Hello, Did the suggested help from Biostars help? https://biostar.usegalaxy.org/p/26197/
Thanks! Jen -- Jennifer Hillman-Jackson Galaxy Application Support http://usegalaxy.org http://galaxyproject.org http://biostar.usegalaxy.org On Wed, Jan 3, 2018 at 6:01 AM, Matthias Enders < m.end...@german-seed-alliance.de> wrote: > Dear Galaxy Dev Mailing List, > > We encountered a problem while installing freebayes and its via Tool Shed. > > Galaxy installed correctly freebayes (1.1.0.46); samtools (0.1.19); gawk > (4.1.3) (all have the Current Installation Status "Installed through > Conda") but then failed on the last dependency "parallel". (Status: "Not > Installed") > > The strange thing is: parallel was installed correctly. Its callable from > the command line, (e.g. parallel --help works fine) and installed with the > latest version. But it's not recognized by Galaxy. > > We are using the Galaxy - Docker image in Version 17.09. > > Can you please assist us in resolving this? > > 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: m.end...@german-seed-alliance.de > > Firmensitz Köln > Amtsgericht Köln, HRB 73844 > > -----Ursprüngliche Nachricht----- > Von: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] Im > Auftrag von galaxy-dev-requ...@lists.galaxyproject.org > Gesendet: Donnerstag, 21. Dezember 2017 18:00 > An: galaxy-dev@lists.galaxyproject.org > Betreff: galaxy-dev Digest, Vol 138, Issue 9 > > Send galaxy-dev mailing list submissions to > galaxy-dev@lists.galaxyproject.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.galaxyproject.org/listinfo/galaxy-dev > or, via email, send a message with subject or body 'help' to > galaxy-dev-requ...@lists.galaxyproject.org > > You can reach the person managing the list at > galaxy-dev-ow...@lists.galaxyproject.org > > When replying, please edit your Subject line so it is more specific than > "Re: Contents of galaxy-dev digest..." > > > HEY! This is important! If you reply to a thread in a digest, please 1. > Change the subject of your response from "Galaxy-dev Digest Vol ..." to the > original subject for the thread. > 2. Strip out everything else in the digest that is not part of the thread > you are responding to. > > Why? > 1. This will keep the subject meaningful. People will have some idea from > the subject line if they should read it or not. > 2. Not doing this greatly increases the number of emails that match search > queries, but that aren't actually informative. > > Today's Topics: > > 1. Re: Galaxy v17.09 impersonation doesn't work (Ping Luo) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 20 Dec 2017 13:52:45 -0600 > From: Ping Luo <luop0...@gmail.com> > To: Hans-Rudolf Hotz <h...@fmi.ch> > Cc: galaxy-dev <galaxy-dev@lists.galaxyproject.org> > Subject: Re: [galaxy-dev] Galaxy v17.09 impersonation doesn't work > Message-ID: > <CA+58tPaRSi0OPWPE9-YqZJr_o+LY7szbdY3sLz3PkKXY=ADoyw@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hans-Rudolf, > > I just started a brand new galaxy with the default internal database. I > did the minimal change to galaxy.ini so that I could use CAS authentication. > Still, impersonation failed. > > > Ping > > On Wed, Dec 20, 2017 at 3:02 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote: > > > Hi Ping > > > > > > Does it work with a fresh installation ( v17.09) staring with an empty > > PostgrSQL database? > > > > > > Hans-Rudolf > > > > On 12/19/2017 03:41 PM, Ping Luo wrote: > > > >> Hans-Rudolf, > >> > >> Yes, I have set the flag to be true > >> > >> # Allow administrators to log in as other users (useful for > >> debugging) > >> allow_user_impersonation = True > >> > >> We use CAS authentication and our database is Postgresql. Our current > >> Galaxy is v15.07 and impersonation works well. I have tried v16.10 > >> before and impersonation didn't work either. > >> > >> Thanks, > >> > >> Ping > >> > >> On Tue, Dec 19, 2017 at 5:12 AM, Hans-Rudolf Hotz <h...@fmi.ch > >> <mailto:h...@fmi.ch>> wrote: > >> > >> Hi Ping > >> > >> The 'impersonate a user' function works for me with v17.09. > >> > >> > >> I assume, you have set: "allow_user_impersonation = True" in the > >> galaxy.ini file? > >> > >> > >> Do you encounter this problem, for the first time, i.e did it work > >> before using (v17.05 or earlier) and you only have the issues after > >> upgrading? > >> > >> What database do you use? > >> > >> Do you use external authentication? > >> > >> > >> Regards, Hans-Rudolf > >> > >> > >> > >> > >> > >> > >> On 12/18/2017 05:22 PM, Ping Luo wrote: > >> > >> The impersonation feature in Galaxy v17.09 doesn't work as > >> expected. > >> > >> After clicking the person to impersonate, the webpage shows "you > >> have > >> now logged in as xxx, return to home page', where 'xxx' is the > >> name of > >> the person I want to impersonate. So far so good. But after I > >> click > >> home, and check the login information, the login name is still > >> myself. > >> > >> Is there anything I missed in the configuration file? > >> > >> Thanks, > >> > >> Ping > >> > >> > >> ___________________________________________________________ > >> 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/ > >> <https://lists.galaxyproject.o rg/> > >> > >> To search Galaxy mailing lists use the unified search at: > >> http://galaxyproject.org/search/ > >> <http://galaxyproject.org/sear ch/> > >> > >> > >> > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <https://lists.galaxyproject.org/pipermail/galaxy-dev/ > attachments/20171220/a562a405/attachment-0001.html> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > galaxy-dev mailing list > galaxy-dev@lists.galaxyproject.org > https://lists.galaxyproject.org/listinfo/galaxy-dev > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > ------------------------------ > > End of galaxy-dev Digest, Vol 138, Issue 9 > ****************************************** > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. 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