Re: errors installing tool dependencies...

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Re: errors installing tool dependencies...

fernandez Edgar

Hello guys,

 

Happy new year everyone!

Wish you all the best!

 

I have a couple of small problems I’ve attached as pictures…

Can you please help me?

 

INFO: My galaxy installation and database is updated today!

 

My sincere salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568        


___________________________________________________________
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package_perl_5_18.jpg (236K) Download Attachment
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Re: errors installing tool dependencies...

Martin Čech
Hi Edgar,

for the package_perl issue please try installing updates to the dependencies (package_gnu_coreutils and package_perl in their respective versions) and then return to this screen and click the 'repository action' button and then 'manage dependencies' from the menu. Uninstall both dependencies (gnu_coreutil and perl) and then install them again.
That should pick up the newest versions and you should be set.

Regarding the hmmer that is a more prosaic problem, at the time of the installation the software was not available at the given URL. Check the machine's internet connection and if it is ok try downloading the file manually. If it succeeds the problem might have been on their side and is ok now. If it does not the problem can still be on their side and in that case either wait a bit and try again or report the issue at https://github.com/galaxyproject/tools-iuc/issues

thank you for using Galaxy.

Martin

On Fri, Jan 22, 2016 at 2:24 PM Fernandez Edgar <[hidden email]> wrote:

Hello guys,

 

Happy new year everyone!

Wish you all the best!

 

I have a couple of small problems I’ve attached as pictures…

Can you please help me?

 

INFO: My galaxy installation and database is updated today!

 

My sincere salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568        

___________________________________________________________
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: errors installing tool dependencies...

fernandez Edgar

Hello Martin,

 

Thank you!

Your instructions for my problem with Perl package worked.

For the URL of hmmer, it is wrong and I will report it like you suggested it.

 

Finally, a new error occurred for bowtie.

Would you please take a look?

 

My Sincere Salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Martin Čech [mailto:[hidden email]]
Sent: January-22-16 2:34 PM
To: Fernandez Edgar <[hidden email]>; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,

for the package_perl issue please try installing updates to the dependencies (package_gnu_coreutils and package_perl in their respective versions) and then return to this screen and click the 'repository action' button and then 'manage dependencies' from the menu. Uninstall both dependencies (gnu_coreutil and perl) and then install them again.

That should pick up the newest versions and you should be set.

 

Regarding the hmmer that is a more prosaic problem, at the time of the installation the software was not available at the given URL. Check the machine's internet connection and if it is ok try downloading the file manually. If it succeeds the problem might have been on their side and is ok now. If it does not the problem can still be on their side and in that case either wait a bit and try again or report the issue at https://github.com/galaxyproject/tools-iuc/issues

 

thank you for using Galaxy.

 

Martin

On Fri, Jan 22, 2016 at 2:24 PM Fernandez Edgar <[hidden email]> wrote:

Hello guys,

 

Happy new year everyone!

Wish you all the best!

 

I have a couple of small problems I’ve attached as pictures…

Can you please help me?

 

INFO: My galaxy installation and database is updated today!

 

My sincere salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568        

___________________________________________________________
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:
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Re: errors installing tool dependencies...

Martin Čech
Hi Edgar,

I am not sure about this one. Please try setting 'new_file_path' in your galaxy.ini to an absolute path, try again and check whether something changes.

Martin

On Mon, Jan 25, 2016 at 9:23 AM Fernandez Edgar <[hidden email]> wrote:

Hello Martin,

 

Thank you!

Your instructions for my problem with Perl package worked.

For the URL of hmmer, it is wrong and I will report it like you suggested it.

 

Finally, a new error occurred for bowtie.

Would you please take a look?

 

My Sincere Salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Martin Čech [mailto:[hidden email]]
Sent: January-22-16 2:34 PM
To: Fernandez Edgar <[hidden email]>; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,

for the package_perl issue please try installing updates to the dependencies (package_gnu_coreutils and package_perl in their respective versions) and then return to this screen and click the 'repository action' button and then 'manage dependencies' from the menu. Uninstall both dependencies (gnu_coreutil and perl) and then install them again.

That should pick up the newest versions and you should be set.

 

Regarding the hmmer that is a more prosaic problem, at the time of the installation the software was not available at the given URL. Check the machine's internet connection and if it is ok try downloading the file manually. If it succeeds the problem might have been on their side and is ok now. If it does not the problem can still be on their side and in that case either wait a bit and try again or report the issue at https://github.com/galaxyproject/tools-iuc/issues

 

thank you for using Galaxy.

 

Martin

On Fri, Jan 22, 2016 at 2:24 PM Fernandez Edgar <[hidden email]> wrote:

Hello guys,

 

Happy new year everyone!

Wish you all the best!

 

I have a couple of small problems I’ve attached as pictures…

Can you please help me?

 

INFO: My galaxy installation and database is updated today!

 

My sincere salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568        

___________________________________________________________
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: errors installing tool dependencies...

fernandez Edgar

Hello Martin.

 

I changed the setting “new_file_path” like you said and the same error occurs (with the full path obviously).

I check that the full path exists. And is rwx for the galaxy user.

Any other ideas I could try?

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Martin Čech [mailto:[hidden email]]
Sent: January-25-16 9:33 AM
To: Fernandez Edgar <[hidden email]>; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,

 

I am not sure about this one. Please try setting 'new_file_path' in your galaxy.ini to an absolute path, try again and check whether something changes.

 

Martin

 

On Mon, Jan 25, 2016 at 9:23 AM Fernandez Edgar <[hidden email]> wrote:

Hello Martin,

 

Thank you!

Your instructions for my problem with Perl package worked.

For the URL of hmmer, it is wrong and I will report it like you suggested it.

 

Finally, a new error occurred for bowtie.

Would you please take a look?

 

My Sincere Salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Martin Čech [mailto:[hidden email]]
Sent: January-22-16 2:34 PM
To: Fernandez Edgar <[hidden email]>; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,

for the package_perl issue please try installing updates to the dependencies (package_gnu_coreutils and package_perl in their respective versions) and then return to this screen and click the 'repository action' button and then 'manage dependencies' from the menu. Uninstall both dependencies (gnu_coreutil and perl) and then install them again.

That should pick up the newest versions and you should be set.

 

Regarding the hmmer that is a more prosaic problem, at the time of the installation the software was not available at the given URL. Check the machine's internet connection and if it is ok try downloading the file manually. If it succeeds the problem might have been on their side and is ok now. If it does not the problem can still be on their side and in that case either wait a bit and try again or report the issue at https://github.com/galaxyproject/tools-iuc/issues

 

thank you for using Galaxy.

 

Martin

On Fri, Jan 22, 2016 at 2:24 PM Fernandez Edgar <[hidden email]> wrote:

Hello guys,

 

Happy new year everyone!

Wish you all the best!

 

I have a couple of small problems I’ve attached as pictures…

Can you please help me?

 

INFO: My galaxy installation and database is updated today!

 

My sincere salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568        

___________________________________________________________
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: errors installing tool dependencies...

fernandez Edgar
In reply to this post by Martin Čech

No wait my mistake: the path doesn’t exists:

[Errno 2] No such file or directory: '/home/galaxy/galaxy-prod/database/tmp/tmp-toolshed-mtdb6vbEI/bowtie2-2.2.6/bowtie2-2.2.6/'

Because you have twice "bowtie2-2.2.6" in the full path…

Is that normal?

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Fernandez Edgar
Sent: January-25-16 11:11 AM
To: 'Martin Čech' <[hidden email]>; [hidden email]
Subject: RE: [galaxy-dev] errors installing tool dependencies...

 

Hello Martin.

 

I changed the setting “new_file_path” like you said and the same error occurs (with the full path obviously).

I check that the full path exists. And is rwx for the galaxy user.

Any other ideas I could try?

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Martin Čech [[hidden email]]
Sent: January-25-16 9:33 AM
To: Fernandez Edgar <[hidden email]>; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,

 

I am not sure about this one. Please try setting 'new_file_path' in your galaxy.ini to an absolute path, try again and check whether something changes.

 

Martin

 

On Mon, Jan 25, 2016 at 9:23 AM Fernandez Edgar <[hidden email]> wrote:

Hello Martin,

 

Thank you!

Your instructions for my problem with Perl package worked.

For the URL of hmmer, it is wrong and I will report it like you suggested it.

 

Finally, a new error occurred for bowtie.

Would you please take a look?

 

My Sincere Salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Martin Čech [mailto:[hidden email]]
Sent: January-22-16 2:34 PM
To: Fernandez Edgar <[hidden email]>; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,

for the package_perl issue please try installing updates to the dependencies (package_gnu_coreutils and package_perl in their respective versions) and then return to this screen and click the 'repository action' button and then 'manage dependencies' from the menu. Uninstall both dependencies (gnu_coreutil and perl) and then install them again.

That should pick up the newest versions and you should be set.

 

Regarding the hmmer that is a more prosaic problem, at the time of the installation the software was not available at the given URL. Check the machine's internet connection and if it is ok try downloading the file manually. If it succeeds the problem might have been on their side and is ok now. If it does not the problem can still be on their side and in that case either wait a bit and try again or report the issue at https://github.com/galaxyproject/tools-iuc/issues

 

thank you for using Galaxy.

 

Martin

On Fri, Jan 22, 2016 at 2:24 PM Fernandez Edgar <[hidden email]> wrote:

Hello guys,

 

Happy new year everyone!

Wish you all the best!

 

I have a couple of small problems I’ve attached as pictures…

Can you please help me?

 

INFO: My galaxy installation and database is updated today!

 

My sincere salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568        

___________________________________________________________
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: errors installing tool dependencies...

Martin Čech
That was my second guess, I wasn't sure whether it should create that dir structure. Are you installing this package at this revision? And what system are you installing it on?

On Mon, Jan 25, 2016 at 11:17 AM Fernandez Edgar <[hidden email]> wrote:

No wait my mistake: the path doesn’t exists:

[Errno 2] No such file or directory: '/home/galaxy/galaxy-prod/database/tmp/tmp-toolshed-mtdb6vbEI/bowtie2-2.2.6/bowtie2-2.2.6/'

Because you have twice "bowtie2-2.2.6" in the full path…

Is that normal?

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Fernandez Edgar
Sent: January-25-16 11:11 AM
To: 'Martin Čech' <[hidden email]>; [hidden email]
Subject: RE: [galaxy-dev] errors installing tool dependencies...

 

Hello Martin.

 

I changed the setting “new_file_path” like you said and the same error occurs (with the full path obviously).

I check that the full path exists. And is rwx for the galaxy user.

Any other ideas I could try?

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Martin Čech [[hidden email]]
Sent: January-25-16 9:33 AM


To: Fernandez Edgar <[hidden email]>; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,

 

I am not sure about this one. Please try setting 'new_file_path' in your galaxy.ini to an absolute path, try again and check whether something changes.

 

Martin

 

On Mon, Jan 25, 2016 at 9:23 AM Fernandez Edgar <[hidden email]> wrote:

Hello Martin,

 

Thank you!

Your instructions for my problem with Perl package worked.

For the URL of hmmer, it is wrong and I will report it like you suggested it.

 

Finally, a new error occurred for bowtie.

Would you please take a look?

 

My Sincere Salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Martin Čech [mailto:[hidden email]]
Sent: January-22-16 2:34 PM
To: Fernandez Edgar <[hidden email]>; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,

for the package_perl issue please try installing updates to the dependencies (package_gnu_coreutils and package_perl in their respective versions) and then return to this screen and click the 'repository action' button and then 'manage dependencies' from the menu. Uninstall both dependencies (gnu_coreutil and perl) and then install them again.

That should pick up the newest versions and you should be set.

 

Regarding the hmmer that is a more prosaic problem, at the time of the installation the software was not available at the given URL. Check the machine's internet connection and if it is ok try downloading the file manually. If it succeeds the problem might have been on their side and is ok now. If it does not the problem can still be on their side and in that case either wait a bit and try again or report the issue at https://github.com/galaxyproject/tools-iuc/issues

 

thank you for using Galaxy.

 

Martin

On Fri, Jan 22, 2016 at 2:24 PM Fernandez Edgar <[hidden email]> wrote:

Hello guys,

 

Happy new year everyone!

Wish you all the best!

 

I have a couple of small problems I’ve attached as pictures…

Can you please help me?

 

INFO: My galaxy installation and database is updated today!

 

My sincere salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568        

___________________________________________________________
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:
  http://galaxyproject.org/search/mailinglists/
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Re: errors installing tool dependencies...

Nicola Soranzo-2
In reply to this post by fernandez Edgar
Hi Edgar,
this smells like an old fixed bug, what version of Galaxy are you running?

Cheers,
Nicola

On 25/01/16 14:22, Fernandez Edgar wrote:

Hello Martin,

 

Thank you!

Your instructions for my problem with Perl package worked.

For the URL of hmmer, it is wrong and I will report it like you suggested it.

 

Finally, a new error occurred for bowtie.

Would you please take a look?

 

My Sincere Salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Martin Čech [[hidden email]]
Sent: January-22-16 2:34 PM
To: Fernandez Edgar [hidden email]; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,

for the package_perl issue please try installing updates to the dependencies (package_gnu_coreutils and package_perl in their respective versions) and then return to this screen and click the 'repository action' button and then 'manage dependencies' from the menu. Uninstall both dependencies (gnu_coreutil and perl) and then install them again.

That should pick up the newest versions and you should be set.

 

Regarding the hmmer that is a more prosaic problem, at the time of the installation the software was not available at the given URL. Check the machine's internet connection and if it is ok try downloading the file manually. If it succeeds the problem might have been on their side and is ok now. If it does not the problem can still be on their side and in that case either wait a bit and try again or report the issue at https://github.com/galaxyproject/tools-iuc/issues

 

thank you for using Galaxy.

 

Martin

On Fri, Jan 22, 2016 at 2:24 PM Fernandez Edgar <[hidden email]> wrote:

Hello guys,

 

Happy new year everyone!

Wish you all the best!

 

I have a couple of small problems I’ve attached as pictures…

Can you please help me?

 

INFO: My galaxy installation and database is updated today!

 

My sincere salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568        

___________________________________________________________
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:
  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: errors installing tool dependencies...

Nicola Soranzo-2
Hi Edgar,
indeed your bug was fixed long ago, please see http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html

You should really move to the GitHub repository and update to the latest 15.07 or (better) to 15.10 .

Cheers,
Nicola

On 25/01/16 17:09, Fernandez Edgar wrote:

[galaxy@galaxy_sever galaxy-prod]$ hg id -i

f6683935f81a+

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Nicola Soranzo [[hidden email]] On Behalf Of Nicola Soranzo
Sent: January-25-16 12:05 PM
To: Fernandez Edgar [hidden email]; Martin Čech [hidden email]; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,
this smells like an old fixed bug, what version of Galaxy are you running?

Cheers,
Nicola

On 25/01/16 14:22, Fernandez Edgar wrote:

Hello Martin,

 

Thank you!

Your instructions for my problem with Perl package worked.

For the URL of hmmer, it is wrong and I will report it like you suggested it.

 

Finally, a new error occurred for bowtie.

Would you please take a look?

 

My Sincere Salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Martin Čech [[hidden email]]
Sent: January-22-16 2:34 PM
To: Fernandez Edgar [hidden email]; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,

for the package_perl issue please try installing updates to the dependencies (package_gnu_coreutils and package_perl in their respective versions) and then return to this screen and click the 'repository action' button and then 'manage dependencies' from the menu. Uninstall both dependencies (gnu_coreutil and perl) and then install them again.

That should pick up the newest versions and you should be set.

 

Regarding the hmmer that is a more prosaic problem, at the time of the installation the software was not available at the given URL. Check the machine's internet connection and if it is ok try downloading the file manually. If it succeeds the problem might have been on their side and is ok now. If it does not the problem can still be on their side and in that case either wait a bit and try again or report the issue at https://github.com/galaxyproject/tools-iuc/issues

 

thank you for using Galaxy.

 

Martin

On Fri, Jan 22, 2016 at 2:24 PM Fernandez Edgar <[hidden email]> wrote:

Hello guys,

 

Happy new year everyone!

Wish you all the best!

 

I have a couple of small problems I’ve attached as pictures…

Can you please help me?

 

INFO: My galaxy installation and database is updated today!

 

My sincere salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568        

___________________________________________________________
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:
  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:
  http://galaxyproject.org/search/mailinglists/
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Open this post in threaded view
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Re: errors installing tool dependencies...

fernandez Edgar

How would I safely make the transition from mercurial to github without my installation?

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Nicola Soranzo [mailto:[hidden email]] On Behalf Of Nicola Soranzo
Sent: January-25-16 12:22 PM
To: Fernandez Edgar <[hidden email]>; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,
indeed your bug was fixed long ago, please see http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html

You should really move to the GitHub repository and update to the latest 15.07 or (better) to 15.10 .

Cheers,
Nicola

On 25/01/16 17:09, Fernandez Edgar wrote:

[galaxy@galaxy_sever galaxy-prod]$ hg id -i

f6683935f81a+

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Nicola Soranzo [[hidden email]] On Behalf Of Nicola Soranzo
Sent: January-25-16 12:05 PM
To: Fernandez Edgar [hidden email]; Martin Čech [hidden email]; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,
this smells like an old fixed bug, what version of Galaxy are you running?

Cheers,
Nicola

On 25/01/16 14:22, Fernandez Edgar wrote:

Hello Martin,

 

Thank you!

Your instructions for my problem with Perl package worked.

For the URL of hmmer, it is wrong and I will report it like you suggested it.

 

Finally, a new error occurred for bowtie.

Would you please take a look?

 

My Sincere Salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Martin Čech [[hidden email]]
Sent: January-22-16 2:34 PM
To: Fernandez Edgar [hidden email]; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,

for the package_perl issue please try installing updates to the dependencies (package_gnu_coreutils and package_perl in their respective versions) and then return to this screen and click the 'repository action' button and then 'manage dependencies' from the menu. Uninstall both dependencies (gnu_coreutil and perl) and then install them again.

That should pick up the newest versions and you should be set.

 

Regarding the hmmer that is a more prosaic problem, at the time of the installation the software was not available at the given URL. Check the machine's internet connection and if it is ok try downloading the file manually. If it succeeds the problem might have been on their side and is ok now. If it does not the problem can still be on their side and in that case either wait a bit and try again or report the issue at https://github.com/galaxyproject/tools-iuc/issues

 

thank you for using Galaxy.

 

Martin

On Fri, Jan 22, 2016 at 2:24 PM Fernandez Edgar <[hidden email]> wrote:

Hello guys,

 

Happy new year everyone!

Wish you all the best!

 

I have a couple of small problems I’ve attached as pictures…

Can you please help me?

 

INFO: My galaxy installation and database is updated today!

 

My sincere salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568        

___________________________________________________________
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:
  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:
  http://galaxyproject.org/search/mailinglists/
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Open this post in threaded view
|

Re: errors installing tool dependencies...

Martin Čech
Edgar,

check 'How to migrate a Galaxy instance from Mercurial Bitbucket to Git GitHub' at https://wiki.galaxyproject.org/Develop/SourceCode

Thanks

M.
On Mon, Jan 25, 2016 at 12:29 PM Fernandez Edgar <[hidden email]> wrote:

How would I safely make the transition from mercurial to github without my installation?

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Nicola Soranzo [mailto:[hidden email]] On Behalf Of Nicola Soranzo
Sent: January-25-16 12:22 PM
To: Fernandez Edgar <[hidden email]>; [hidden email]


Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,
indeed your bug was fixed long ago, please see http://dev.list.galaxyproject.org/Bismark-installation-dependencies-error-td4668186.html

You should really move to the GitHub repository and update to the latest 15.07 or (better) to 15.10 .

Cheers,
Nicola

On 25/01/16 17:09, Fernandez Edgar wrote:

[galaxy@galaxy_sever galaxy-prod]$ hg id -i

f6683935f81a+

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Nicola Soranzo [[hidden email]] On Behalf Of Nicola Soranzo
Sent: January-25-16 12:05 PM
To: Fernandez Edgar [hidden email]; Martin Čech [hidden email]; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,
this smells like an old fixed bug, what version of Galaxy are you running?

Cheers,
Nicola

On 25/01/16 14:22, Fernandez Edgar wrote:

Hello Martin,

 

Thank you!

Your instructions for my problem with Perl package worked.

For the URL of hmmer, it is wrong and I will report it like you suggested it.

 

Finally, a new error occurred for bowtie.

Would you please take a look?

 

My Sincere Salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Martin Čech [[hidden email]]
Sent: January-22-16 2:34 PM
To: Fernandez Edgar [hidden email]; [hidden email]
Subject: Re: [galaxy-dev] errors installing tool dependencies...

 

Hi Edgar,

for the package_perl issue please try installing updates to the dependencies (package_gnu_coreutils and package_perl in their respective versions) and then return to this screen and click the 'repository action' button and then 'manage dependencies' from the menu. Uninstall both dependencies (gnu_coreutil and perl) and then install them again.

That should pick up the newest versions and you should be set.

 

Regarding the hmmer that is a more prosaic problem, at the time of the installation the software was not available at the given URL. Check the machine's internet connection and if it is ok try downloading the file manually. If it succeeds the problem might have been on their side and is ok now. If it does not the problem can still be on their side and in that case either wait a bit and try again or report the issue at https://github.com/galaxyproject/tools-iuc/issues

 

thank you for using Galaxy.

 

Martin

On Fri, Jan 22, 2016 at 2:24 PM Fernandez Edgar <[hidden email]> wrote:

Hello guys,

 

Happy new year everyone!

Wish you all the best!

 

I have a couple of small problems I’ve attached as pictures…

Can you please help me?

 

INFO: My galaxy installation and database is updated today!

 

My sincere salutations,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568        

___________________________________________________________
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:
  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:
  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:
  http://galaxyproject.org/search/mailinglists/