galaxy-user December 2011

galaxy-user@lists.galaxyproject.org

63 participants
78 discussions

upload files
by Bao-Hua Song 05 Dec '11

05 Dec '11

Dear Galaxy experts, I have a question regarding uploading my illumina data (over 3G) using FTP. It was not uploaded completely and stopped. I tried a couple of times..still not working. Can anyone tell me what can cause the problems? Many thanks, Bao

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public interface issues
by Cittaro Davide 05 Dec '11

05 Dec '11

Hi all, I can't use the public interface in an effective way: items in history (i.e. the green boxes) cannot be expanded. More important, names of the items remind me something that has to deal with the tool/library path (e.g. 2010_03/pilot2/README_pilot2_snps). This happens on OS X and MS Windows systems, Firefox and Safari. Thanks d /* Davide Cittaro, PhD Head of Bioinformatics Core Center for Translational Genomics and Bioinformatics San Raffaele Scientific Institute Via Olgettina 58 20132 Milano Italy Office: +39 02 26439140 Mail: cittaro.davide(a)hsr.it<mailto:cittaro.davide@hsr.it> Skype: daweonline */

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Re: [galaxy-user] problems loading galaxy histories
by Dave Clements 05 Dec '11

05 Dec '11

Dear Gretel, I am copying this question to the Galaxy-User mailing list, which is the best place to discuss it. Also, see http://galaxyproject.org/wiki/Supportfor other ways to get information. Can you post some additional information to this thread? In particular: * What steps are missing from the histories? Do the steps have anything in common? * Are you trying to view histories that were created on, and have always been stored, on the public Galaxy list; or are you loading a history into that server that was exported from another Galaxy Server? Thanks, Dave C. On Mon, Dec 5, 2011 at 7:26 AM, Gretel Kamm <grtkamm(a)gmx.net> wrote: > Dear Dave Clements, > > I am writing to you because I have been having some problems loading my > user histories at galaxy site. I can log to my count but there are just > some tracks available (the rest of them are not displayed). I don't know > where the problem could be? Perhaps it is the size of the tracks. If that > were the problem, I could delete some of them (if I could see them). I > would appreciate any help you could give me. > > > Regard, > > Gretel Kamm > > > > -- > > Lic. Gretel Kamm > > INGEBI-CONICET > > Vuelta de Obligado 2490 > > 1428 Buenos Aires > > 4783-2871 int. 15 > > Fax 4786-8578 > > e-mail kamm(a)dna.uba.ar > > > NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie! > Jetzt informieren: http://www.gmx.net/de/go/freephone > > > -- > > Lic. Gretel Kamm > > INGEBI-CONICET > > Vuelta de Obligado 2490 > > 1428 Buenos Aires > > 4783-2871 int. 15 > > Fax 4786-8578 > > e-mail kamm(a)dna.uba.ar > > > Empfehlen Sie GMX DSL Ihren Freunden und Bekannten und wir > belohnen Sie mit bis zu 50,- Euro! https://freundschaftswerbung.gmx.de > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

2 2

Request to Add Reference Genome
by Matthew Biggs 05 Dec '11

05 Dec '11

Hello Galaxy Team, I am writing to request that the genome of *Sinorhizobium meliloti *1021 be added to the "Map with Bowtie for Illumina" tool. I am using the main server http://main.g2.bx.psu.edu/ and my user name is mbiggs. Please let me know if this email is received. Thanks, Matt Biggs

2 1

Define a path for the command files
by Toqa Manasrah 05 Dec '11

05 Dec '11

Hi everybody, I am integrating a new tool which depends on several other libraries (part of the tool). when galaxy run my tool, it can find main command but not the deepest. where should I define the path of the libraries and command folders I need. by teh way, all these commands and libraries are copied inside the tool directory. Thank you,

2 2

there was a wrong link in my previous mail - gtf file issues
by Noa Sher 04 Dec '11

04 Dec '11

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Problem creating GTF file for use with cufflinks
by Noa Sher 04 Dec '11

04 Dec '11

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Galaxy-Announce: A new, moderated, low-volume Galaxy Mailing List
by Dave Clements 02 Dec '11

02 Dec '11

Hello all, There is a new mailing list in the Galaxy: Galaxy-Announce. Galaxy-Announce is a *moderated, low-volume *mailing list. Galaxy-Announce complements the existing Galaxy-User (about the public server at UseGalaxy.org) and Galaxy-Dev (deployment and development) mailing lists. However, unlike those relatively high-volume mailing lists, Galaxy-Announce will only have a few messages each month. If you are looking for a Galaxy list that just covers the big stuff, this is your list. To subscribe to the list please add your email address to the list here: http://lists.bx.psu.edu/listinfo/galaxy-announce See http://wiki.g2.bx.psu.edu/Mailing%20Lists for more information on this and other Galaxy mailing lists, including links to searchable archives of all Galaxy lists. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/

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galaxy-user December 2011