June 2013 - galaxy-user - lists.galaxyproject.org

Newbie: summary or metrics of Galaxy use & adoption?
by Ramon Felciano 03 Jun '13

03 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 03 Jun '13

03 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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