Following the suggestion from Devon Ryan @ https://biostar.usegalaxy.org/p/26197/ Our IT-people re-do the installation several times, until it works out.
So it works on occasion..
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.enders@german-seed-alliance.de
Firmensitz Köln Amtsgericht Köln, HRB 73844
-----Ursprüngliche Nachricht----- Von: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] Im Auftrag von galaxy-dev-request@lists.galaxyproject.org Gesendet: Donnerstag, 11. Januar 2018 18:00 An: galaxy-dev@lists.galaxyproject.org Betreff: galaxy-dev Digest, Vol 139, Issue 4 Priorität: Hoch
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Today's Topics:
1. Re: Problem with dependencies: Conda/freebayes (Björn Grüning) 2. Re: Problem with dependencies: Conda/freebayes (Devon Ryan) 3. Re: Problems installing conda dependencies for seq2hla tool (Peter Briggs) 4. Re: Problem with dependencies: Conda/freebayes (Jennifer Hillman-Jackson)
----------------------------------------------------------------------
Message: 1 Date: Thu, 11 Jan 2018 09:44:10 +0100 From: Björn Grüning bjoern.gruening@gmail.com To: Matthias Enders m.enders@german-seed-alliance.de, "galaxy-dev@lists.galaxyproject.org" galaxy-dev@lists.galaxyproject.org Cc: Fabian Kaiser f.kaiser@npz-innovation.de Subject: Re: [galaxy-dev] Problem with dependencies: Conda/freebayes Message-ID: 2b047e78-2a48-02e2-b413-8c597d0d5a89@gmail.com Content-Type: text/plain; charset=utf-8; format=flowed
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.enders@german-seed-alliance.de
Firmensitz Köln Amtsgericht Köln, HRB 73844
-----Ursprüngliche Nachricht----- Von: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] Im Auftrag von galaxy-dev-request@lists.galaxyproject.org Gesendet: Donnerstag, 21. Dezember 2017 18:00 An: galaxy-dev@lists.galaxyproject.org Betreff: galaxy-dev Digest, Vol 138, Issue 9
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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:
- Re: Galaxy v17.09 impersonation doesn't work (Ping Luo)
Message: 1 Date: Wed, 20 Dec 2017 13:52:45 -0600 From: Ping Luo luop0812@gmail.com To: Hans-Rudolf Hotz hrh@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 hrh@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 <hrh@fmi.ch mailto:hrh@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/>
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Message: 2 Date: Thu, 11 Jan 2018 09:47:42 +0100 From: Devon Ryan dpryan@dpryan.com To: Björn Grüning bjoern.gruening@gmail.com Cc: Fabian Kaiser f.kaiser@npz-innovation.de, "galaxy-dev@lists.galaxyproject.org" galaxy-dev@lists.galaxyproject.org, Matthias Enders m.enders@german-seed-alliance.de Subject: Re: [galaxy-dev] Problem with dependencies: Conda/freebayes Message-ID: CADus9os+Adb=ciHgQaCaDqejn7tbe2ns5dS45TGjPv2iDa1taQ@mail.gmail.com Content-Type: text/plain; charset="UTF-8"
This is presumably the same question elsewhere: https://biostar.usegalaxy.org/p/26197/ -- Devon Ryan, Ph.D. Email: dpryan@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.gruening@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.enders@german-seed-alliance.de
Firmensitz Köln Amtsgericht Köln, HRB 73844
-----Ursprüngliche Nachricht----- Von: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] Im Auftrag von galaxy-dev-request@lists.galaxyproject.org Gesendet: Donnerstag, 21. Dezember 2017 18:00 An: galaxy-dev@lists.galaxyproject.org Betreff: galaxy-dev Digest, Vol 138, Issue 9
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When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-dev digest..."
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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:
- Re: Galaxy v17.09 impersonation doesn't work (Ping Luo)
Message: 1 Date: Wed, 20 Dec 2017 13:52:45 -0600 From: Ping Luo luop0812@gmail.com To: Hans-Rudolf Hotz hrh@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 hrh@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 <hrh@fmi.ch mailto:hrh@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/>
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End of galaxy-dev Digest, Vol 138, Issue 9
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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/
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------------------------------
Message: 3 Date: Thu, 11 Jan 2018 10:19:46 +0000 From: Peter Briggs peter.briggs@manchester.ac.uk To: "galaxy-dev@lists.galaxyproject.org" galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Problems installing conda dependencies for seq2hla tool Message-ID: E20AB71CD352854B9E24B5830826BC43C8564673@MBXP13.ds.man.ac.uk Content-Type: text/plain; charset="us-ascii"
Just to follow up on my own question, in case it's helpful to anyone else:
Re the specific problem with not being able to install the seq2HLA 2.2 dependency via conda: in the end I build my own version and made it available to Galaxy as "Galaxy package" (https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html#gal...), which seemed to work okay.
Re updating to conda 4.3.24: after the update this gave me problems with at least one dependency, due to the "--offline bug" described here: https://github.com/galaxyproject/galaxy/issues/5187
I applied Norbert Eichner's fix in PR #5233 (https://github.com/galaxyproject/galaxy/pull/5233) and reinstalled the conda dependency via "Manage Tool Dependencies" in the "Admin" interface, which seemed to fix that problem. It's not clear to me yet whether other conda dependencies might need to be reinstalled, or if applying the patch is sufficient.
Best wishes
Peter
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
________________________________________ From: galaxy-dev [galaxy-dev-bounces@lists.galaxyproject.org] on behalf of Peter Briggs [peter.briggs@manchester.ac.uk] Sent: Friday, January 05, 2018 12:06 PM To: galaxy-dev@lists.galaxyproject.org Subject: [galaxy-dev] Problems installing conda dependencies for seq2hla tool
Dear Devs
I've been having problems installing the jjohnson/seq2hla tool from the toolshed on our production instance (running release_17.09).
Specifically Galaxy has been unable to successfully install the seq2HLA 2.2 dependency via conda. However it seems to work fine when installing into a clean local instance.
Initially the problem seemed to be that our version of conda was too old (we had 4.2.13), so while the __seq2HLA@2.2 env was being created, the 'seq2hla' package couldn't be installed into it (so Galaxy thought that the requirement was satifsfied but essentially it was broken).
I updated conda to 4.3.24 and checked that our "ensure_conda_channels" setting matched the one in 'galaxy.ini.sample'. Now when I try to reinstall the seq2hla tool, the dependency cannot be installed at all - there seems to be an issue with the R 3.1.2-2 conda package which this needs to pull in:
ERROR conda.core.link:_execute_actions(337): An error occurred while installing package 'defaults::r-3.1.2-2'. PaddingError: Placeholder of length '80' too short in package /XXXXXXXXX/galaxy/production/tool_dependencies/_conda/envs/__seq2HLA@2.2/bin/Rscript. The package must be rebuilt with conda-build > 2.0.
XXXX... above is the path to the Galaxy installation directory, and the full path does exceed 80 characters. Presumably this worked okay on the local Galaxy install because there the path is shorter than the 80 character limit.
Is there any workaround or fix that I can use to get this working on our production instance?
Also, is it generally safe to update the Galaxy conda installation as I have done? Is there a recommended conda version for Galaxy?
Thanks for your help, best wishes
Peter
-- Peter Briggs peter.briggs@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482
___________________________________________________________ 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/
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------------------------------
Message: 4 Date: Thu, 11 Jan 2018 08:40:25 -0800 From: Jennifer Hillman-Jackson jen@galaxyproject.org To: Matthias Enders m.enders@german-seed-alliance.de Cc: Fabian Kaiser f.kaiser@npz-innovation.de, "galaxy-dev@lists.galaxyproject.org" galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Problem with dependencies: Conda/freebayes Message-ID: CAJ_ABepjC4w7ayYu2Hhj3SnoZ+NkAMiE4EH3=iSfM5UTCSQ1RQ@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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.enders@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.enders@german-seed-alliance.de
Firmensitz Köln Amtsgericht Köln, HRB 73844
-----Ursprüngliche Nachricht----- Von: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] Im Auftrag von galaxy-dev-request@lists.galaxyproject.org Gesendet: Donnerstag, 21. Dezember 2017 18:00 An: galaxy-dev@lists.galaxyproject.org Betreff: galaxy-dev Digest, Vol 138, Issue 9
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Why?
- 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:
- Re: Galaxy v17.09 impersonation doesn't work (Ping Luo)
Message: 1 Date: Wed, 20 Dec 2017 13:52:45 -0600 From: Ping Luo luop0812@gmail.com To: Hans-Rudolf Hotz hrh@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 hrh@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 fordebugging) 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 <hrh@fmi.ch mailto:hrh@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 asexpected.
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 afterI 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/>
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Matthias Enders