- galaxy-user - lists.galaxyproject.org

June 3, 2013 Galaxy Distribution
by Jennifer Jackson 04 Jun '13

04 Jun '13

June 3, 2013 Galaxy Distribution <http://wiki.galaxyproject.org/News/2013_06_03_Galaxy_Distribution> *Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_03>* *Highlights:* * Visualization tool updates to Scatterplot <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Scatterplot> and Trackster <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Trackster>. * Job distribution, error tracking/management, and reporting function improvements to Admin <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Admin> & Core <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Core>. * Multiple Tool <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Tools> updates, History and Dataset <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Histories> upgrades, and other related UI <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#UI> enhancements. * New features and fixes added to the Tool Shed <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Tool_Shed> and related components. * Python 2.5 Support /officially ended/ <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Python_2.5_Support_H…>. * Plus newly merged Pull Requests <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Pull_Requests_Merged> and links to tickets covering key Bug Fixes <http://wiki.galaxyproject.org/DevNewsBriefs/2013_06_01#Bug_Fixes>. / http://getgalaxy.org/ /http://bitbucket.org/galaxy/galaxy-dist/ /http://galaxy-dist.readthedocs.org/ // new: $ hg clone https://bitbucket.org/galaxy/galaxy-dist#stable upgrade: $ hg pull $ hg updaterelease_2013.06.03 /Thanks for using Galaxy,/ The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team>

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Newbie: summary or metrics of Galaxy use & adoption?
by Ramon Felciano 04 Jun '13

04 Jun '13

Hello all - I would like to evaluate Galaxy for integration with Ingenuity's NGS analytics platform, and am trying to pull together some macro materials on how Galaxy has been used and adopted by the community at large. Are there any presentations or wiki pages that summarize basic stuff like: # users # of deployments/ instances (public or private) Relative use of CloudMan vs locally deployed Use in any clinical or regulated environments (e.g. CLIA) I've seen the materials at http://wiki.galaxyproject.org/Galaxy%20Project/Statistics but this looks to be only related to the public instance. Are there any similar materials that summarize across all installations, perhaps based on user surveys or the like? Thanks in advance for your help. Ramon ____________________________________ Ramon M. Felciano, PhD Founder and SVP, Research INGENUITY Systems, Inc. 1700 Seaport Blvd., 3rd Floor Redwood City, CA 94063 650.381.5100 phone 650.963.3399 fax E-mail: felciano(a)ingenuity.com<mailto:felciano@ingenuity.com>

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Fwd: galaxy on the cloud
by Dannon Baker 04 Jun '13

04 Jun '13

Hi Alejandro, It should show up if you search for the AMI ID, which is ami-da58aab3. That said, the easiest way to launch a galaxy cloud cluster if you're not already familiar with EC2 is probably using usegalaxy.org/cloudlaunch. This interface will guide you through the launch process without any extra input on your part other than providing your AWS keys.

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galaxy on the cloud
by Colaneri, Alejandro Cesar 03 Jun '13

03 Jun '13

Hello, I'm trying to start an instance of galaxy in the cloud (AMAZON) I'm following the screencast but when I copy the AMI name form the wiki site [cid:8F29F430-A843-4C52-8A1B-3DACF9E074A5] And paste in the Community AMIs search box , it does not work. Can you please tell me which is the lastest AMI name? Thank you Alejandro [cid:4C28C476-6FFD-45DD-9B06-795A2C46266C] Dr. Alejandro Colaneri Departments of Biology University of North Carolina at Chapel Hill 310 Coker Hall, CB# 3280 120 South Road Chapel Hill, NC 27599-3280 Tel: 919-962-2273 fax: 919- 962-1625

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Information for Galaxy Event Horizon
by Sarah Maman 03 Jun '13

03 Jun '13

Dear all, Four days of training in genomics are occurring on our local instance of Galaxy (27-30 May). This training session takes place at INRA, Toulouse Auzeville, France, as part of a collaboration between Sigenae (http://www.sigenae.org/) and GenoToul bioinformatics platform (http://bioinfo.genotoul.fr/) This session is composed of four training days: * Galaxy first step * Reads alignment and SNP calling * RNAseq alignment and transcripts assemblies * sRNAseq Do you think it is possible to list our training session in your "Galaxy Event Horizon"? Sincerely, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*--

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:jeanfrancois.dufayard:
by Jean-François Dufayard 02 Jun '13

02 Jun '13

http://aquaservice.kz/lxvnvdcx/lsvtgbjaalcrkqyz.wtnxp

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List of genomes
by YBao 01 Jun '13

01 Jun '13

Hi All, I was trying to map a set of data to a genome, Klebsiella pneumoniae subsp. Pneumoniae MGH 78578(31). While uploading the reads, I was able to find the reference genome as listed above. However, when I tried to map the data using wither bowtie or BWA, the pull down list did not include this genome. Can someone help or enlighten me as why it did not make into the list? Thanks Yongde -- Yongde Bao DNA Sciences Core Dept. of Microbiology, Immunology, and Cancer Biology UVA

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uploading files to main galaxy at psu
by Colaneri, Alejandro Cesar 01 Jun '13

01 Jun '13

I'm trying to upload fastq files to the server. I have 52 fastq files, Two days ago I started with 8 of them. Two files were upload in the first hs, however after more than 48 hs the rest of the files are still trying to be uploaded. It is this normal? Dr. Alejandro Colaneri Departments of Biology University of North Carolina at Chapel Hill 310 Coker Hall, CB# 3280 120 South Road Chapel Hill, NC 27599-3280 Tel: 919-962-2273 fax: 919- 962-1625

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June 2013 Galaxy Update
by Dave Clements 31 May '13

31 May '13

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Re: [galaxy-user] tophat to cuffdiff without cufflinks
by Colaneri, Alejandro Cesar 31 May '13

31 May '13

Well in that case I will like to use the same gtf file from TAIR 10 that was used by the tophat. But the tophat have the option bult in. How can I point cuffdiff to the same file? Dr. Alejandro Colaneri Departments of Biology University of North Carolina at Chapel Hill 310 Coker Hall, CB# 3280 120 South Road Chapel Hill, NC 27599-3280 Tel: 919-962-2273 fax: 919- 962-1625 From: Jennifer Jackson <jen(a)bx.psu.edu<mailto:jen@bx.psu.edu>> Date: Thursday, May 30, 2013 8:07 PM To: "Colaneri, Alejandro Cesar" <colaneri(a)email.unc.edu<mailto:colaneri@email.unc.edu>> Cc: "galaxy-user(a)bx.psu.edu<mailto:galaxy-user@bx.psu.edu>" <galaxy-user(a)bx.psu.edu<mailto:galaxy-user@bx.psu.edu>> Subject: Re: [galaxy-user] tophat to cuffdiff without cufflinks Hello, You will need to provide a GTF or GFF3 file to Cuffdiff - this is what the tool uses as a reference base to build gene, transcript, and if provided in the annotation attributes, transcript start site and protein groupings to perform the differential analysis. More details can be found here: http://cufflinks.cbcb.umd.edu/manual.html Our tutorial and other wiki help is linked from here, see "Tools on the Main Server": http://wiki.galaxyproject.org/Support#Interpreting_scientific_results Hopefully this helps, Jen Galaxy team On 5/30/13 3:15 PM, Colaneri, Alejandro Cesar wrote: Hi I comparing gen expression data (RNA-seq) in Arabidopsis. Different genotypes, different conditions. Since Arabidopsis is very well annotated I decided to do cuffdiff directly after tophat. However when building my workflow I found that the cuffdiff said a gtf file is necessary. Please see the picture in this email, under INPUT FORMAT. My question is if I can still compare my libraries in the way I designed below. [cid:part1.04070709.03020802@bx.psu.edu] Dr. Alejandro Colaneri Departments of Biology University of North Carolina at Chapel Hill 310 Coker Hall, CB# 3280 120 South Road Chapel Hill, NC 27599-3280 Tel: 919-962-2273 fax: 919- 962-1625 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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