[galaxy-dev] Trying to install GATK on up-to-date Galaxy install

I seem to run into a bottleneck with the .’package_pixman_0_32_4’. This seems to happen with both boris and devteam versions? The same error is preventing cairo from installing. libpng

[galaxy-dev] R: Planemo 0.19.0 testing tools that produce dataset collections

Hi Greg, in the inputs the param has name "input_gff", while in the test you are using name "input". Cheers, Nicola Von Kuster, Greg ha scritto >Hello Galaxy devs, > >I’m developing a tool that uses a multi-select list to accept any number of >input datasets. The tool works fine w

[galaxy-dev] Planemo 0.19.0 testing tools that produce dataset collections

Hello Galaxy devs, I’m developing a tool that uses a multi-select list to accept any number of input datasets. The tool works fine when executing it within Galaxy, but when running it through planemo testing, it never passes, so I’m wondering if there are known issues with planemo testing tool

Re: [galaxy-dev] installable revisions for repository suite definitions

Okay, that makes sense. I'll switch over to making sure each tool dependency is in a separate repository with version names. It was just one repo which we were updating a lot that ended up with multiple versions so it's an easy thing to do. Thanks, Aaron On Wed, Nov 4, 2015 at 12:18 PM, Marti

[galaxy-dev] GCC2016 Training Topic Voting CLOSES THIS FRIDAY

Hello all, *Voting * on what training topics are offered at GCC2016 Training *closes this Friday*. Please vote in the next two d

Re: [galaxy-dev] installable revisions for repository suite definitions

Hi Aaron, I think Galaxy will always install the latest revision of the selected installable revision. Our approach was that tool dependencies have versioned repositories (with versions in the names) so that it cannot happen that abyss 2.0 would be in the package_abyss_1_9_0 repo. With this in pla

Re: [galaxy-dev] installable revisions for repository suite definitions

Thanks Martin, that helps me out. However, the issue I'm running into is that it seems like specific revisions in my repository suite definition are being ignored and it's only using the latest one. I think what may be happening is as follows. In my repository suite I have a dependency like: ht

Re: [galaxy-dev] support for newer versions of Torque

Any suggestions on how to handle this? Without being to integrate Galaxy with our queuing system it's hard to use it as a production environment. Cheers, Malcolm On Friday, October 30, 2015 08:16:17 AM Malcolm Tobias wrote: > I'm having trouble "scrambling my eggs". > > I'm trying to build PB

Re: [galaxy-dev] installable revisions for repository suite definitions

Hi Aaron, we touched this recently here: https://github.com/galaxyproject/tools-devteam/pull/267 I believe that if you specify the repository_dependencies.xml of your suite in the following way: http://toolshed.g2.bx.psu.edu"; /> you will pin the exact revision of the tool (fasta_clipping_hist

Re: [galaxy-dev] Galaxy Startup Failing

Hi Will, I tried that and it didn’t work for me. Are you using start-stop-daemon to launch python? Or do you run “python scripts/paster.py serve” from /etc/init.d/galaxy? If I use start-stop-daemon then python does not seem to be picking up the .venv. I suspect it has something to do with .

Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused

I am not very good with Apache rewrite rules, but I think there is a problem with (at least) the first rule. I see in the Apache documentation [1] that the following “doesn’t make sense, not supported": ^/somepath(.*) http://thishost/otherpath$1 [P] The [P] flag is for forwarding to a proxy, b

Re: [galaxy-dev] installable revisions for repository suite definitions

Okay, thanks Dave. That makes sense. Moving forward I'll just make a new suite with a version number in the name. Another question, does the same apply for tool dependency definitions? I've upgraded a suite of tools + dependency definitions, and now even if I make a new repository suite (to allo

Re: [galaxy-dev] login problem (redirection to the login page)

Update : When I clic several time on the galaxy name, I got this on the log : Exception happened during processing of request from ('127.0.0.1', 45055) Traceback (most recent call last): File path/to/galaxy-master/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_i

Re: [galaxy-dev] login problem (redirection to the login page)

Here is some details : when I enable the access to Galaxy without authentication I'm redirected to the welcome page, but still I'm not connected (I can login/register) 2015-11-04 14:42 GMT+01:00 Floreline TOUCHARD : > Thanks for the "bidouille" ;) > > It didn't work for me. > I have my Galaxy in

[galaxy-dev] FASTQ Groomer tool

Hello gents, I just installed "FASTQ Groomer tool" for the teachers to try it out and I've been getting the following error than I do not understand: galaxy.jobs DEBUG 2015-11-04 08:16:19,957 (756) Working directory for job is: /home/galaxy/galaxy-prod/database/job_working_directory/000/756 gal

Re: [galaxy-dev] login problem (redirection to the login page)

Thanks for the "bidouille" ;) It didn't work for me. I have my Galaxy instance configured to run jobs on a cluster. I don't know where the problem come from. 2015-11-04 14:19 GMT+01:00 Yvan Le Bras : > Hi Floreline, > > Did you use several workers and/or handler ? I have had the same issue on >

Re: [galaxy-dev] login problem (redirection to the login page)

Hi Floreline, Did you use several workers and/or handler ? I have had the same issue on Galaxy instances from our cloud, and a "not beautiful manner" I found to succeed authenticate was to clic several times on the galaxy name (top left of your instance) to force reload the page before login..

[galaxy-dev] login problem (redirection to the login page)

Hi, this is not the first time I encounter this problem : I change the authentication mode (external to internal). And since then I cannot login with any account. Each time I'm redirected to the login page. Yet I haven't any log error. I have the galaxy-master 15.07 version. I cleared the firefox

Re: [galaxy-dev] Galaxy on Centos via Apache - connection refused

So yeah you might be on to something here. When I commented the Rewrite rules I could access my galaxy instance from myservername:8081 with or without the index.html file placed in /var/www/html. When I did place it in the directory though and I tried with the rewrite rules my server gave me the

Re: [galaxy-dev] atlas 3.10 IUC error

Thanks Peter, Nicola, Ok, I'll try to switch on an 64bits computer then, maybe there's some other errors due to this. Thanks a lot. Olivier -Message d'origine- De : Peter Cock [mailto:p.j.a.c...@googlemail.com] Envoyé : mardi 3 novembre 2015 19:24 À : o.cla...@outlook.fr Cc : Nicola So