February 2011 - galaxy-user - lists.galaxyproject.org

Question About FTP
by Danny Park 15 Feb '11

15 Feb '11

Hey guys, I was trying to connect to the public instance of galaxy via FTP but was not able to do so successfully. I tried both FTP and SFTP. Is there something I am missing? Thanks, Danny

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Gene Name in Cufflink/compare/diff
by Matteo Bovolenta 15 Feb '11

15 Feb '11

Hi all, when I run a RNASeq analysis using tophat, cufflink, coffcompare and cuffdiff by aligning my data to the RefSeq genes I obtain tables from cufflink/compare/diff which does not include the gene name, but only the NM_. Does someone knows how I can obtain all the tables with the gene name? Thank you all very much for the support, Best Regards, Matteo -- Matteo Bovolenta, PhD Dipartimento di Medicina Sperimentale e Diagnostica Sezione di Genetica Medica Università di Ferrara Via Fossato di Mortara, 74 44100 Ferrara tel +39 0532 974449(office) tel +39 0532 974502 (lab) fax +39 0532 236157 email bvlmtt(a)unife.it http://www.unife.it/medicina/geneticamedica http://www.bio-nmd.eu registered in ORPHANET http://www.orpha.net NOTA DI RISERVATEZZA: ai sensi del D.Lgs. 196/2003 si precisa che le informazioni contenute in questo messaggio e nei relativi allegati sono riservate ed a uso esclusivo del destinatario. Qualora il messaggio in parola Le fosse pervenuto per errore, La invitiamo ad eliminarlo senza copiarlo, a non inoltrarlo a terzi e a non farne alcun uso, dando gentilmente comunicazione all'indirizzo del mittente: bvlmtt(a)unife.it Grazie. CONFIDENTIALITY NOTICE: this message together with its annexes may contain confidential, proprietary or legally privileged information and is intended only for the use of the addressee named above. No confidentiality or privilege is waived or lost by any mistransmission. If you are not the intended recipient of this message you are hereby notified that you must not use, disseminate, copy it in any form or take any action in reliance on it. If you have received this message in error please delete it and any copies of it and kindly inform the sender of this e-mail by bvlmtt(a)unife.it Thank you

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how can I display wig tracks in UCSC browser?
by yang yu 15 Feb '11

15 Feb '11

Hi, I have uploaded a 2GB wiggle file to Galaxy. Can I display the Wig track in UCSC genome browser directly via Galaxy? thx Yu Yang

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extract genomic DNA
by Keith E. Giles 14 Feb '11

14 Feb '11

a few days ago I was able to extract genomic DNA from a bed file in either fasta or interval format. But today, that same file, and subsets of that larger file are giving me errors. It doens't tell me much. What is so incredibly frustrating is that the datasets are identical!!! One day they seem to work, the next not. Any ideas?

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extract gDNA
by Keith E. Giles 14 Feb '11

14 Feb '11

this is the error I'm getting An error occurred running this job: Traceback (most recent call last): File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py", line 259, in <module> if __name__ == "__main__": __main__() File "/galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py"

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March 2011 GMOD Meeting early registration closes this Friday
by Dave Clements 14 Feb '11

14 Feb '11

Hello all, *Register for the March 2011 GMOD Meeting ( http://gmod.org/wiki/March_2011_GMOD_Meeting) by this Friday, Feb 18, and save over 15%.* The March meeting is part of GMOD Americas 2011 ( http://gmod.org/wiki/GMOD_Americas_2011) an event that includes Satellite Meetings, a GMOD Course (already full), and for the first time, an "Introduction to GMOD" session the night before the meeting for GMOD newcomers. GMOD Americas 2011 events are being held at the US National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, United States. Also, if you have a topic you want to discuss at the meeting, please send it to Scott Cain <scott(a)scottcain.net> ASAP so he can get you on the program. *About GMOD:* GMOD is the Generic Model Organism Database project, a collection of interoperable open-source software components for annotating, visualizing, managing and analyzing biological data. GMOD is also an active community of software developers and biologists addressing common challenges with their data. The GMOD suite includes widely used tools such as GBrowse and JBrowse (and WebGBrowse) for genome browsing, Apollo and MAKER for genome annotation, GBrowse_syn and CMap for comparative genomics visualization, Chado, BioMart and InterMine for data integration, management, and querying, and Galaxy and Ergatis (and ISGA) for data analysis. *Meeting Overview: *As with previous GMOD meetings, this meeting will have a mixture of project talks, component talks, and user talks. Our guest speaker is Dr. Eric Stone of North Carolina State University. Dr. Stone will talk about his experience on the "Drosophila Genome Reference Panel," a project that is sequencing and annotating almost 200 inbred lines. The agenda is driven by attendee suggestions, and you are encouraged to add your suggestions now. For an idea of what happens at a GMOD meeting, see the writeup of the September 2010 GMOD Meeting. GMOD meetings are an excellent way to meet GMOD developers and users and to learn (and affect) what's coming in the project. *Registration: *Registration for the March 2011 GMOD Meeting is $80 on or before February 18 $95 after February 18 Please register early, both to save money, and ensure a spot. You are also strongly encouraged to submit a talk and/or sign up for (or propose) a Satellite Meeting. Details on transportation, suggested lodging, and other logistics are on the GMOD Americas 2011 page. This meeting, and all GMOD Americas 2011 events, are jointly sponsored by NESCent and the Galaxy Project. Hope to see you in North Carolina! Dave Clements Galaxy Project PS: And I hope to see you in the Netherlands as well! *The abstract submission deadline for the Galaxy Community Conference is Feb 28.* See http://galaxy.psu.edu/gcc2011/Abstracts.html -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/

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temp files for workflows
by Keith Sheppard 14 Feb '11

14 Feb '11

Hi All, I'm fairly new to galaxy and trying to understand it from both a user and tool developer perspective. Does galaxy have a way to mark tool outputs within a workflow as temporary (ie they should be deleted after the workflow finishes running)? If not is there some way to facilitate this as a tool developer? It's pretty frequent for us to have workflows where the intermediate tool output is not important and we would rather have the disk space. Thank you Keith

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fission yeast genome
by Sanjay P Khadayate 13 Feb '11

13 Feb '11

Dear Galaxy team, We would hereby like to request you to include Schizosaccharomyces pombe genome into the public and development version of galaxy. Here is the genome page http://www.sanger.ac.uk/Projects/S_pombe/ Thanks & Regards Sanjay

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entrez ID to Refseq or gene symbol
by Ajish George 12 Feb '11

12 Feb '11

Giovanni: The conversion table can be found at NCBI's FTP site for Entrez gene. ftp://ftp.ncbi.nih.gov/gene/DATA/gene2refseq.gz This should be updated daily and the EntrezID will correspond to the GeneID in this table. Just subset for the TaxID of c-elegans, 6239, and you should be able to pull out just what you need. -'jish -- Ajish D. George Postdoctoral Fellow Dept. of Genetics & Genomic Sciences Mt. Sinai School of Medicine 1425 Madison Ave, New York, NY 10029 > > ------------------------------ > > Message: 2 > Date: Thu, 10 Feb 2011 18:17:54 -0500 > From: giovanni stefani <giovanni.stefani(a)yale.edu> > To: galaxy-user(a)bx.psu.edu > Subject: [galaxy-user] entrez ID to Refseq or gene symbol > Message-ID: <0DEE6BFA-902B-4CA6-9582-8E5352A53E38(a)yale.edu> > Content-Type: text/plain; charset=us-ascii > > Hello, > > does anyone know how to convert entrez I.D. to either Refseq ID or Gene Symbols? > I have found resources on Refseq to Gene Symbol conversion, but I can't find anything on Entrez I.D. > The genome I work with is C. elegans. > Any suggestion will be greatly appreciated. > Best, > > Giovanni >

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Re: [galaxy-user] Running Tophat
by Jeremy Goecks 12 Feb '11

12 Feb '11

> > I have shared my hisotry with you yesterday, can you help me to take a look to > see what is the problem for my tophat analysis? Thank you very much! Ying, Unfortunately, your job is too large for our cluster. Our cluster has a limit of 250GB of disk space, and Tophat is exceeding this limit while running your job (Tophat generates many intermediary files when running, including a very large SAM file). Your best bet is to set up and use our cloud instance ( https://bitbucket.org/galaxy/galaxy-central/wiki/cloud ); otherwise, if you have enough resources locally, you can set up a local instance ( https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy ) . Thanks, J.

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