[galaxy-dev] Can't view file_name in histories via API unless admin?

2014-01-16 Thread Neil.Burdett
Hi, it seems that the entry "file_name:" does not appear when running the command /home/galaxy/milxcloud/scripts/api/display.py http://barium-rbh:9100/extras/api/histories/ebfb8f50c6abde6d/contents/4a56addbcc836c23 unless you are stated as as admin user in the "universe_wsgi.ini" i.e. admi

[galaxy-dev] Import workflows via API

2014-01-16 Thread Neil.Burdett
Hi, I execute workflows via the API. However, if I want another user to use my workflows, I can publish my workflows, but the new user then has to go on to the web browser and import this workflow. Is there a method/script which I can call via the API which can import all available (publish

Re: [galaxy-dev] making tools with Galaxy

2014-01-16 Thread Björn Grüning
Hi Lionel, here is a simple example of an graphicsmagic wrapper, that consumes an image and produce one. Maybe its useful for you. https://github.com/bgruening/galaxytools/tree/master/image_processing Cheers, Bjoern > Hello Lionel, > > Please send correspondence like this to the galaxy-dev@lis

Re: [galaxy-dev] making tools with Galaxy

2014-01-16 Thread Greg Von Kuster
Hello Lionel, Please send correspondence like this to the galaxy-dev@lists.bx.psu.edu mailing list rather than individual email accounts as doing so will ensure more timely and optimal repoonses. I'm not quite sure what code you are reading, so could you please clarify? In general, though, w

Re: [galaxy-dev] creating a hierarchy of students teachers and courses

2014-01-16 Thread Fernandez Edgar
Hello Dannon, You are right, I've just tried it and it is extremely lighter than my previous solution. I've successfully made a teacher share a complete history with her students and vice-versa a student sharing its history with teacher. Cordialement / Regards, Edgar Fernandez De : Dannon Bake

Re: [galaxy-dev] sanitize_all_html option

2014-01-16 Thread Lukasse, Pieter
Thanks Greg and John! I think the trello card summarizes it well. Looking forward to the solution ;) -Original Message- From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton Sent: woensdag 15 januari 2014 16:01 To: Greg Von Kuster Cc: Lukasse, Pieter; galaxy-dev

[galaxy-dev] moving galaxy instance to different location

2014-01-16 Thread Ido Tamir
Hi, I have to move my galaxy instance to a different file system location. Is there anything that I have to look out for besides the obvious like absolute paths in some data configs? thank you very much, ido ___ Please keep all replies o

Re: [galaxy-dev] "allow_user_impersonation" (was: creating a hierarchy of students teachers and courses)

2014-01-16 Thread Dannon Baker
Imagine that, actually two cards for it! On Thu, Jan 16, 2014 at 8:33 AM, John Chilton wrote: > Card exists and it has 10 votes, that is the most I have seen in a while. > > https://trello.com/c/zwqNwflD > > I have added myself as a member to the card, I will see if I can find > some time to wo

Re: [galaxy-dev] "allow_user_impersonation" (was: creating a hierarchy of students teachers and courses)

2014-01-16 Thread John Chilton
Card exists and it has 10 votes, that is the most I have seen in a while. https://trello.com/c/zwqNwflD I have added myself as a member to the card, I will see if I can find some time to work on this. -John On Thu, Jan 16, 2014 at 7:27 AM, Dannon Baker wrote: > On Thu, Jan 16, 2014 at 3:39 AM,

Re: [galaxy-dev] "allow_user_impersonation" (was: creating a hierarchy of students teachers and courses)

2014-01-16 Thread Dannon Baker
On Thu, Jan 16, 2014 at 3:39 AM, Hans-Rudolf Hotz wrote: > "allow_user_impersonation" does not work when using external > authentication. Are there any fixes for this in progress? > > If not shall I create a Trello card? > If there's no Trello card for it, I doubt it's currently being worked on.

Re: [galaxy-dev] creating a hierarchy of students teachers and courses

2014-01-16 Thread Dannon Baker
Would direct-sharing histories work as a significantly lighter weight solution? Each student could just create a history named "DannonBaker_SharedResults" or the like, share it directly with their instructor, and put via dataset copy and/or perform any work to be shared in that? -Dannon On Wed,

Re: [galaxy-dev] Avoid integrated_tool_panel.xml update

2014-01-16 Thread Björn Grüning
Hi Christian, afaik that is not possible. It is regenerated each time changes happen to your tool_conf files. Please have a closer look to: https://wiki.galaxyproject.org/GalaxyToolPanel#Managing_the_layout_of_your_Galaxy_tool_panel Hope that link helps to avoid some issues. Bjoern > Hi all, >

[galaxy-dev] "allow_user_impersonation" (was: creating a hierarchy of students teachers and courses)

2014-01-16 Thread Hans-Rudolf Hotz
Hi I am sorry for hijacking someone else's thread: 3. teachers having read access to students’ work This one is why I would give the teachers admin access - I think they could impersonate the students to access their work (set allow_user_impersonation = True in universe_wsgi.ini). It

Re: [galaxy-dev] Avoid integrated_tool_panel.xml update

2014-01-16 Thread Hans-Rudolf Hotz
Hi Christian Have a look at the file: .hgignore Regards, Hans-Rudolf On 01/16/2014 03:23 AM, Cristian Alejandro Rojas wrote: Hi all, There is a setting on somewhere to skip the integrated_tool_panel.xml file update? Best regards, -- *Cristian Alejandro Rojas Quintero* /*Estudiante Ingeni