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April, 25th, 2017

  • The Tophat2 tool (from NGS: RNA Analysis/Tophat2 Gapped-read mapper for RNA-seq data) is no longer available. Please use the one available in NGS: Mapping/TopHat Gapped-read mapper for RNA-seq data.
  • Annotation files (GTF) for various genomes and Ensembl releases are available in Data libraries (top menu)/GTF. Help yourself!

March, 7th, 2017

We have recently updated the authentication procedure for the FTP server. From now on, to authenticate on the FTP server you will have to use your Galaxeast username. Your email address won’t work as a login anymore.

Please follow this procedure to connect to the FTP server.

February, 6th, 2017

To Tophat2 users

We have noticed that the possibility of using annotation files with the Tophat2 tool (available in the tool menu NGS: RNA Analysis/Tophat2 Gapped-read mapper for RNA-seq data) is not working. Be careful if you have used Tophat2 with annotations provided from Use Own Junctions/Use Gene Annotation Model/Select a reference annotation because annotations were not used! This tool will be uninstall on the 13th of February. We have installed a working Tophat2 tool available in NGS: Mapping/TopHat Gapped-read mapper for RNA-seq data.

November, 15th, 2016

MAINTENANCE ON THE 16th OF NOVEMBER

A maintenance is scheduled on the 16th of November from 8am to 12am. As the maintenance will be made on the storage facility all jobs not finished by tomorrow morning will be killed. We are sorry for any inconvenience.

October, 27th, 2016

Two new E. coli genomes are now available: K-12 and BW25113.

March, 14th, 2016

To users with a Galaxeast account created before 16th of November: During our last major upgrade (in November 2015), we have changed the way passwords are encoded in the Galaxeast database. To log in to the FTP server again, you have to change your Galaxeast password (going to User > Preferences > Manage User information).

November, 16th, 2015

The GalaxEast platform has been fully upgraded.

During this upgrade, the whole platform has been transferred on new hardwares to improve computing power and increase dataset storage space. The platform itself has also been updated i.e Galaxy source code has been updated and all tools available in the old GalaxEast platform have been re-installed in the new one. You will thus see some new functionalities and tools available. All your datasets and workflows are transferred and available in the updated instance.

Remark: as the tools reinstallation may have involved an update of the tools, you may encounter issues when trying to re-run jobs from your old histories or Galaxy may be unable to find tools used in your workflows. If you end up with such issues, you’ll be able to find desired tools by doing a search and selecting your tool of interest in the tool panel.

August 3rd, 2015

A new tool is now available: Bed closest (find closest intervals) which can be used to search for overlapping features between two sets of genomic intervals (in “NGS: BED Tools” section). See documentation of the tool.

July 12th, 2015

A new genome is now available: Vitis Vinifera (Assembly 12X.2)

April 10th, 2015

A new tool is now available: Fasta to fastq which can be used to convert fasta files into fastq files (in “FASTA manipulation” section)

February 13rd, 2015

A new genome is now available: Chlamydomonas reinhardtii (Chlre5)

A new tool is now available: bcftools view which can be used to convert BCF format to VCF format (in “NGS: SAM Tools” section)

January 5th, 2015

The GalaxEast team would like to wish you all Season's Greetings and a Happy New Year 2015!

December 18th, 2014

  • The GalaxEast team released documentation on file/table manipulation tools. Just check it out on our wiki.
  • A new tool - Shuffle from the BEDtools suite - has just been added to GalaxEast. The tool is design to randomly select chromosomal coordinates. See BEDtools shuffle documentation. The program requiers a bed,vcf,gff file and a *.len file that you can either provide or take from our data library (Shared data (top menu)/Data Libraries/Chromosome length).

September 18th, 2014

Our Galaxy platform, GalaxEast was presented at the ECCB 2014 conference, in Strasbourg on the 8th of September. Check out our poster.

May 6th, 2014

DeepTools which is available in our Galaxy instance has just been accepted for publication:

Ramírez F, Dündar F, Diehl S, Grüning BA, Manke T: deepTools: a flexible platform for exploring deep-sequencing data. Nucleic Acids Research (2014). doi:10.1093/nar/gku365 (http://nar.oxfordjournals.org/content/early/2014/05/05/nar.gku365)

April 30th, 2014

A new genome is now available: Arabidopsis Thaliana (TAIR10)

A new tool is now available: Union of two datasets based on common field (in “Join, Subtract and Group” section)

April 4th, 2014

Our workgroup has been improving the robustness of your Galaxy instance with some infrastructure maintenances and an update of the Galaxy platform.

Infrastructure maintenance

  • Uploading big files through the “Get Data/Upload file” tool is now working;
  • The web server has been improved to be more reliable when running many jobs at the same time;
  • Secure FTP transfer allowed with explicit TLS (make sure to accept the self-signed certificate).

Galaxy Update

Galaxy has been updated to the official 2014-02-10 release

This new version includes the following main features and improvements :

  • Visualization upgrades, including Trackster CSS styling;
  • Multiple Tools migrated to the Tool Shed for a leaner distribution;
  • Redesign of UI rendering: new icons, new font, history panel updates;
  • Check out the new “Upload file” utility - Upload file has become as simple as “drag and drop”;

Make sure to select a reference genome when uploading your data.
Upload is limited to 2GB per file with this tool. For bigger files please use FTP.

  • Check out the new “Operation on multiple datasets » utility;

For more detailed information about this update, please read the complete release note.

January 17th, 2014

The IGBMC Galaxy wiki has now a new URL (http://wiki.galaxy-igbmc.fr) and is accessible from a simple Internet connection.

November 21st, 2013

Galaxy storage space has been increased to 3Tb.

November 15th, 2013

Galaxy has been updated to the official 2013.11.04 release.

This new version includes the following main features and improvements :

  • A security vulnerability with filter tools has been trapped and fixed ;
  • The bug concerning the change of a dataset datatype attribute has been fixed ;
  • 48 tools have been migrated to the official Tool Shed ;
  • Many component of the platform have been upgraded for performance and scalability ;
  • The Galaxy UI has been enhanced and includes now a new windowing system named Scratchbook that let you preview your datasets simultaneously.

For more detailed information about this update, please read the official Galaxy release note

November 6th, 2013

October 2nd, 2013

  • New tools available in NGS: SAM Tools and NGS: Picard.

September 26th, 2013

  • Galaxy maintenance (Short restart): SAM-to-BAM tool works with more genomes

June 26th, 2013

  • Update of the IGBMC Galaxy platform (Log out bug is solved).
  • Addition of a new genome : Saccharomyces cerevisiae Apr. 2011 (sacCer3).
  • Addition of Google Analytics tracking

Warning : A known problem appeared with this new version of Galaxy. When changing the datatype attribute of a dataset, the selected dataset appears as a running job (yellow box with spinning icon) for ever. You'll have to refresh the history manually to get the dataset available for further work (in green).

June 5th, 2013

The IGBMC Galaxy platform is launched.

news.txt · Last modified: 2017/04/25 15:00 by slegras