Problem with dependencies: Conda/freebayes
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 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-request@lists.galaxyproject.org You can reach the person managing the list at galaxy-dev-owner@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 <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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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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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-request@lists.galaxyproject.org
You can reach the person managing the list at galaxy-dev-owner@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 <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/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/sear ch/>
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Subject: Digest Footer
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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/
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
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-request@lists.galaxyproject.org
You can reach the person managing the list at galaxy-dev-owner@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 <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/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/sear ch/>
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Subject: Digest Footer
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------------------------------
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/
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
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-request@lists.galaxyproject.org
You can reach the person managing the list at galaxy-dev-owner@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 <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/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/sear ch/>
participants (4)
-
Björn Grüning -
Devon Ryan -
Jennifer Hillman-Jackson -
Matthias Enders