- galaxy-user - lists.galaxyproject.org

Tool without input parameters
by Jelle Scholtalbers 15 Jan '10

15 Jan '10

Hi, Is there a way to provide a tool through galaxy that doesn't need any input parameters? If I just don't specify a parameter I get an error: "AttributeError: Tool instance has no attribute 'inputs'" Specifying a hidden input parameter will load the xml, but in galaxy it won't show a tool overview or execute the tool for you when you click on its name. Cheers, Jelle

2 1

Is there any way to calculate % AT or GC of a group of sequences?
by Noa Sher 13 Jan '10

13 Jan '10

I am looking at a file of peaks from ChIP-chip data and would like to know whether there is a way to take all the sequeneces associated with these peaks and to calculate the total %AT and %GC, to see if there is enrichment compared with the entire genome? Thanks Noa

2 1

Re: [galaxy-user] Suggestion on functionality for published workflows
by Jeremy Goecks 12 Jan '10

12 Jan '10

Hi Assaf, I'm cc'ing the galaxy-user list because this is a good discussion to have and because this is good information to share. To your questions: > I make a history 'importable via link' and it appears on the public list, but what's now ? > how does somebody else import it ? there's no clickable URL or button. First, to be clear: we've not broken/replaced/removed any functionality with any recent changes; these changes provide enhancements. I assume we're starting from the history grid. When you make a history importable from the grid, you can see the link to its public location by clicking on the text "importable" in the history's status column. This link takes you to a page where you can see two links for each importable history: a link for importing the history and a link for viewing the history. The view link takes you to a page where you can view the history *or* import the history (there's a link at the top of the page to import it). > Also, > will there be a way to make a history importable but *not* public ? > I use the 'import' link a lot, but I don't want to make my histories public for everyone. This is a difficult issue and one that's in flux and open for discussion. Right now, when you make a history importable, it is public in the sense that anyone can import it. Yes, they have to know the history's encoded ID, but "security through obscurity" is not a model that Galaxy employs. If someone wants to share a history with a limited subset of people and keep the history private, they can do so via the history sharing mechanism. Because "enable import" already makes a history accessible by everyone, it is reasonable that doing so makes the history "public." The basic sharing categories, then, haven't changed. What's changed, of course, is that Galaxy now makes it possible to find public/importable items. As I said, we're in the process of changing the history sharing language to make clearer what is happening; hopefully these changes will help users decide when to make a history public and when to share it with a limited set of other people. Another option is to allow users to make a history public but hide it from the list of public items. This is effectively what making a history importable does, and it's not a great solution. FYI, there are distinct advantages when users can view a history rather than having to import it: (a) it's less work to view the history; (b) it's not necessary to clutter your histories with imported histories; (c) it's not necessary to understand how to use Galaxy to view a history; and (d) users can (eventually) annotate/rate/comment on shared/public histories, thereby providing a single place to work with a shared history. Best, J. On Jan 12, 2010, at 12:41 PM, Assaf Gordon wrote: > Hello Jeremy, > > I must be missing something: > I make a history 'importable via link' and it appears on the public list, but what's now ? > how does somebody else import it ? there's no clickable URL or button. > > Also, > will there be a way to make a history importable but *not* public ? > I use the 'import' link a lot, but I don't want to make my histories public for everyone. > > Thanks, > -gordon > > > > Jeremy Goecks wrote, On 01/12/2010 11:55 AM: >> Hi Tim, >> >> A progress report: we've put in place much of the infrastructure for >> viewing and searching public items in Galaxy. On our main server, there >> are now lists of public histories and public pages (with pages you can >> author webpages using different Galaxy objects, including histories and >> (soon) workflows): >> >> http://main.g2.bx.psu.edu/history/list_public >> http://main.g2.bx.psu.edu/page/list_published >> >> The list of public workflows will show up in the next week or so: >> >> http://main.g2.bx.psu.edu/workflow/list_public >> >> Local instances of Galaxy have their own lists of public items as well. >> We'll publicize these lists/links in coming iterations of Galaxy. >> >> However, please note that these lists are not (currently) retroactive; >> only histories/pages/workflows shared after these lists were put in >> place are visible. Hence, as of now, there are no public histories on >> main. To make a history/workflow public, the owner must "enable import >> by link"; we're in the process of updating this language to make it >> clearer what it means to make public and/or enable import by link. >> >> There is the ability to tag public items as well and search on item >> name, owner, and tag. There is not a description field for items yet, >> but this is coming soon. >> >> Thanks much for your input; keep it coming. >> >> Best, >> J. >> >> >> >> On Tue, Nov 10, 2009 at 5:36 PM, Timothy Hughes >> <timothy.hughes(a)medisin.uio.no <mailto:timothy.hughes@medisin.uio.no>> >> wrote: >> >> I have heard from jgoecks <http://bitbucket.org/jgoecks/> that the >> galaxy team are working on a repository for all galaxy objects. I >> would like to suggest that all workflows that are shared publically >> (published) have a mandatory field that briefly describes their >> functionality and that the repository have search functionality >> which enables a search of published workflows using this field. I am >> sure their are loads of great workflows out there which are either >> immediately usable or are easily adaptable. Getting access to such >> workflows would also be an excellent way to learn Galaxy in a >> complementary way to the screencasts. >> >> >> While we are waiting for such functionality, perhaps Galaxy >> developers could set up a simple page where the public histories / >> workflows can be posted. The simplest solution might be just a check >> box on the sharing page ("post link to publicly accessible page"), >> alternatively just a piece of text on the sharing page encouraging >> users to manually post on specific forum or mailing list. >> >> Tim. >> >> -- >> Tim Hughes PhD (http://digitised.info) >> Medical Genetics Department >> Oslo University Hospital Ullevål >> Kirkeveien 166 >> 0407 Oslo >> Norway >> >> >> >> _______________________________________________ >> galaxy-user mailing list >> galaxy-user(a)lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu> >> http://lists.bx.psu.edu/listinfo/galaxy-user >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> galaxy-user mailing list >> galaxy-user(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-user > >

2 3

Suggestion on functionality for published workflows
by Timothy Hughes 12 Jan '10

12 Jan '10

I have heard from jgoecks <http://bitbucket.org/jgoecks/> that the galaxy team are working on a repository for all galaxy objects. I would like to suggest that all workflows that are shared publically (published) have a mandatory field that briefly describes their functionality and that the repository have search functionality which enables a search of published workflows using this field. I am sure their are loads of great workflows out there which are either immediately usable or are easily adaptable. Getting access to such workflows would also be an excellent way to learn Galaxy in a complementary way to the screencasts. While we are waiting for such functionality, perhaps Galaxy developers could set up a simple page where the public histories / workflows can be posted. The simplest solution might be just a check box on the sharing page ("post link to publicly accessible page"), alternatively just a piece of text on the sharing page encouraging users to manually post on specific forum or mailing list. Tim. -- Tim Hughes PhD (http://digitised.info) Medical Genetics Department Oslo University Hospital Ullevål Kirkeveien 166 0407 Oslo Norway

3 2

Fetching promoters
by Linda Barnum 08 Jan '10

08 Jan '10

Hello, Is there a way to fetch the promoter regions for homologous genes from different species. E.g. say I'd like to fetch the promoter region for a drosophila gene CG13222 from drosophila as well as its CG13222 homologues in other flies from UCSC genome browser? Thanks, Lin

3 2

Galaxy and GMOD at PAG
by Dave Clements, GMOD Help Desk 06 Jan '10

06 Jan '10

Hello all, GMOD will once again have a strong presence at the Plant and Animal Genome Conference (PAG 2010), being held January 9-13 in San Diego. There will be over 45 talks, workshops, demonstrations and posters about GMOD Components and projects that use them. This includes a workshop on Galaxy: Animal Genomics With Galaxy: Analyze, Publish, And Visualize Saturday, Jan 9, 1:30-2-30, California Room Anton will be presenting the workshop. See the PAG 2010 page on the GMOD wiki for a full listing and a flier showing highlights: http://gmod.org/wiki/PAG_2010 If you are attending PAG, please consider going to this and the other GMOD-related presentations. Thanks, Dave C. -- Please keep responses on the list! http://gmod.org/wiki/January_2010_GMOD_Meeting http://gmod.org/wiki/GMOD_News Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback

2 1

reduced datasets
by Douglas Rhoads 26 Dec '09

26 Dec '09

In the Metagenomic Analysis tutorial they used a reduced dataset to speed things up. I am going to be using Galaxy as part of my hands-on Genomics and Bioinformatics course. In the lab portion, students (20-30) will be doing their own analyses. If everyone is trying to do a full dataset on the Windshield Splatter we will never get done with the Megablast. Is there a simple way, maybe using Galaxy to reduce the size of the 454 data and QV? Even if I have to make the reduced data sets myself.

2 1

Reduced Dataset
by drhoads＠uark.edu 25 Dec '09

25 Dec '09

In the Metagenomic Analysis tutorial they used a reduced dataset to speed things up. I am going to be using Galaxy as part of my hands- on Genomics and Bioinformatics course. In the lab portion, students (20-30) will be doing their own analyses. If everyone is trying to do a full dataset on the Windshield Splatter we will never get done with the Megablast. Is there a simple way, maybe using Galaxy to reduce the size of the 454 data and QV? Even if I have to make the reduced data sets myself. Douglas Rhoads, Professor of Biological Sciences Director of Graduate Program in Cell and Molecular Biology 601 SCEN, Dept. of Biological Sciences, 1 University of Arkansas, Fayetteville, AR 72701 drhoads(at)uark.edu, http://biscweb.uark.edu/drhoads phone: 479-575-3251 FAX: 479-575-4010

1 0

Re: [galaxy-user] Fetching promoters
by Anton Nekrutenko 25 Dec '09

25 Dec '09

Yes. This will be happening shortly. a. On Dec 25, 2009, at 1:14 PM, Linda Barnum wrote: > is there any plan to update the dm2 build to dm3 in Galaxy? Anton Nekrutenko http://nekrut.bx.psu.edu http://galaxyproject.org

1 0

Dataset visivility policy
by MORITA Hideyuki 25 Dec '09

25 Dec '09

Hi, In Galaxy demonstrated now, everyone can see data, if they can know URL. (e.g. http://main.g2.bx.psu.edu/datasets/**********/display/) A user can set the permission to the dataset with "edit attibutes". However, it is not effective for above-mentioned URL. I am expecting as default function that only I can see the data that I made. And, I think it is insufficient only to make it to a difficult forecast of the ID part of URL. Please tell me your policies concerning the data visibility. And, do you have the plan to implement the function that I expect it? Thanks. MORITA Hideyuki.

2 2