This is presumably the same question elsewhere: https://biostar.usegalaxy.org/p/26197/ -- Devon Ryan, Ph.D. Email: dpr...@dpryan.com Data Manager/Bioinformatician Max Planck Institute of Immunobiology and Epigenetics Stübeweg 51 79108 Freiburg Germany
On Thu, Jan 11, 2018 at 9:44 AM, Björn Grüning <bjoern.gruen...@gmail.com> wrote: > Hi Matthias, > > sorry for answering so late! > > Do you have any error message from the logs during installation? > > What means it is not recognised by Galaxy? > Do you see the conda environment in /tool_deps/_conda/ ? > > Is freebayes crashing? > > Ciao, > Bjoern > > >> 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=ad...@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. 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/ >> > ___________________________________________________________ > 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/ ___________________________________________________________ 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/
