Re: [galaxy-dev] Docker for Mac

Hi Philipp I have successfully used "Docker for Mac (beta)” on 10.11.5, but I have always used the traditional location for the image to fetch from: https://index.docker.io/u/bgruening/galaxy-stable/ (i.e just following the excellent

Re: [galaxy-dev] Docker for Mac

Hi Hans-Rudolph, This means you use Docker pull bgruening/galaxy-stable:latest to get the image? I just noticed that the “latest” image is 6 weeks old and the other only 9 days… Anyway, I will try if the problems occur with the old one as well. Did you ever tried to use Docker for

Re: [galaxy-dev] Docker for Mac

> On 29 Jun 2016, at 15:57, Philipp Rathert > wrote: > > Hi Hans-Rudolph, > This means you use > Docker pull bgruening/galaxy-stable:latest to get the image? > yesy > I just noticed that the “latest” image is 6 weeks old and the other only 9 > days…

[galaxy-dev] Auto detection of output format Galaxy custom tool

Hi everyone, I am looking to auto-detect the file format of a file outputted by a python tool I have written. Does anyone have any idea how to do this? I have tried setting the format attribute to "auto" with no luck. Let me know if you would like to see my tool config file. Cheers, Katherine

Re: [galaxy-dev] Docker for Mac

> On Jun 29, 2016, at 7:02 AM, Philipp Rathert > wrote: > > Hi Ido, > > I get no error message, but the command does not change anything. Rights are > still assigned to host user and not to postgresql. > > Could it be that, since galaxy and other

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

The auto-detection is only used when importing a file into Galaxy (e.g. by uploading it). If you are writing a tool which produces output in your format, then the tool's XML should specify that output format. Which of these are you trying to do? Or both? Peter On Wed, Jun 29, 2016 at 3:36 PM,

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

OK. What happens? Can you select the correct datatype in the upload tool? If not, check the file format definition as some file formats are configured not to appear here. Are you leaving the datatype as "auto"? If so, does Galaxy fail to identify the file, and leave it as the default generic

Re: [galaxy-dev] Docker for Mac

I don’t know anything about docker - yet. best, ido > On 29 Jun 2016, at 13:02, Philipp Rathert > wrote: > > Hi Ido, > > I get no error message, but the command does not change anything. Rights are > still assigned to host user and not to postgresql. >

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

Ok, so I don't give the user the option to select the correct data type to reduce the amount of stuff the user has to know when using the tool. I do leave the format as auto and Galaxy just leaves it as the generic data type 'data'. As for how the format is defined in Galaxy, I'm not quite sure

Re: [galaxy-dev] Docker for Mac

> > On 29 Jun 2016, at 10:23, Rathert, Philipp, Dr. > wrote: > > And I have the additional problem that I have to assign ownership rights to > the folders in /export and I get the following error: >  > > chown -R postgres:postgres /postgresql > chown:

Re: [galaxy-dev] Docker for Mac

Hi Ido, I get no error message, but the command does not change anything. Rights are still assigned to host user and not to postgresql. Could it be that, since galaxy and other program were running in a docker container, none of these users are known in the actual host environment? Cheers,