September 2016 - galaxy-dev - lists.galaxyproject.org

Can't display tools in the middle panel of Galaxy
by Stephanie LE GRAS 13 Sep '16

13 Sep '16

Hi there (again again), The last problem we are facing is that sometime when clicking on a tool name in the tool panel, the form don’t get displayed in the middle panel. We’ve checked the log of galaxy and it seems that the HTML request arrives but nothing happens. We have noticed that this seems to occur more ofter when the history is empty and we can correct the phenomenon if we use a non empty url such as : http://use.galaxeast.fr/root?job_id=c72a8935c65f68c1 or if we load an history and click on the [i] (view details) of a dataset. Versions of Galaxy : release_16.04 (production instance), release_16.07 (test instance). Any idea about what the problem can be ? Many thanks in advance for any help, Best regards, Stephanie -- Stephanie Le Gras INSERM Computational scientist - Bioinformatician GenomEast platform (former Microarray and Sequencing platform) IGBMC 1, rue Laurent Fries 67404 ILLKIRCH Cedex France Tel. : +33 (0)3 88 65 32 73

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Galaxy Proteomics Hackathon
by Björn Grüning 09 Sep '16

09 Sep '16

Hi all! I would like to spread the news from the GalaxyP team about a new hackthon. Please join and help us if you have some time! ********************* The first Galaxy-P CONDA hackathon will be held on September 27th and 28th. Galaxy-P and proteomics tool developers will participate in this hackathon to "CONDA-package" some of the prioritized proteomics tools within Galaxy. The hackathon will be an online event which will start with an introduction to Galaxy structure and CONDA packaging by Bjoern Gruening. https://github.com/galaxyproteomics/tools-galaxyp/issues/57 Details soon. Please see if you would like to publicize this. Thanks and Regards, Pratik

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delete user and all trace of user
by Fernandez Edgar 09 Sep '16

09 Sep '16

Hello gents! I’ve successfully got my version 16.04 up and running and everything is still there (user, groups roles, data and tools). Unfortunately , I’m still having a problem with deleting a user. I’ve purge him and then I deleted him. but, he still shows up in my list of users as "purged". Is there a way to completely remove him from galaxy? Do I need to run a script in a cron job to clean my galaxy periodically? Thanks in advance! Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON ROGER-GAUDRY, bureau X-210 • Bur. : 1-514-343-6111 poste 16568

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How to set up handler and web server process within a virtual machine
by Katherine Beaulieu 08 Sep '16

08 Sep '16

Hi Everyone, I am looking to set up a web server and handler process for galaxy within a virtual machine. I've tried following the instructions written here: https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling#Starting_an… But, I can still start Galaxy with sh run.sh, also the commands associated with supervisord don't seem to work, I keep getting this error: "Error: positional arguments are not supported:" Lastly, how can I confirm that this is working? Will I see two 'python' processes running when I run top? Katherine

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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 05 Sep '16

05 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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