- galaxy-dev - lists.galaxyproject.org

Html page in galaxy-dist
by Mohamed Kassam 08 Sep '16

08 Sep '16

Dear all, I've created different pages in html and php, and I put them in apache by changing the port. Now I changed the SSL certifcate and I moved galaxy web adress to https. However my other page are not recognized because they are still in http. Do you know where I can put my php and html pages in galay-dist can be picked up by apache like the welcome.html files then I can transfer them to https. Thanks in advance, Mohamed

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Converting an internal user to an external user
by Ryan G 07 Sep '16

07 Sep '16

Hi all - I'm having a problem with a user account and Galaxy getting confused with it being internal vs external. When we first set up galaxy, we were using Galaxy's internal authentication system. This worked well but all our users then had another password to keep track of. We activated external user authentication a few months ago and it works fine for us. This user hasn't logged in since and recently tried but is unable to. I discovered her account in Galaxy appears as an internal account eg created before we were using external authentication. Now that we have external authentication, Galaxy doesn't recognize her and she gets the user_disabled page whenever she tries to log in. Is there a way I can change her account in Galaxy from being an internal to an external account? Ryan

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History refresh in multi-thread mode and concurrent access
by Christophe Caron 06 Sep '16

06 Sep '16

Hi we run a Galaxy instance (16.04) in multi-thread mode ( 8 x web handler / 2 jobs handler) to manage scalability, with Apache in frontend, and a cluster (SGE like). We test the load of our infrastructure by running several workflows in simultaneous : 50 workflow with 35 steps (light cpu consuming for each steps) All jobs are successfull but some steps remain in grey (it seems jobs are really ended because the next streps runs), before to appear in green (no yellow). If we force the refresh history (refresh button on the interface), jobs appear in green. When we run only one (or 2:)) workflow, each workflow follow the chain : grey, yellow, green. Maybe, there is some mechanisms to optimize between web handler/apache and clients to avoid this and to get the right color status ? Any clue ? Thanks -- Christophe Caron INRA

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Development/production instances updates management
by Mathieu Bahin 06 Sep '16

06 Sep '16

Hi all, First of all, I'm new to this list and already posted my question on biostar. Thanks to Hans-Rudolf for his answer but I'm not sure we have exactly the same constraints here and I send this message to try to get other answers and see what is the best solution for us. I'm trying to setup a good galaxy environment for a biology institute. To do so, I need to have a development and a production instances that are clones on the structure side. I'd like to update regularly these instances (following more or less galaxy main updates) and track them with git repos. I'm pretty sure lot of galaxy admins are trying to do that but I can't find the answer. My idea was to have a local git repo to save the development instance (not the data). When there is a new update, I git pull it from galaxy GitHub, compare what changed in the sample files and make the appropriate changes in the config files corresponding to these samples. Then I would git push towards the production instance. To do so, I need to have a proper .gitignore file (listing especially the data files). I saw that there is a .gitignore in the galaxy GitHub repo. It's probably relevant when I want to pull the updates but I'm not sure it is regarding the transfers between the development and production instances (for example, the config files have to be tracked I guess). Cheers, Mathieu -- --------------------------------------------------------------------------------------- | Mathieu Bahin | IE CNRS | | Institut de Biologie de l'Ecole Normale Supérieure (IBENS) | Biocomp team | 46 rue d'Ulm | 75230 PARIS CEDEX 05 | 01.44.32.23.56 ---------------------------------------------------------------------------------------

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September 2016 Galactic News
by Dave Clements 06 Sep '16

06 Sep '16

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Galaxy Tools XSD - searching for help!
by Björn Grüning 05 Sep '16

05 Sep '16

Dear community, is there someone that is familiar with XSD files and validating XML files? We need help in updating our Galaxy Tools XSD file: https://github.com/galaxyproject/Galaxy-XSD/blob/master/galaxy.xsd The idea is to auto generate documentation out of it and improve planemo lint. If you have these skills please get in touch with us :) Thanks! Bjoern

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Galaxy Docker 16.07
by Björn Grüning 04 Sep '16

04 Sep '16

Hi all! We are proud to present you the next release of our Galaxy Docker Image. https://github.com/bgruening/docker-galaxy-stable/releases/tag/16.07 https://registry.hub.docker.com/u/bgruening/galaxy-stable/ A few highlights: * based on Galaxy 16.07, with all it's new features and enhancements * SFTP Integration (by Alexander Lenail) * enhanced SLURM documentation (by Marius van den Beek) * initial Docker compose support Moreover, our workshop slides with a general Docker introduction and how to manage the Galaxy Docker container is available here: https://galaxy.slides.com/bgruening/the-galaxy-docker-project/live#/ Don't forget to checkout our general readme file: https://github.com/bgruening/docker-galaxy-stable/blob/master/README.md Thanks to all contributors [1] and enjoy this release! Bjoern [1] https://github.com/bgruening/docker-galaxy-stable/graphs/contributors

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Re: [galaxy-dev] how to create users through Galaxy API?
by Martin Čech 03 Sep '16

03 Sep '16

Hi, you specify username, password and email in the body (payload) of the POST as Key:Value pairs. Code from the API method: ( https://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/webapps/ga…) username = payload[ 'username' ] email = payload[ 'email' ] password = payload[ 'password' ] There are also other conditions that need to be fulfilled (e.g. user creation has to be turned on in the configuration) - you will find these when you look at the source code of the method (because the documentation is not perfect yet, sorry). M. On Sun, Dec 29, 2013 at 11:22 PM, xlwang <xlwang_0903(a)163.com> wrote: > hi, > I still have some confusion. > post /api/users , when i use postman, it seems like this: > > > No other parameters? How to confirm the new user's information?Such as > user name, password. > Can you give me a example please?Thank you! > > At 2013-12-30 06:04:15,"Martin Čech" <marten(a)bx.psu.edu> wrote: > > Hello, > > to create a user through API you send a POST request to /api/users > > More information about User API here: > > > https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.… > > Martin > > > On Fri, Dec 27, 2013 at 5:11 AM, xlwang <xlwang_0903(a)163.com> wrote: > >> hello, >> I want to create users through Galaxy API.For example, I can get users >> information through url like this(use postman): >> http://localhost:8080/api/users?key=my_key >> But how to create a user? >> >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. 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/ >> > > > >

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Send repeat parameter to code file for multiple select list
by Katherine Beaulieu 03 Sep '16

03 Sep '16

Hello Galaxy Community, I was wondering if anyone had ever come across a situation where they have had to pass the contents of a repeat parameter to a code file in a Galaxy tool config? Is there any way to do this? Katherine

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Testtoolshed status
by Steve Cassidy 02 Sep '16

02 Sep '16

I’m getting a 500 response from the testtoolshed when I try to upload a tool via planemo: ➜ alveo-galaxy-tools git:(master) ✗ planemo shed_update --shed_target testtoolshed apitools cd '/Users/steve/projects/alveo-galaxy-tools/apitools' && git rev-parse HEAD cd '/Users/steve/projects/alveo-galaxy-tools/apitools' && git diff --quiet Could not update alveoimport Unexpected HTTP status code: 500: <html> <head><title>Internal Server Error</title></head> <body> <h1>Internal Server Error</h1> <p>The server has either erred or is incapable of performing the requested operation. <br/> </p> <hr noshade> <div align="right">WSGI Server</div> </body> </html> Repository metadata updated successfully for repository alveoimport. Failed to update a repository. In addition, I just got a “Tool Shed could not be reached” message via the web interface, so i’m wondering if something is up. Thanks, Steve — Department of Computing, Macquarie University http://web.science.mq.edu.au/~cassidy

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