Dear all, finally a restart of the container solved the issue with the database/blast.
Regarding the problem with the command line: For other tools, the command line showed up, but not for blastn, as the wrapper encountered the error before creating the command line (this is my interpretation). So the error: "An invalid option was selected for database, 'myCoolDatabaseName', please verify." Was produced by the wrapper, which did not find the new database before restarting the galaxy container. So the real issue here is perhaps more on "How could blast+ be made aware of new integrated databases, without restarting"? Mit freundlichen Grüßen Matthias Enders ----------------------------------------------------------------------- GERMAN SEED ALLIANCE GmbH c/o Norddeutsche Pflanzenzucht Hans-Georg Lembke KG Hohenlieth, 24363 Holtsee Tel.: +49 (0)4351/ 736-189 Fax: + 49 (0)4351/ 736-271 Mobil: +49 (0)151/ 14247360 Email: [email protected] Firmensitz Köln Amtsgericht Köln, HRB 73844 -----Ursprüngliche Nachricht----- Von: Peter Cock <[email protected]> Gesendet: Dienstag, 10. Juli 2018 12:11 An: Matthias Enders <[email protected]> Cc: Björn Grüning <[email protected]>; [email protected] Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy There is a setting to enable showing the command line string and full paths on disk via the "i" icon from a history entry, see https://docs.galaxyproject.org/en/master/admin/options.html#expose-dataset-path # This option allows users to see the full path of datasets via the # "View Details" option in the history. This option also exposes the # command line to non-administrative users. Administrators can always # see dataset paths. #expose_dataset_path: false https://github.com/galaxyproject/galaxy/blob/release_18.05/config/galaxy.yml.sample#L1495 It existed in galaxy.ini too, which has since be replaced by galaxy.yml Peter On Tue, Jul 10, 2018 at 8:19 AM, Matthias Enders <[email protected]> wrote: > Dear Björn, > > thanks for the very fast reply. Unfortunately, this part is not visible in > our instance. (see screenshot). As you can see in the topmost bar, this is > done, while being loged in as admin. > > Mit freundlichen Grüßen > > Matthias Enders > ---------------------------------------------------------------------- > - > > > GERMAN SEED ALLIANCE GmbH > c/o Norddeutsche Pflanzenzucht > Hans-Georg Lembke KG > Hohenlieth, 24363 Holtsee > Tel.: +49 (0)4351/ 736-189 > Fax: + 49 (0)4351/ 736-271 > Mobil: +49 (0)151/ 14247360 > > Email: [email protected] > > Firmensitz Köln > Amtsgericht Köln, HRB 73844 > > -----Ursprüngliche Nachricht----- > Von: Björn Grüning <[email protected]> > Gesendet: Dienstag, 10. Juli 2018 09:15 > An: Matthias Enders <[email protected]>; > [email protected] > Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy > Priorität: Hoch > > Hi Matthias, > > please have a look at the attached screenshot. Given that you are an admin > and click on the info-symbol of the dataset you should see the commandline. > > This is with a 18.05 Docker. > Cheers, > Bjoern > > Am 10.07.2018 um 08:58 schrieb Matthias Enders: >> Dear Galaxy Community, >> >> is there any possibility to expose the command line call, generated >> within galaxy? >> >> We searched the net and found this discussions: >> https://github.com/galaxyproject/galaxy/issues/3252 >> https://github.com/galaxyproject/galaxy/issues/2954 >> >> But both are on the exposure to non-admin users. Within our instance >> we see the command line call nor for admin, neither for normal users! >> >> ... ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
