL Queensland]]   [[http://galaxy-qld.genome.edu.au/|Genomics Virtual Lab GVL-QLD]]
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One new [[[[Community/Logs|Log Board entry]] was added in June: One new [[Community/Logs|Log Board entry]] was added in June:
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 * ''From [[]]''
   * [[]]:

=== Datatypes ===

 * ''From [[]]''
   * [[]]:

=== Workflows ===

 * ''From [[]]''
   * [[]]:

=== Packages ===

 * ''From [[]]''
   * [[]]:
 * ''From [[http://toolshed.g2.bx.psu.edu/view/qfab/|qfab]]''
   * [[http://toolshed.g2.bx.psu.edu/view/qfab/pynast|pynast]]: PyNAST is a sequence aligner for adding new 16S rDNA sequences to existing 16S rDNA alignments - GVL
   * [[http://toolshed.g2.bx.psu.edu/view/qfab/fasttree_linux_64bit|fasttree_linux_64bit]]: !FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL
   * [[http://toolshed.g2.bx.psu.edu/view/qfab/rarefaction|rarefaction]]: Rarefaction calculation based on mothur's rarefaction.single command - GVL

 * ''From [[http://toolshed.g2.bx.psu.edu/view/crs4/|crs4]]''
   * [[http://toolshed.g2.bx.psu.edu/view/crs4/hadoop_galaxy|hadoop_galaxy]]: Hadoop-Galaxy integration

 * ''From [[https://toolshed.g2.bx.psu.edu/view/evan/|evan]]''
   * [[https://toolshed.g2.bx.psu.edu/view/evan/bwa_wrappers|bwa_wrappers]]: Galaxy wrappers for the BWA short read aligner.

 * ''From [[http://toolshed.g2.bx.psu.edu/view/anton/|anton]]''
   * [[http://toolshed.g2.bx.psu.edu/view/anton/vcfprimers|vcfprimers]]: Extract flanking sequences for each VCF record
   * [[http://toolshed.g2.bx.psu.edu/view/anton/vcffixup|vcffixup]]: Count the allele frequencies across alleles present in each record in the VCF file.
   * [[http://toolshed.g2.bx.psu.edu/view/anton/vcfsort|vcfsort]]: Sort VCF dataset by coordinate
   * [[http://toolshed.g2.bx.psu.edu/view/anton/vcfallelicprimitives|vcfallelicprimitives]]: Splits alleleic primitives (gaps or mismatches) into multiple VCF lines
   * [[http://toolshed.g2.bx.psu.edu/view/anton/vcfaddinfo|vcfaddinfo]]: Adds info fields from the second dataset which are not present in the first dataset.
   * plus [[http://toolshed.g2.bx.psu.edu/view/anton/|18 more VCF related tools from anton]]

 * ''From [[http://toolshed.g2.bx.psu.edu/view/superyuan/|superyuan]]''
   * [[http://toolshed.g2.bx.psu.edu/view/superyuan/refeditor|refeditor]]: Produces a personalized diploid reference genome based on all known genetic variants of that particular individual.

 * ''From [[http://toolshed.g2.bx.psu.edu/view/iracooke/|iracooke]]''
   * [[http://toolshed.g2.bx.psu.edu/view/iracooke/make_protein_decoys|make_protein_decoys]]: Generate a decoy database from an input set of protein sequences. Decoys generated using this tool can be used for tandem ms searches.
   * [[http://toolshed.g2.bx.psu.edu/view/iracooke/proteindb_from_gff3|proteindb_from_gff3]]: Convert Augustus Generated gff3 to a Protein Database
   * [[http://toolshed.g2.bx.psu.edu/view/iracooke/protxml_to_gff|protxml_to_gff]]: Map peptides from a protXML file to genomic coordinates
   * [[http://toolshed.g2.bx.psu.edu/view/iracooke/sixframe_translate|sixframe_translate]]: Translates sequences in a nucleotide fasta file to protein

 * ''From [[https://toolshed.g2.bx.psu.edu/view/hyungrolee/|hyungrolee]]''
   * [[https://toolshed.g2.bx.psu.edu/view/hyungrolee/mgescan|mgescan]]: MGEScan: Identifying long terminal repeats (LTR) and non-LTR retroelements in eukaryotic genomic sequences.

 * ''From [[http://toolshed.g2.bx.psu.edu/view/iuc/|iuc]]''
   * [[http://toolshed.g2.bx.psu.edu/view/iuc/samtools_sort|samtools_sort]]: Sort alignments by leftmost coordinates or read name.

 * ''From [[https://toolshed.g2.bx.psu.edu/view/devteam/|devteam]]''
   * [[https://toolshed.g2.bx.psu.edu/view/devteam/bamleftalign|bamleftalign]]: utility for leftaligning indels in BAM datasets. Based on bamleftalign utility for !FreeBayes package.

=== Packages / Tool Dependency Definitions ===

 * ''From [[http://toolshed.g2.bx.psu.edu/view/qfab/|qfab]]''
   * [[http://toolshed.g2.bx.psu.edu/view/qfab/package_numpy_1_8|package_numpy_1_8]]: Tool dependency definition; downloads and compiles the python numpy package 1.8.1 - GVL
   * [[http://toolshed.g2.bx.psu.edu/view/qfab/package_pycogent_1_5_2|package_pycogent_1_5_2]]: Tool dependency definition; installs the !PyCogent package version 1.5.2 and its dependencies - GVL
   * [[http://toolshed.g2.bx.psu.edu/view/qfab/package_uclust_1_2_22q|package_uclust_1_2_22q]]: Tool dependency definition; installs uclust v1.2.22q for PyNAST - GVL
   * [[http://toolshed.g2.bx.psu.edu/view/qfab/package_mothur|package_mothur]]: mothur is an open-source, expandable software to fill the bioinformatics needs of the microbial ecology community
   * [[http://toolshed.g2.bx.psu.edu/view/qfab/collector_curve|collector_curve]]: Collector's curve calculation based on mothur's collect.single command - GVL

 * ''From [[http://toolshed.g2.bx.psu.edu/view/biopython/|biopython]]''
   * [[http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_64|package_biopython_1_64]]: Downloads and compiles version 1.64 of the Biopython package.
 * ''From [[http://toolshed.g2.bx.psu.edu/view/jankanis/|jankanis]]''
   * [[http://toolshed.g2.bx.psu.edu/view/jankanis/package_libxml2_2_9_1|package_libxml2_2_9_1]]: fork of existing package_libxml2_2_9_1 from devteam with some additional environment variable exports

 * ''From [[http://toolshed.g2.bx.psu.edu/view/iuc/|iuc]]''
   * [[http://toolshed.g2.bx.psu.edu/view/iuc/package_gnu_coreutils_8_22|package_gnu_coreutils_8_22]]: downloads and compiles version 8.22 of the GNU coreutils.
   * [[https://toolshed.g2.bx.psu.edu/view/iuc/package_libpng_1_2|package_libpng_1_2]]: Provides the 1.2.x branch of libpng for compatibility with older software.
   * [[https://toolshed.g2.bx.psu.edu/view/iuc/package_tpp_4_6_3|package_tpp_4_6_3]]: Downloads and compiles version 4.6.3 of the Trans-Proteomic Pipeline.

 * ''From [[https://toolshed.g2.bx.psu.edu/view/iracooke/|iracooke]]''
   * [[https://toolshed.g2.bx.psu.edu/view/iracooke/package_protk_1_2_6|package_protk_1_2_6]]: Installs the version 1.2.6 of the protk rubygem

 * ''From [[http://toolshed.g2.bx.psu.edu/view/anton/|anton]]''
   * [[http://toolshed.g2.bx.psu.edu/view/anton/package_vcflib|package_vcflib]]: Compiled binary files for vcflib toolkit.

 * ''From [[http://toolshed.g2.bx.psu.edu/view/jeremie/|jeremie]]''
   * [[http://toolshed.g2.bx.psu.edu/view/jeremie/package_pindel_0_2_5|package_pindel_0_2_5]]: downloads and compiles version 0.2.5 of Pindel.

 * ''From [[http://toolshed.g2.bx.psu.edu/view/devteam/|devteam]]''
   * [[http://toolshed.g2.bx.psu.edu/view/devteam/freebayes_0_9_14_8a407cf5f4|freebayes_0_9_14_8a407cf5f4]]: Dependencies for !FreeBayes and !LeftAlign wrappers
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 * ''From [[]]''
   * [[]]: updated to ...
 * ''From [[https://toolshed.g2.bx.psu.edu/view/vipints/|vipints]]''
   * [[https://toolshed.g2.bx.psu.edu/view/vipints/fml_gff3togtf|fml_gff3togtf]]: Uploaded version 2.0.0 of gfftools to integrate local Galaxy instances.
 * ''From [[http://toolshed.g2.bx.psu.edu/view/peterjc/|peterjc]]''
   * [[http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr|blastxml_to_top_descr]]: Uploaded v0.1.0, now also handles extended tabular BLAST output.

Hey! This is under construction!

July 2014 Galaxy Update

Galaxy Updates

Welcome to the July 2014 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.  

The Galaxy Update is going out a few days early this month because the usual release date is during GCC2014.

Events


GCC2014: June 30 - July 2

GCC2014: June 30 - July 2, Baltimore

The 2014 Galaxy Community Conference (GCC2014) starts on Monday, June 30, and runs through July 2, at the Homewood Campus of Johns Hopkins University, in Baltimore, Maryland, United States. The program is online and all titles and abstracts for accepted talks and posters are now online.

Fifteen Training sessions on 12 topics, several Birds of a Feather, two lightning talk sessions, and the very first Galaxy Project Hackathon are also happening.


Galaxy @ ISBMB and BOSC 2014

BOSC 2013    ISMB 2014

There will be at least six talks and five posters related to Galaxy at ISMB and BOSC 2014 this year. Talks include

Other Events

http://bit.ly/gxycal

Over the rest of the summer there are other Galaxy related events in Leiden, Sydney, Brisbane, São Paulo, and Rio de Janeiro. Also see the Galaxy Events Google Calendar for details on other events of interest to the community.


Date

Topic/Event

Venue/Location

Contact

June 28-30

Galaxy Hackathon

Homewood Campus of Johns Hopkins University, Baltimore, Maryland, United States

Organizers

June 30 -
July 2

2014 Galaxy Community Conference (GCC2014)

Organizers

July 7-9

NBIC/BioSB RNA- seq data analysis course

Leiden, the Netherlands

NBIC/BioSB <education AT biosb DOT nl>

July 10

An Introduction to Galaxy with the Genomics Virtual Lab

Post-GSA 2014 Workshop, Sydney, Australia

Mark Crowe

July 11-15

ISMB and BOSC 2014

At least six talks and five posters

Boston, Massachussetts, United States

See presenter list

July 18

Workshop: RNA-Seq analysis using Galaxy

Brisbane, Australia

Mark Crowe

July 28 - August 1

Workshop: DNA Sequence Bioinformatics Analysis with the Galaxy Platform

University of São Paulo (USP), São Paulo, Brazil

Dave Clements

August 25-27

Análise e anotação funcional de seqüências NGS usando Stingray@Galaxy

Fiocruz, Rio de Janeiro, Brasil

Plataforma de Bioinformática do IOC <bioinformatica@ioc.fiocruz.br>

September 6-10

T07 - Scientific Workflows for Analysing, Integrating and Scaling Bioinformatics Data: a Practical Introduction to Galaxy, Taverna and WS-PGRADE

European Conference on Computational Biology (ECCB'14), Strasbourg, France

Hailiang (Leon) Mei

September 30 - October 2

RNA-Seq & ChIP-Seq analysis course using Galaxy

PRABI, Lyon, France

Navratil V <navratil AT prabi DOT fr>., Oger C. <oger AT prabi DOT fr>, Veber P. <veber AT prabi DOT fr>, Deschamps C. <deschamps AT prabi DOT fr>, Perriere G. <perriere AT prabi DOT fr>

September 30 - October 2

Galaxy Training and Demo Day

Bern (Switzerland)

Hans-Rudolf Hotz and Bjoern Gruening

(second Swiss) Galaxy Workshop

SyBIT Tech Day, Bern (Switzerland)

German Galaxy Developers Day

Freiburg (Germany)

New Papers

48 papers were added to the Galaxy CiteULike Group in June. Some papers that may be particularly interesting to the Galaxy community:

The new papers were tagged in many different areas:

#

Tag

  

#

Tag

  

#

Tag

  

#

Tag

2

Cloud 

1

Project 

3

Tools 

4

UsePublic

2

HowTo 

3

RefPublic 

-

UseCloud 

-

Visualization

1

IsGalaxy 

1

Reproducibility 

2

UseLocal 

17

Workbench

16

Methods 

1

Shared 

7

UseMain

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

One new public Galaxy server was added to the published list in June:

GVL QLD

Genomics Virtual Lab


Galaxy Distributions

BioBlend 0.4.3 was released on April 11, 2014.

The most recent version of CloudMan was released in January 2014.

Galaxy Community Hubs

   Galaxy Community Log Board
Galaxy Deployment Catalog   

   Share your experience now   
Describe your instance now



One new Log Board entry was added in June:

The Community Log Board and Deployment Catalog Galaxy community hubs were launched last your. If you have a Galaxy deployment, or experience you want to share then please publish them.


Galaxy ToolShed

ToolShed Contributions

Galaxy Project ToolShed Repos

In no particular order:

Tools

  • From qfab

    • pynast: PyNAST is a sequence aligner for adding new 16S rDNA sequences to existing 16S rDNA alignments - GVL

    • fasttree_linux_64bit: FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL

    • rarefaction: Rarefaction calculation based on mothur's rarefaction.single command - GVL

  • From crs4

  • From evan

    • bwa_wrappers: Galaxy wrappers for the BWA short read aligner.

  • From anton

  • From superyuan

    • refeditor: Produces a personalized diploid reference genome based on all known genetic variants of that particular individual.

  • From iracooke

    • make_protein_decoys: Generate a decoy database from an input set of protein sequences. Decoys generated using this tool can be used for tandem ms searches.

    • proteindb_from_gff3: Convert Augustus Generated gff3 to a Protein Database

    • protxml_to_gff: Map peptides from a protXML file to genomic coordinates

    • sixframe_translate: Translates sequences in a nucleotide fasta file to protein

  • From hyungrolee

    • mgescan: MGEScan: Identifying long terminal repeats (LTR) and non-LTR retroelements in eukaryotic genomic sequences.

  • From iuc

    • samtools_sort: Sort alignments by leftmost coordinates or read name.

  • From devteam

    • bamleftalign: utility for leftaligning indels in BAM datasets. Based on bamleftalign utility for FreeBayes package.

Packages / Tool Dependency Definitions

Tool Updates:

Other News