November 2013 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Tool XML form building bug with <options from_data_table="..."> ?
by damion＠learningpoint.ca 01 Nov '13

01 Nov '13

John, thanks for following up. I myself abashedly sent out a followup mail which maybe didn't get to this list (from the other galaxy-user(a)lists.bx.pu.edu list). Yes indeed, I'd closed my one-liner options tag. Problem fixed now. Regards, Damion ---------------------------------------- From: "John Chilton" <chilton(a)msi.umn.edu> Sent: 01 November 2013 09:48 To: Cc: "Galaxy Dev" <galaxy-dev(a)bx.psu.edu>, damion(a)learningpoint.ca Subject: Re: [galaxy-dev] Tool XML form building bug with <options from_data_table="..."> ? Hey Damion, Because this wasn't explicitly shown in your example e-mail, can you verify for me that you are putting the filter elements inside of the options element and not inside of the param element? -John

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Tool XML form building bug with <options from_data_table="..."> ?
by Jennifer Jackson 01 Nov '13

01 Nov '13

Moving this over to galaxy-dev(a)bx.psu.edu, the best list for tool design questions. Best! Jen, Galaxy team On 10/30/13 2:24 PM, damion(a)learningpoint.ca wrote: > Has anyone run into this? I'm building a general-purpose filter > control on my galaxy tool xml template for enabling numeric fields to > be filtered by > < etc. parameters - in a user friendly way. I have a > select list <para> driven by a data table: > ... > <param name="filter_column" type="select" label="Col"> > <options from_data_table="bccdc_blast_fields" /> > </param> > ... > This works fine in building a list of fields to select from. Then I add > <filter type="sort_by" column="1"/> > <filter type="add_value" name="TESTESTTEST" value="WHWHWHW" /> > > but nothing happens, sort remains incorrect and no extra value. I try > these same filters on a previous <param> in form that is driven > by <options from_file="bccdc_blast_bins.loc"> and they work fine. > > I also tried applying <fiilter type="static_value" ...> to no avail on > from_data_table options tag, but from from_file options, no problem. > > So I start to think there's a bug whereby NO filters work on <options > from_data_table="bccdc_blast_fields" /> input? I've surveyed the > galaxy.tools.parameters.dynamic_options > python code, but can't see a decision point there in which > from_data_table work vs from_file choice is made; is it in another > script file? > > I'm using a BioLinux 2012 install that includes Galaxy. > > Help appreciated! > > Regards, > > Damion Dooley > BC Centre for Disease Control > Vancouver, BC > > > ___________________________________________________________ > 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 http://galaxyproject.org

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Workflows with multiple editors
by Eric Rasche 01 Nov '13

01 Nov '13

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I'm working with a number of people in my department to develop a single workflow that will be used for a course we teach. So far I've found that "sharing" a workflow with individual users/roles isn't very optimal. They email me with changes they'd like to happen, or they create their own copies which immediately branch off and don't help everyone else who might need them. As such, I'd like to propose changes and would like community feedback on my proposed changes so when I create the trello card/maybe try my hand at implementing them, they aren't completely specific to my use case. In my mind, the 'optimal' version of managing workflows would be something along the following lines: Top priorities: - - workflows can be shared as "write" or "read only" with multiple users/roles. - This would allow there to be a single copy of a workflow in cases where multiple people might make changes to a single workflow - For "read only", this allows the previous/traditional model of sharing a workflow and the receiver being able to run it as is, or to copy and modify it. Note: For my case at least, realtime multiple person editing is not needed. If a banner shows up which reads "someone started editing before you, either ask them to save + leave or save as a copy" would work in my case. Wishlist features: - - workflows are treated as VCS repositories - Note that full merge/branching probably not really necessary for this case (that would be really nice, but probably too much of a nightmare to code...) - - You can see previous iterations of workflows. - - Workflows can be "owned" by either a user or a role - users could create a workflow and transfer ownership to a role - role owned workflows are delete-able (or maybe require some X% of users in that role to confirmation deletion?) - This would sort of work like a group owned VCS repository, where multiple users can create workflows of interest to a group of people (role) and have them, by default, be available. Anyone have input on this proposal? Cheers, Eric - -- Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr(a)tamu.edu rasche.eric(a)yandex.ru -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iQIcBAEBAgAGBQJScWXTAAoJEMqDXdrsMcpVFH4QAMO0V4tSJGzM3PGGIwdonY0v nyuHTCJJ5qliWuapUJUK9E0UQBblnaJYooLjh2l1vgo95JaXdHEAC9NVecQLH8J2 ey5cu1xODf6JmBGlicRGxQWlLZmo9U3R4T/OhHco40I239aTpuSDPcwcBJUm1cAE czz+/2pgdCpkJqYQJ9EE956TAYdyPBYFvSrIO7ebWkSvC5He40qca0x06tgq14uR Dta+8QH8brVYX1G+TAgdh3hGlLUwIlPMiZsWOEMcwSUtyXP3I7OKx/XIOy3ZYVTu Py/XlvNlZ87yiaiwDSxjxR9qaDeGQ3J8CRCG9mqWu8O5Y9QKkyrC410I+hZH5lE+ my28z7l5rK0i05pR6o8euASJ7D1eFHEDYmBmN6j3qRcOgzzdup2oQpm6TA7ue1sd NAS4rnW7QGmfNj+9xNSQhDWSj7CeIUeHXbDe55suBX3JofCNg8Qq6uYzPd7KGj7n jvWp8tGnpwbgTmvDPlR03gJiXMZld+gGwKrlCyn1kdBkfI1r5l0UfoaIUE+8HDm3 wXviQ8GU7seYU5bJFK798owVNawjY1H3JenzIYt1XvF1z53Uc39x58Q9lxXbVfSe KgiqCfF0YuvVtOczGTAQ57qCFwlpKg2ra+X+HtAZyMDNMsb3ANgfogTqsB+7HYvF czq2QJHq9mBC5N9JLhRo =conD -----END PGP SIGNATURE-----

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browse directories on galaxy server
by David Hoover 01 Nov '13

01 Nov '13

Is there any desire to create a way in galaxy to browse local directories on the galaxy server itself? Not the client machine running the web browwser, but the machine on which galaxy is running. I've created a tool that allows a user to upload a single file from their own personal directory on the galaxy server into galaxy directly, without going through Apache. However, this is very limiting. It would be very helpful to be able to browse directories that are deemed accessible to the galaxy user, and before I begin trying to develop anything I'd like to know if there is any support for such a feature. David Hoover Helix Systems Staff National Institutes of Health

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User activations
by jordi＠biociphers.org 01 Nov '13

01 Nov '13

Hi all, Recently I have updated our test galaxy server in order to check some new features like user email activation using emails. I saw that in the admin page http://wiki.galaxyproject.org/Admin/UserAccounts . But I download the last version and the conf values that are supose to be in the universe_wsgi.ini are not present ( at least in the sample file). Do you know if this is a future feature or there is anything I need to do for testing it? thanks everyone for your help Jordi

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