Re: [galaxy-dev] Setting up Galaxy without e-mail

Hi Dannon, On Thu, Jul 30, 2015 at 4:28 AM, Dannon Baker dannon.ba...@gmail.com wrote: Regarding activation, you mean you set user_activation_on = True, right? You can just leave 'user_activation_on = False', which is the default (and the value if left commented), which will disable any

[galaxy-dev] Working with SLURM (same partition as cmd line)?

Hi all, I was wondering if anyone has experience with setting up Galaxy with SLURM. I'm not sure if this is the same for other DRMAAs, but what I would like to do is use a server for both Galaxy and command-line job execution. Thus, I would like both to add jobs on to the *same* queue (i.e.,

Re: [galaxy-dev] Advice on Galaxy administration

advice! Ray On Wed, Sep 23, 2015 at 12:12 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote: > On Tue, Sep 22, 2015 at 4:38 PM, Raymond Wan <rwan.w...@gmail.com> wrote: >> Hi Peter, >> >> >> On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock <p.j.a.c...@googlema

Re: [galaxy-dev] Advice on Galaxy administration

Hi Peter, On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock wrote: > Hi Ray, > > You will absolutely need command line access to the Galaxy > server for some of the administration tasks - the web admin > controls and web report tool only let you do some of the likely >

Re: [galaxy-dev] Apache proxy under Ubuntu

Hi Mic, On Wed, Dec 16, 2015 at 10:35 AM, Mic wrote: > Where do I insert the following settings? > > RewriteEngine on > RewriteRule ^/static/style/(.*) > /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L] ... They should probably go in

Re: [galaxy-dev] Error installing cummeRbund tool

of problem in the Tool Shed? Thank you for your help! Ray On Fri, Jun 3, 2016 at 1:08 AM, Raymond Wan <rwan.w...@gmail.com> wrote: > Dear all, > > I'm trying to install a Galaxy tool (cummeRbund; the one from devteam) > and I'm getting the following error during installation:

Re: [galaxy-dev] Error installing cummeRbund tool

managed by the Galaxy developers > themselves, then reporting it on this mailing list should also > reach the relevant people.) > > Peter > > > On Tue, Jun 7, 2016 at 4:40 AM, Raymond Wan <rwan.w...@gmail.com> wrote: >> Dear all, >> >> Sorry to bring thi

[galaxy-dev] Error running JBrowse

Dear all, I'm trying to run the JBrowse tool within Galaxy. The installation was fine (I think), but when I run the tool, I get this error: Fatal error: Exit code 1 () Traceback (most recent call last): File

Re: [galaxy-dev] Bypassing Data Managers?

ery long. Since I have the FASTA file already, it might be easier to upload one myself; but if that's not something Data Managers can do, I guess I can just start the download and set it aside... Thank you! Ray On Thu, Feb 18, 2016 at 8:36 AM, Raymond Wan <rwan.w...@gmail.com> wrote: >

Re: [galaxy-dev] Bypassing Data Managers?

n (and which is >> unrelated to Galaxy), download times are very long. Since I have the >> FASTA file already, it might be easier to upload one myself; but if >> that's not something Data Managers can do, I guess I can just start >> the download and set it aside... >> >>

Re: [galaxy-dev] Bypassing Data Managers?

Hi Peter, On Thu, Feb 18, 2016 at 4:13 PM, Peter van Heusden wrote: > Hi Ray > > Data Managers are designed to co-exist with manually editing the .loc files. > So don't worry, edit away. Thank you for the clarification! That made me feel better and I pressed ahead and just

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

Hi Peter, On Tue, May 24, 2016 at 6:29 PM, Peter Cock wrote: > In case you didn't know, Galaxy likes to keep all BAM files in > coordinate sorted order with a BAI index (using samtools). > Somehow this is failing on your system (perhaps a suitable > version of

[galaxy-dev] Unsorted BAM file --> Galaxy crash?

Dear all, We are experiencing a crash of our Galaxy instance (latest git log is early January 2016) and it seems unable to restart. The last entries in paster.log says the following: galaxy.web.framework.base DEBUG 2016-05-24 17:46:42,593 Enabling 'histories' API controller, class:

Re: [galaxy-dev] Allow users to see the job queue?

age. > > This is probably the easiest way - though you need to consider, that all > users can see each other jobs (i.e the executed command line) on that extra > web site > > > Regards, Hans-Rudolf > > > > > On 04/15/2016 09:22 AM, Raymond Wan wrot

Re: [galaxy-dev] Trying to understand python dependencies

Hi Anthony, On Wed, Jul 27, 2016 at 11:16 PM, Tony Schreiner wrote: > I have galaxy server 15.10 running on Ubuntu 14.04, which has python 2.7.5. > > I was in the process of adding matplotlib from the toolchest. It has a > dependency on package_python_2_7. > > Before

Re: [galaxy-dev] showing progress on running tasks

Hi Ryan, On Sat, Jul 9, 2016 at 12:40 AM, Ryan G wrote: > Hi Martin - I was actually thinking to let the tool itself tell Galaxy about > the progress instead of Galaxy estimating that. > > If instance, if the tool know it has 5 stages, it can report back to Galaxy >

Re: [galaxy-dev] Error running JBrowse

Hi Eric, On Wed, Aug 17, 2016 at 4:31 AM, Eric Rasche <e...@tamu.edu> wrote: > Hi Ray, > > Sorry I missed this mail. No problem! Thanks for getting back to me! > On 23. juni 2016 10:27, Raymond Wan wrote: > I'm trying to run the JBrowse tool within Galaxy. The insta

Re: [galaxy-dev] apache on ubuntu

Hi Jochen, On Fri, Sep 2, 2016 at 8:32 PM, Jochen Bick wrote: > yes exactly. So my problem is that I have no idea where to copy those > settings. I have tutorial how it works on Centos but the file structure is > different on Ubuntu. Slightly different, but not too

Re: [galaxy-dev] apache on ubuntu

Hi Jochen, On Sat, Sep 3, 2016 at 2:31 AM, Bick Jochen wrote: > RewriteEngine on > RewriteRule ^(.*) http://localhost:8080$1 [P] ... > but it does not have any effect. Here the error.log but there is no error: > [Fri Sep 02 15:28:21.677881 2016]

Re: [galaxy-dev] apache on ubuntu

Hi Jochen, I presume you looked at this already: https://wiki.galaxyproject.org/Admin/Config/ApacheProxy Those instructions work for Ubuntu as well. What do your Apache2 error logs says (in /var/log/apache2/)? And what have you tried in your configuration files? And are you trying to forward