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DeepTools installation error

Timo Janßen
Hi all,

trying to install the deeptools_suite from the toolshed I only get the
following error:

"500 Internal Server Error

nginx/1.11.10"

This happens as well for the dependencies, e.g. deeptools_bigwig_compare.

I am currently using Galaxy 16.10 with nginx proxy.

Also the installation of the dependency
package_python_2_7_matplotlib_1_4 fails because of a missing dependency:

"Error installing tool dependency python version 2.7.10: Unable to
locate required tool shed repository named package_python_2_7_10 owned
by iuc with revision 80931fb5f433."

Has anyone seen these problems before and knows a solution?

Best regards,
Timo Janßen

--
------------------------------------------------------------------------
Timo Janßen
Wissenschaftliche Hilfskraft
Arbeitsgruppe "Anwendungs- und Informationssysteme"
Tel.: +49(0)551/201-1791
E-Mail: [hidden email]
------------------------------------------------------------------------
Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen
(GWDG)
Am Faßberg 11, 37077 Göttingen, URL: http://www.gwdg.de
Tel.: +49 551 201-1510, Fax: +49 551 201-2150, E-Mail: [hidden email]
Service-Hotline: Tel.: +49 551 201-1523, E-Mail: [hidden email]

Geschäftsführer: Prof. Dr. Ramin Yahyapour
Aufsichtsratsvorsitzender: Prof. Dr. Norbert Lassau
Sitz der Gesellschaft: Göttingen
Registergericht: Göttingen, Handelsregister-Nr. B 598
------------------------------------------------------------------------
Zertifiziert nach ISO 9001
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Re: DeepTools installation error

Devon Ryan-2

Hi Timo,

Use conda for dependency resolution in Galaxy and make your life easier :)

Devon

On 03/08/2017 06:31 PM, Timo Janßen wrote:
Hi all,

trying to install the deeptools_suite from the toolshed I only get the
following error:

"500 Internal Server Error

nginx/1.11.10"

This happens as well for the dependencies, e.g. deeptools_bigwig_compare.

I am currently using Galaxy 16.10 with nginx proxy.

Also the installation of the dependency
package_python_2_7_matplotlib_1_4 fails because of a missing dependency:

"Error installing tool dependency python version 2.7.10: Unable to
locate required tool shed repository named package_python_2_7_10 owned
by iuc with revision 80931fb5f433."

Has anyone seen these problems before and knows a solution?

Best regards,
Timo Janßen



___________________________________________________________
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/mailinglists/

-- 
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: [hidden email]

___________________________________________________________
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:
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Re: DeepTools installation error

Md. Rezaul Karim
Hi Devon, 

I'm also experiencing similar issues. Could you please briefly explain how to use Condo with Galaxy? 

Is there any other versions where Conda is integrated apart from the regular Galaxy distributions? 

On Mar 8, 2017 7:38 PM, "Devon Ryan" <[hidden email]> wrote:

Hi Timo,

Use conda for dependency resolution in Galaxy and make your life easier :)

Devon

On 03/08/2017 06:31 PM, Timo Janßen wrote:
Hi all,

trying to install the deeptools_suite from the toolshed I only get the
following error:

"500 Internal Server Error

nginx/1.11.10"

This happens as well for the dependencies, e.g. deeptools_bigwig_compare.

I am currently using Galaxy 16.10 with nginx proxy.

Also the installation of the dependency
package_python_2_7_matplotlib_1_4 fails because of a missing dependency:

"Error installing tool dependency python version 2.7.10: Unable to
locate required tool shed repository named package_python_2_7_10 owned
by iuc with revision 80931fb5f433."

Has anyone seen these problems before and knows a solution?

Best regards,
Timo Janßen



___________________________________________________________
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/mailinglists/

-- 
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: [hidden email]

___________________________________________________________
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/mailinglists/

___________________________________________________________
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:
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Re: DeepTools installation error

Devon Ryan-2

The documentation here is quite good: https://docs.galaxyproject.org/en/master/admin/conda_faq.html

As an aside, the dockerized version of Galaxy (https://github.com/bgruening/docker-galaxy-stable) from Björn Gruening makes this convenient.

Devon


On 03/08/2017 08:55 PM, Md. Rezaul Karim wrote:
Hi Devon, 

I'm also experiencing similar issues. Could you please briefly explain how to use Condo with Galaxy? 

Is there any other versions where Conda is integrated apart from the regular Galaxy distributions? 

On Mar 8, 2017 7:38 PM, "Devon Ryan" <[hidden email]> wrote:

Hi Timo,

Use conda for dependency resolution in Galaxy and make your life easier :)

Devon

On 03/08/2017 06:31 PM, Timo Janßen wrote:
Hi all,

trying to install the deeptools_suite from the toolshed I only get the
following error:

"500 Internal Server Error

nginx/1.11.10"

This happens as well for the dependencies, e.g. deeptools_bigwig_compare.

I am currently using Galaxy 16.10 with nginx proxy.

Also the installation of the dependency
package_python_2_7_matplotlib_1_4 fails because of a missing dependency:

"Error installing tool dependency python version 2.7.10: Unable to
locate required tool shed repository named package_python_2_7_10 owned
by iuc with revision 80931fb5f433."

Has anyone seen these problems before and knows a solution?

Best regards,
Timo Janßen

___________________________________________________________
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/mailinglists/
-- 
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: [hidden email]
___________________________________________________________ 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/mailinglists/
-- 
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: [hidden email]

___________________________________________________________
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/mailinglists/
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Re: DeepTools installation error

Timo Janßen
In reply to this post by Devon Ryan-2
On 03/08/2017 08:38 PM, Devon Ryan wrote:
> Hi Timo,
>
> Use conda for dependency resolution in Galaxy and make your life easier :)
>
> Devon

Hi Devon,

thanks for the suggestion. I think that wasn't the actual issue but I
managed to solve it now. I installed DeepTools via the command line api
and despite getting errors all tools have been installed. The matplotlib
package still complains about the missing dependency but seems to work
anyhow.

Timo

--
------------------------------------------------------------------------
Timo Janßen
Wissenschaftliche Hilfskraft
Arbeitsgruppe "Anwendungs- und Informationssysteme"
Tel.: +49(0)551/201-1791
E-Mail: [hidden email]
------------------------------------------------------------------------
Gesellschaft für wissenschaftliche Datenverarbeitung mbH Göttingen
(GWDG)
Am Faßberg 11, 37077 Göttingen, URL: http://www.gwdg.de
Tel.: +49 551 201-1510, Fax: +49 551 201-2150, E-Mail: [hidden email]
Service-Hotline: Tel.: +49 551 201-1523, E-Mail: [hidden email]

Geschäftsführer: Prof. Dr. Ramin Yahyapour
Aufsichtsratsvorsitzender: Prof. Dr. Norbert Lassau
Sitz der Gesellschaft: Göttingen
Registergericht: Göttingen, Handelsregister-Nr. B 598
------------------------------------------------------------------------
Zertifiziert nach ISO 9001
------------------------------------------------------------------------


___________________________________________________________
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/mailinglists/

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