tophat2 install

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tophat2 install

Briand, Sheldon

Hi,

 

I ran into a problem installing tophat2 here:

tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found

 

I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.

 

Repairing the repository doesn’t make any difference.

 

Thanks!

-Sheldon

 

Sheldon Briand

NRC Research Computing Support Analyst

Research Computing Support / Soutien Informartique a la Recherche

Operations, Science Portfolio / Operations, Portefeuil des sciences

SSC-NRC / SPC-CNRC

Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford

Halifax, NS  B3H 3Z1

902 426-1677

[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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: tophat2 install

Briand, Sheldon

Hi,

 

Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven’t had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!

-Sheldon  

 

1. Manually remove the installed repository subdirectory hierarchy from disk.
2. If the repository included any tools, manually remove entries for each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories )
3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required:

The following assumes you're using postgres:

update tool_shed_repository set deleted=True, uninstalled=True, status='Uninstalled', error_message=Null  where name = 'bcftools_view';

 

 

 

From: Briand, Sheldon
Sent: Wednesday, March 12, 2014 11:44 AM
To: [hidden email]
Subject: tophat2 install

 

Hi,

 

I ran into a problem installing tophat2 here:

tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found

 

I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.

 

Repairing the repository doesn’t make any difference.

 

Thanks!

-Sheldon

 

Sheldon Briand

NRC Research Computing Support Analyst

Research Computing Support / Soutien Informartique a la Recherche

Operations, Science Portfolio / Operations, Portefeuil des sciences

SSC-NRC / SPC-CNRC

Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford

Halifax, NS  B3H 3Z1

902 426-1677

[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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: tophat2 install

Greg Von Kuster
<base href="x-msg://230/">Hi Sheldon,

I recommend not manually changing any database entries.  You should be able to install the repository and all of its dependencies using the Repair Repository feature.  See https://wiki.galaxyproject.org/RepairingInstalledRepositories

Greg Von Kuster

On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]> wrote:

Hi,
 
Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven’t had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!
-Sheldon  
 
1. Manually remove the installed repository subdirectory hierarchy from disk. 
2. If the repository included any tools, manually remove entries for each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories ) 
3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required: 

The following assumes you're using postgres: 

update tool_shed_repository set deleted=True, uninstalled=True, status='Uninstalled', error_message=Null  where name = 'bcftools_view';
 
 
 
From: Briand, Sheldon 
Sent: Wednesday, March 12, 2014 11:44 AM
To: [hidden email]
Subject: tophat2 install
 
Hi,
 
I ran into a problem installing tophat2 here:
tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found
 
I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.
 
Repairing the repository doesn’t make any difference.
 
Thanks!
-Sheldon
 
Sheldon Briand
NRC Research Computing Support Analyst
Research Computing Support / Soutien Informartique a la Recherche
Operations, Science Portfolio / Operations, Portefeuil des sciences
SSC-NRC / SPC-CNRC
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS  B3H 3Z1
902 426-1677
 
___________________________________________________________
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:
 http://lists.bx.psu.edu/

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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: tophat2 install

Briand, Sheldon
<base href="x-msg://230/">

Hi,

 

The repair operation doesn’t seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.

 

-Sheldon

 

 

From: Greg Von Kuster [mailto:[hidden email]]
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

Hi Sheldon,

 

I recommend not manually changing any database entries.  You should be able to install the repository and all of its dependencies using the Repair Repository feature.  See https://wiki.galaxyproject.org/RepairingInstalledRepositories

 

Greg Von Kuster

 

On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]> wrote:



Hi,

 

Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven’t had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!

-Sheldon  

 

1. Manually remove the installed repository subdirectory hierarchy from disk. 
2. If the repository included any tools, manually remove entries for each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories ) 
3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required: 

The following assumes you're using postgres: 

update tool_shed_repository set deleted=True, uninstalled=True, status='Uninstalled', error_message=Null  where name = 'bcftools_view';

 

 

 

From: Briand, Sheldon 
Sent: Wednesday, March 12, 2014 11:44 AM
To: [hidden email]
Subject: tophat2 install

 

Hi,

 

I ran into a problem installing tophat2 here:

tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found

 

I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.

 

Repairing the repository doesn’t make any difference.

 

Thanks!

-Sheldon

 

Sheldon Briand

NRC Research Computing Support Analyst

Research Computing Support / Soutien Informartique a la Recherche

Operations, Science Portfolio / Operations, Portefeuil des sciences

SSC-NRC / SPC-CNRC

Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford

Halifax, NS  B3H 3Z1

902 426-1677

 

___________________________________________________________
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:
 http://lists.bx.psu.edu/

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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

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Re: tophat2 install

Greg Von Kuster
<base href="x-msg://230/">You should be able to click on the missing tool dependency and see its installation log.  It should show you whatever error is occuring that is not allowing successful installation.

Greg Von Kuster

On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" <[hidden email]> wrote:

Hi,
 
The repair operation doesn’t seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.
 
-Sheldon
 
 
From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install
 
Hi Sheldon,
 
I recommend not manually changing any database entries.  You should be able to install the repository and all of its dependencies using the Repair Repository feature.  See https://wiki.galaxyproject.org/RepairingInstalledRepositories
 
Greg Von Kuster
 
On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]> wrote:


Hi,
 
Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven’t had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!
-Sheldon  
 
1. Manually remove the installed repository subdirectory hierarchy from disk. 
2. If the repository included any tools, manually remove entries for each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories ) 
3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required: 

The following assumes you're using postgres: 

update tool_shed_repository set deleted=True, uninstalled=True, status='Uninstalled', error_message=Null  where name = 'bcftools_view';
 
 
 
From: Briand, Sheldon 
Sent: Wednesday, March 12, 2014 11:44 AM
To: [hidden email]
Subject: tophat2 install
 
Hi,
 
I ran into a problem installing tophat2 here:
tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found
 
I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.
 
Repairing the repository doesn’t make any difference.
 
Thanks!
-Sheldon
 
Sheldon Briand
NRC Research Computing Support Analyst
Research Computing Support / Soutien Informartique a la Recherche
Operations, Science Portfolio / Operations, Portefeuil des sciences
SSC-NRC / SPC-CNRC
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS  B3H 3Z1
902 426-1677
 
___________________________________________________________
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:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/
 
<Screenshot.png>


___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: tophat2 install

Briand, Sheldon
<base href="x-msg://230/">

Hi,

 

Yes the error is:

Error installing tool dependency package tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found

 

-Sheldon

 

From: Greg Von Kuster [mailto:[hidden email]]
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

You should be able to click on the missing tool dependency and see its installation log.  It should show you whatever error is occuring that is not allowing successful installation.

 

Greg Von Kuster

 

On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" <[hidden email]> wrote:



Hi,

 

The repair operation doesn’t seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.

 

-Sheldon

 

 

From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

Hi Sheldon,

 

I recommend not manually changing any database entries.  You should be able to install the repository and all of its dependencies using the Repair Repository feature.  See https://wiki.galaxyproject.org/RepairingInstalledRepositories

 

Greg Von Kuster

 

On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]> wrote:




Hi,

 

Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven’t had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!

-Sheldon  

 

1. Manually remove the installed repository subdirectory hierarchy from disk. 
2. If the repository included any tools, manually remove entries for each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories ) 
3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required: 

The following assumes you're using postgres: 

update tool_shed_repository set deleted=True, uninstalled=True, status='Uninstalled', error_message=Null  where name = 'bcftools_view';

 

 

 

From: Briand, Sheldon 
Sent: Wednesday, March 12, 2014 11:44 AM
To: [hidden email]
Subject: tophat2 install

 

Hi,

 

I ran into a problem installing tophat2 here:

tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found

 

I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.

 

Repairing the repository doesn’t make any difference.

 

Thanks!

-Sheldon

 

Sheldon Briand

NRC Research Computing Support Analyst

Research Computing Support / Soutien Informartique a la Recherche

Operations, Science Portfolio / Operations, Portefeuil des sciences

SSC-NRC / SPC-CNRC

Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford

Halifax, NS  B3H 3Z1

902 426-1677

 

___________________________________________________________
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:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

 

<Screenshot.png>

 


___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: tophat2 install

Briand, Sheldon
<base href="x-msg://230/">

Hi,

 

Here is the error from the paster.log:

 

Traceback (most recent call last):

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", line 496, in handle_tool_dependencies

    from_install_manager=from_install_manager )

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 318, in install_package

    from_install_manager=from_install_manager )

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 245, in handle_complex_repository_d

ependency_for_package

    tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 126, in get_absolute_path_to_file_i

n_repository

    for root, dirs, files in os.walk( repo_files_dir ):

  File "/opt/local/python-2.7.5/lib/python2.7/os.py", line 276, in walk

    names = listdir(top)

TypeError: coercing to Unicode: need string or buffer, NoneType found

 

-Sheldon

 

From: [hidden email] [mailto:[hidden email]] On Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 10:52 AM
To: 'Greg Von Kuster'
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

Hi,

 

Yes the error is:

Error installing tool dependency package tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found

 

-Sheldon

 

From: Greg Von Kuster [[hidden email]]
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

You should be able to click on the missing tool dependency and see its installation log.  It should show you whatever error is occuring that is not allowing successful installation.

 

Greg Von Kuster

 

On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" <[hidden email]> wrote:

 

Hi,

 

The repair operation doesn’t seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.

 

-Sheldon

 

 

From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

Hi Sheldon,

 

I recommend not manually changing any database entries.  You should be able to install the repository and all of its dependencies using the Repair Repository feature.  See https://wiki.galaxyproject.org/RepairingInstalledRepositories

 

Greg Von Kuster

 

On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]> wrote:



Hi,

 

Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven’t had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!

-Sheldon  

 

1. Manually remove the installed repository subdirectory hierarchy from disk. 
2. If the repository included any tools, manually remove entries for each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories ) 
3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required: 

The following assumes you're using postgres: 

update tool_shed_repository set deleted=True, uninstalled=True, status='Uninstalled', error_message=Null  where name = 'bcftools_view';

 

 

 

From: Briand, Sheldon 
Sent: Wednesday, March 12, 2014 11:44 AM
To: [hidden email]
Subject: tophat2 install

 

Hi,

 

I ran into a problem installing tophat2 here:

tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found

 

I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.

 

Repairing the repository doesn’t make any difference.

 

Thanks!

-Sheldon

 

Sheldon Briand

NRC Research Computing Support Analyst

Research Computing Support / Soutien Informartique a la Recherche

Operations, Science Portfolio / Operations, Portefeuil des sciences

SSC-NRC / SPC-CNRC

Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford

Halifax, NS  B3H 3Z1

902 426-1677

 

___________________________________________________________
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:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

 

<Screenshot.png>

 


___________________________________________________________
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: tophat2 install

Greg Von Kuster
<base href="x-msg://230/">It looks like your database and file system are out of sync.  Your database seems to think you have an installed repository but your file system does not seem to have the repository's installation directory.  Can you confirm that this is the case?


On Mar 20, 2014, at 11:53 AM, "Briand, Sheldon" <[hidden email]> wrote:

Hi,
 
Here is the error from the paster.log:
 
Traceback (most recent call last):
  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", line 496, in handle_tool_dependencies
    from_install_manager=from_install_manager )
  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 318, in install_package
    from_install_manager=from_install_manager )
  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 245, in handle_complex_repository_d
ependency_for_package
    tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 126, in get_absolute_path_to_file_i
n_repository
    for root, dirs, files in os.walk( repo_files_dir ):
  File "/opt/local/python-2.7.5/lib/python2.7/os.py", line 276, in walk
    names = listdir(top)
TypeError: coercing to Unicode: need string or buffer, NoneType found
 
-Sheldon
 
From: [hidden email] [mailto:galaxy-[hidden email]] On Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 10:52 AM
To: 'Greg Von Kuster'
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install
 
Hi,
 
Yes the error is:
Error installing tool dependency package tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found
 
-Sheldon
 
From: Greg Von Kuster [[hidden email]] 
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install
 
You should be able to click on the missing tool dependency and see its installation log.  It should show you whatever error is occuring that is not allowing successful installation.
 
Greg Von Kuster
 
On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" <[hidden email]> wrote:

 

Hi,
 
The repair operation doesn’t seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.
 
-Sheldon
 
 
From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install
 
Hi Sheldon,
 
I recommend not manually changing any database entries.  You should be able to install the repository and all of its dependencies using the Repair Repository feature.  See https://wiki.galaxyproject.org/RepairingInstalledRepositories
 
Greg Von Kuster
 
On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]> wrote:



Hi,
 
Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven’t had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!
-Sheldon  
 
1. Manually remove the installed repository subdirectory hierarchy from disk. 
2. If the repository included any tools, manually remove entries for each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories ) 
3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required: 

The following assumes you're using postgres: 

update tool_shed_repository set deleted=True, uninstalled=True, status='Uninstalled', error_message=Null  where name = 'bcftools_view';
 
 
 
From: Briand, Sheldon 
Sent: Wednesday, March 12, 2014 11:44 AM
To: [hidden email]
Subject: tophat2 install
 
Hi,
 
I ran into a problem installing tophat2 here:
tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found
 
I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.
 
Repairing the repository doesn’t make any difference.
 
Thanks!
-Sheldon
 
Sheldon Briand
NRC Research Computing Support Analyst
Research Computing Support / Soutien Informartique a la Recherche
Operations, Science Portfolio / Operations, Portefeuil des sciences
SSC-NRC / SPC-CNRC
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS  B3H 3Z1
902 426-1677
 
___________________________________________________________
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:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/
 
<Screenshot.png>
 
___________________________________________________________
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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To search Galaxy mailing lists use the unified search at:
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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:
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Re: tophat2 install

Briand, Sheldon
<base href="x-msg://230/">

Hi,

 

dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473

contains only:

env.sh

 

If that isn’t the right place to look let me know.

 

-Sheldon

 

From: Greg Von Kuster [mailto:[hidden email]]
Sent: Thursday, March 20, 2014 2:04 PM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

It looks like your database and file system are out of sync.  Your database seems to think you have an installed repository but your file system does not seem to have the repository's installation directory.  Can you confirm that this is the case?

 

 

On Mar 20, 2014, at 11:53 AM, "Briand, Sheldon" <[hidden email]> wrote:



Hi,

 

Here is the error from the paster.log:

 

Traceback (most recent call last):

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", line 496, in handle_tool_dependencies

    from_install_manager=from_install_manager )

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 318, in install_package

    from_install_manager=from_install_manager )

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 245, in handle_complex_repository_d

ependency_for_package

    tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 126, in get_absolute_path_to_file_i

n_repository

    for root, dirs, files in os.walk( repo_files_dir ):

  File "/opt/local/python-2.7.5/lib/python2.7/os.py", line 276, in walk

    names = listdir(top)

TypeError: coercing to Unicode: need string or buffer, NoneType found

 

-Sheldon

 

From: [hidden email] [mailto:galaxy-[hidden email]] On Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 10:52 AM
To: 'Greg Von Kuster'
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

Hi,

 

Yes the error is:

Error installing tool dependency package tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found

 

-Sheldon

 

From: Greg Von Kuster [[hidden email]] 
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

You should be able to click on the missing tool dependency and see its installation log.  It should show you whatever error is occuring that is not allowing successful installation.

 

Greg Von Kuster

 

On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" <[hidden email]> wrote:

 

Hi,

 

The repair operation doesn’t seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.

 

-Sheldon

 

 

From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

Hi Sheldon,

 

I recommend not manually changing any database entries.  You should be able to install the repository and all of its dependencies using the Repair Repository feature.  See https://wiki.galaxyproject.org/RepairingInstalledRepositories

 

Greg Von Kuster

 

On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]> wrote:




Hi,

 

Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven’t had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!

-Sheldon  

 

1. Manually remove the installed repository subdirectory hierarchy from disk. 
2. If the repository included any tools, manually remove entries for each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories ) 
3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required: 

The following assumes you're using postgres: 

update tool_shed_repository set deleted=True, uninstalled=True, status='Uninstalled', error_message=Null  where name = 'bcftools_view';

 

 

 

From: Briand, Sheldon 
Sent: Wednesday, March 12, 2014 11:44 AM
To: [hidden email]
Subject: tophat2 install

 

Hi,

 

I ran into a problem installing tophat2 here:

tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found

 

I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.

 

Repairing the repository doesn’t make any difference.

 

Thanks!

-Sheldon

 

Sheldon Briand

NRC Research Computing Support Analyst

Research Computing Support / Soutien Informartique a la Recherche

Operations, Science Portfolio / Operations, Portefeuil des sciences

SSC-NRC / SPC-CNRC

Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford

Halifax, NS  B3H 3Z1

902 426-1677

 

___________________________________________________________
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:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

 

<Screenshot.png>

 

___________________________________________________________
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:
 http://lists.bx.psu.edu/

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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: tophat2 install

Greg Von Kuster
<base href="x-msg://230/">What version of Galaxy are you running?  You want to look in the tophat2 repository directory, not its package dependency.  There should be a tool_dependencies.xml file in the tophat2's installation directory hierarchy somewhere.

On Mar 20, 2014, at 1:12 PM, "Briand, Sheldon" <[hidden email]> wrote:

Hi,
 
dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473
contains only:
env.sh
 
If that isn’t the right place to look let me know.
 
-Sheldon
 
From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Thursday, March 20, 2014 2:04 PM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install
 
It looks like your database and file system are out of sync.  Your database seems to think you have an installed repository but your file system does not seem to have the repository's installation directory.  Can you confirm that this is the case?
 
 
On Mar 20, 2014, at 11:53 AM, "Briand, Sheldon" <[hidden email]> wrote:


Hi,
 
Here is the error from the paster.log:
 
Traceback (most recent call last):
  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", line 496, in handle_tool_dependencies
    from_install_manager=from_install_manager )
  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 318, in install_package
    from_install_manager=from_install_manager )
  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 245, in handle_complex_repository_d
ependency_for_package
    tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 126, in get_absolute_path_to_file_i
n_repository
    for root, dirs, files in os.walk( repo_files_dir ):
  File "/opt/local/python-2.7.5/lib/python2.7/os.py", line 276, in walk
    names = listdir(top)
TypeError: coercing to Unicode: need string or buffer, NoneType found
 
-Sheldon
 
From: [hidden email] [mailto:galaxy-[hidden email]] On Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 10:52 AM
To: 'Greg Von Kuster'
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install
 
Hi,
 
Yes the error is:
Error installing tool dependency package tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found
 
-Sheldon
 
From: Greg Von Kuster [[hidden email]] 
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install
 
You should be able to click on the missing tool dependency and see its installation log.  It should show you whatever error is occuring that is not allowing successful installation.
 
Greg Von Kuster
 
On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" <[hidden email]> wrote:

 

Hi,
 
The repair operation doesn’t seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.
 
-Sheldon
 
 
From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install
 
Hi Sheldon,
 
I recommend not manually changing any database entries.  You should be able to install the repository and all of its dependencies using the Repair Repository feature.  See https://wiki.galaxyproject.org/RepairingInstalledRepositories
 
Greg Von Kuster
 
On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]> wrote:




Hi,
 
Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven’t had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!
-Sheldon  
 
1. Manually remove the installed repository subdirectory hierarchy from disk. 
2. If the repository included any tools, manually remove entries for each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories ) 
3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required: 

The following assumes you're using postgres: 

update tool_shed_repository set deleted=True, uninstalled=True, status='Uninstalled', error_message=Null  where name = 'bcftools_view';
 
 
 
From: Briand, Sheldon 
Sent: Wednesday, March 12, 2014 11:44 AM
To: [hidden email]
Subject: tophat2 install
 
Hi,
 
I ran into a problem installing tophat2 here:
tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found
 
I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.
 
Repairing the repository doesn’t make any difference.
 
Thanks!
-Sheldon
 
Sheldon Briand
NRC Research Computing Support Analyst
Research Computing Support / Soutien Informartique a la Recherche
Operations, Science Portfolio / Operations, Portefeuil des sciences
SSC-NRC / SPC-CNRC
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS  B3H 3Z1
902 426-1677
 
___________________________________________________________
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:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/
 
<Screenshot.png>
 
___________________________________________________________
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:
 http://lists.bx.psu.edu/

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:
 http://lists.bx.psu.edu/

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:
  http://lists.bx.psu.edu/

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: tophat2 install

Briand, Sheldon
<base href="x-msg://230/">

$ hg summary

parent: 12441:dc067a95261d

 

From the tool_dependencies.xml:

 

<package name="tophat2" version="2.0.9">

      <repository changeset_revision="8549fd545473" name="package_tophat2_2_0_9" owner="devteam" prior_installation_required="False" toolshed

="http://toolshed.g2.bx.psu.edu" />

 

 

From: Greg Von Kuster [mailto:[hidden email]]
Sent: Thursday, March 20, 2014 2:23 PM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

What version of Galaxy are you running?  You want to look in the tophat2 repository directory, not its package dependency.  There should be a tool_dependencies.xml file in the tophat2's installation directory hierarchy somewhere.

 

On Mar 20, 2014, at 1:12 PM, "Briand, Sheldon" <[hidden email]> wrote:



Hi,

 

dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473

contains only:

env.sh

 

If that isn’t the right place to look let me know.

 

-Sheldon

 

From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Thursday, March 20, 2014 2:04 PM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

It looks like your database and file system are out of sync.  Your database seems to think you have an installed repository but your file system does not seem to have the repository's installation directory.  Can you confirm that this is the case?

 

 

On Mar 20, 2014, at 11:53 AM, "Briand, Sheldon" <[hidden email]> wrote:




Hi,

 

Here is the error from the paster.log:

 

Traceback (most recent call last):

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", line 496, in handle_tool_dependencies

    from_install_manager=from_install_manager )

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 318, in install_package

    from_install_manager=from_install_manager )

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 245, in handle_complex_repository_d

ependency_for_package

    tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 126, in get_absolute_path_to_file_i

n_repository

    for root, dirs, files in os.walk( repo_files_dir ):

  File "/opt/local/python-2.7.5/lib/python2.7/os.py", line 276, in walk

    names = listdir(top)

TypeError: coercing to Unicode: need string or buffer, NoneType found

 

-Sheldon

 

From: [hidden email] [mailto:galaxy-[hidden email]] On Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 10:52 AM
To: 'Greg Von Kuster'
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

Hi,

 

Yes the error is:

Error installing tool dependency package tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found

 

-Sheldon

 

From: Greg Von Kuster [[hidden email]] 
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

You should be able to click on the missing tool dependency and see its installation log.  It should show you whatever error is occuring that is not allowing successful installation.

 

Greg Von Kuster

 

On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" <[hidden email]> wrote:

 

Hi,

 

The repair operation doesn’t seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.

 

-Sheldon

 

 

From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

Hi Sheldon,

 

I recommend not manually changing any database entries.  You should be able to install the repository and all of its dependencies using the Repair Repository feature.  See https://wiki.galaxyproject.org/RepairingInstalledRepositories

 

Greg Von Kuster

 

On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]> wrote:





Hi,

 

Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven’t had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!

-Sheldon  

 

1. Manually remove the installed repository subdirectory hierarchy from disk. 
2. If the repository included any tools, manually remove entries for each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories ) 
3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required: 

The following assumes you're using postgres: 

update tool_shed_repository set deleted=True, uninstalled=True, status='Uninstalled', error_message=Null  where name = 'bcftools_view';

 

 

 

From: Briand, Sheldon 
Sent: Wednesday, March 12, 2014 11:44 AM
To: [hidden email]
Subject: tophat2 install

 

Hi,

 

I ran into a problem installing tophat2 here:

tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found

 

I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.

 

Repairing the repository doesn’t make any difference.

 

Thanks!

-Sheldon

 

Sheldon Briand

NRC Research Computing Support Analyst

Research Computing Support / Soutien Informartique a la Recherche

Operations, Science Portfolio / Operations, Portefeuil des sciences

SSC-NRC / SPC-CNRC

Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford

Halifax, NS  B3H 3Z1

902 426-1677

 

___________________________________________________________
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:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

 

<Screenshot.png>

 

___________________________________________________________
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:
 http://lists.bx.psu.edu/

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:
 http://lists.bx.psu.edu/

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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
Reply | Threaded
Open this post in threaded view
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Re: tophat2 install

Greg Von Kuster
<base href="x-msg://230/">There have been several fixes released to the stable branch that you do not have in 12441.  I would recommend doing the following:

hg pull
hg update stable

Then uninstall the tophat2 repository and reinstall it.  See if that makes a difference.


On Mar 20, 2014, at 1:30 PM, "Briand, Sheldon" <[hidden email]> wrote:

$ hg summary
parent: 12441:dc067a95261d
 
From the tool_dependencies.xml:
 
<package name="tophat2" version="2.0.9">
      <repository changeset_revision="8549fd545473" name="package_tophat2_2_0_9" owner="devteam" prior_installation_required="False" toolshed
 
 
From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Thursday, March 20, 2014 2:23 PM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install
 
What version of Galaxy are you running?  You want to look in the tophat2 repository directory, not its package dependency.  There should be a tool_dependencies.xml file in the tophat2's installation directory hierarchy somewhere.
 
On Mar 20, 2014, at 1:12 PM, "Briand, Sheldon" <[hidden email]> wrote:


Hi,
 
dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473
contains only:
env.sh
 
If that isn’t the right place to look let me know.
 
-Sheldon
 
From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Thursday, March 20, 2014 2:04 PM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install
 
It looks like your database and file system are out of sync.  Your database seems to think you have an installed repository but your file system does not seem to have the repository's installation directory.  Can you confirm that this is the case?
 
 
On Mar 20, 2014, at 11:53 AM, "Briand, Sheldon" <[hidden email]> wrote:



Hi,
 
Here is the error from the paster.log:
 
Traceback (most recent call last):
  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", line 496, in handle_tool_dependencies
    from_install_manager=from_install_manager )
  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 318, in install_package
    from_install_manager=from_install_manager )
  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 245, in handle_complex_repository_d
ependency_for_package
    tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 126, in get_absolute_path_to_file_i
n_repository
    for root, dirs, files in os.walk( repo_files_dir ):
  File "/opt/local/python-2.7.5/lib/python2.7/os.py", line 276, in walk
    names = listdir(top)
TypeError: coercing to Unicode: need string or buffer, NoneType found
 
-Sheldon
 
From: [hidden email] [mailto:galaxy-[hidden email]] On Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 10:52 AM
To: 'Greg Von Kuster'
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install
 
Hi,
 
Yes the error is:
Error installing tool dependency package tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found
 
-Sheldon
 
From: Greg Von Kuster [[hidden email]] 
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install
 
You should be able to click on the missing tool dependency and see its installation log.  It should show you whatever error is occuring that is not allowing successful installation.
 
Greg Von Kuster
 
On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" <[hidden email]> wrote:

 

Hi,
 
The repair operation doesn’t seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.
 
-Sheldon
 
 
From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install
 
Hi Sheldon,
 
I recommend not manually changing any database entries.  You should be able to install the repository and all of its dependencies using the Repair Repository feature.  See https://wiki.galaxyproject.org/RepairingInstalledRepositories
 
Greg Von Kuster
 
On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]> wrote:





Hi,
 
Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven’t had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!
-Sheldon  
 
1. Manually remove the installed repository subdirectory hierarchy from disk. 
2. If the repository included any tools, manually remove entries for each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories ) 
3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required: 

The following assumes you're using postgres: 

update tool_shed_repository set deleted=True, uninstalled=True, status='Uninstalled', error_message=Null  where name = 'bcftools_view';
 
 
 
From: Briand, Sheldon 
Sent: Wednesday, March 12, 2014 11:44 AM
To: [hidden email]
Subject: tophat2 install
 
Hi,
 
I ran into a problem installing tophat2 here:
tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found
 
I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.
 
Repairing the repository doesn’t make any difference.
 
Thanks!
-Sheldon
 
Sheldon Briand
NRC Research Computing Support Analyst
Research Computing Support / Soutien Informartique a la Recherche
Operations, Science Portfolio / Operations, Portefeuil des sciences
SSC-NRC / SPC-CNRC
Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
Halifax, NS  B3H 3Z1
902 426-1677
 
___________________________________________________________
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:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/
 
<Screenshot.png>
 
___________________________________________________________
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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To search Galaxy mailing lists use the unified search at:
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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:
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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
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Re: tophat2 install

Briand, Sheldon
<base href="x-msg://230/">

pulling from https://bitbucket.org/galaxy/galaxy-dist

searching for changes

no changes found

 

From: Greg Von Kuster [mailto:[hidden email]]
Sent: Thursday, March 20, 2014 2:36 PM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

There have been several fixes released to the stable branch that you do not have in 12441.  I would recommend doing the following:

 

hg pull

hg update stable

 

Then uninstall the tophat2 repository and reinstall it.  See if that makes a difference.

 

 

On Mar 20, 2014, at 1:30 PM, "Briand, Sheldon" <[hidden email]> wrote:



$ hg summary

parent: 12441:dc067a95261d

 

From the tool_dependencies.xml:

 

<package name="tophat2" version="2.0.9">

      <repository changeset_revision="8549fd545473" name="package_tophat2_2_0_9" owner="devteam" prior_installation_required="False" toolshed

 

 

From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Thursday, March 20, 2014 2:23 PM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

What version of Galaxy are you running?  You want to look in the tophat2 repository directory, not its package dependency.  There should be a tool_dependencies.xml file in the tophat2's installation directory hierarchy somewhere.

 

On Mar 20, 2014, at 1:12 PM, "Briand, Sheldon" <[hidden email]> wrote:




Hi,

 

dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473

contains only:

env.sh

 

If that isn’t the right place to look let me know.

 

-Sheldon

 

From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Thursday, March 20, 2014 2:04 PM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

It looks like your database and file system are out of sync.  Your database seems to think you have an installed repository but your file system does not seem to have the repository's installation directory.  Can you confirm that this is the case?

 

 

On Mar 20, 2014, at 11:53 AM, "Briand, Sheldon" <[hidden email]> wrote:





Hi,

 

Here is the error from the paster.log:

 

Traceback (most recent call last):

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", line 496, in handle_tool_dependencies

    from_install_manager=from_install_manager )

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 318, in install_package

    from_install_manager=from_install_manager )

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 245, in handle_complex_repository_d

ependency_for_package

    tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )

  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 126, in get_absolute_path_to_file_i

n_repository

    for root, dirs, files in os.walk( repo_files_dir ):

  File "/opt/local/python-2.7.5/lib/python2.7/os.py", line 276, in walk

    names = listdir(top)

TypeError: coercing to Unicode: need string or buffer, NoneType found

 

-Sheldon

 

From: [hidden email] [mailto:galaxy-[hidden email]] On Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 10:52 AM
To: 'Greg Von Kuster'
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

Hi,

 

Yes the error is:

Error installing tool dependency package tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found

 

-Sheldon

 

From: Greg Von Kuster [[hidden email]] 
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

You should be able to click on the missing tool dependency and see its installation log.  It should show you whatever error is occuring that is not allowing successful installation.

 

Greg Von Kuster

 

On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" <[hidden email]> wrote:

 

Hi,

 

The repair operation doesn’t seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.

 

-Sheldon

 

 

From: Greg Von Kuster [mailto:greg@bx.psu.edu] 
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: '[hidden email]'
Subject: Re: [galaxy-dev] tophat2 install

 

Hi Sheldon,

 

I recommend not manually changing any database entries.  You should be able to install the repository and all of its dependencies using the Repair Repository feature.  See https://wiki.galaxyproject.org/RepairingInstalledRepositories

 

Greg Von Kuster

 

On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]> wrote:






Hi,

 

Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven’t had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!

-Sheldon  

 

1. Manually remove the installed repository subdirectory hierarchy from disk. 
2. If the repository included any tools, manually remove entries for each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories ) 
3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required: 

The following assumes you're using postgres: 

update tool_shed_repository set deleted=True, uninstalled=True, status='Uninstalled', error_message=Null  where name = 'bcftools_view';

 

 

 

From: Briand, Sheldon 
Sent: Wednesday, March 12, 2014 11:44 AM
To: [hidden email]
Subject: tophat2 install

 

Hi,

 

I ran into a problem installing tophat2 here:

tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found

 

I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.

 

Repairing the repository doesn’t make any difference.

 

Thanks!

-Sheldon

 

Sheldon Briand

NRC Research Computing Support Analyst

Research Computing Support / Soutien Informartique a la Recherche

Operations, Science Portfolio / Operations, Portefeuil des sciences

SSC-NRC / SPC-CNRC

Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford

Halifax, NS  B3H 3Z1

902 426-1677

 

___________________________________________________________
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:
 http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/mailinglists/

 

<Screenshot.png>

 

___________________________________________________________
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:
 http://lists.bx.psu.edu/

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:
 http://lists.bx.psu.edu/

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
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Re: tophat2 install

Björn Grüning-3
Hi,

you need to track galaxy-central to make use of the patches that are
applied as bugfixes after the release. You can do that easily with
changing the path in .hg/hgrc ... but I do not know if that is the right
way to do ;) For me it worked.

Cheers,
Bjoern

Am 20.03.2014 18:46, schrieb Briand, Sheldon:

> pulling from https://bitbucket.org/galaxy/galaxy-dist
> searching for changes
> no changes found
>
> From: Greg Von Kuster [mailto:[hidden email]]
> Sent: Thursday, March 20, 2014 2:36 PM
> To: Briand, Sheldon
> Cc: '[hidden email]'
> Subject: Re: [galaxy-dev] tophat2 install
>
> There have been several fixes released to the stable branch that you do not have in 12441.  I would recommend doing the following:
>
> hg pull
> hg update stable
>
> Then uninstall the tophat2 repository and reinstall it.  See if that makes a difference.
>
>
> On Mar 20, 2014, at 1:30 PM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>
>
> $ hg summary
> parent: 12441:dc067a95261d
>
>>From the tool_dependencies.xml:
>
> <package name="tophat2" version="2.0.9">
>        <repository changeset_revision="8549fd545473" name="package_tophat2_2_0_9" owner="devteam" prior_installation_required="False" toolshed
> ="http://toolshed.g2.bx.psu.edu" />
>
>
> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
> Sent: Thursday, March 20, 2014 2:23 PM
> To: Briand, Sheldon
> Cc: '[hidden email]<mailto:[hidden email]>'
> Subject: Re: [galaxy-dev] tophat2 install
>
> What version of Galaxy are you running?  You want to look in the tophat2 repository directory, not its package dependency.  There should be a tool_dependencies.xml file in the tophat2's installation directory hierarchy somewhere.
>
> On Mar 20, 2014, at 1:12 PM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>
>
>
> Hi,
>
> dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473
> contains only:
> env.sh
>
> If that isn't the right place to look let me know.
>
> -Sheldon
>
> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
> Sent: Thursday, March 20, 2014 2:04 PM
> To: Briand, Sheldon
> Cc: '[hidden email]<mailto:[hidden email]>'
> Subject: Re: [galaxy-dev] tophat2 install
>
> It looks like your database and file system are out of sync.  Your database seems to think you have an installed repository but your file system does not seem to have the repository's installation directory.  Can you confirm that this is the case?
>
>
> On Mar 20, 2014, at 11:53 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>
>
>
>
> Hi,
>
> Here is the error from the paster.log:
>
> Traceback (most recent call last):
>    File "/BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", line 496, in handle_tool_dependencies
>      from_install_manager=from_install_manager )
>    File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 318, in install_package
>      from_install_manager=from_install_manager )
>    File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 245, in handle_complex_repository_d
> ependency_for_package
>      tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
>    File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 126, in get_absolute_path_to_file_i
> n_repository
>      for root, dirs, files in os.walk( repo_files_dir ):
>    File "/opt/local/python-2.7.5/lib/python2.7/os.py", line 276, in walk
>      names = listdir(top)
> TypeError: coercing to Unicode: need string or buffer, NoneType found
>
> -Sheldon
>
> From: [hidden email]<mailto:[hidden email]> [mailto:[hidden email]<mailto:[hidden email]>] On Behalf Of Briand, Sheldon
> Sent: Thursday, March 20, 2014 10:52 AM
> To: 'Greg Von Kuster'
> Cc: '[hidden email]<mailto:[hidden email]>'
> Subject: Re: [galaxy-dev] tophat2 install
>
> Hi,
>
> Yes the error is:
> Error installing tool dependency package tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found
>
> -Sheldon
>
> From: Greg Von Kuster [mailto:[hidden email]]
> Sent: Thursday, March 20, 2014 10:49 AM
> To: Briand, Sheldon
> Cc: '[hidden email]<mailto:[hidden email]>'
> Subject: Re: [galaxy-dev] tophat2 install
>
> You should be able to click on the missing tool dependency and see its installation log.  It should show you whatever error is occuring that is not allowing successful installation.
>
> Greg Von Kuster
>
> On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>
> Hi,
>
> The repair operation doesn't seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.
>
> -Sheldon
>
>
> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
> Sent: Thursday, March 20, 2014 10:26 AM
> To: Briand, Sheldon
> Cc: '[hidden email]<mailto:[hidden email]>'
> Subject: Re: [galaxy-dev] tophat2 install
>
> Hi Sheldon,
>
> I recommend not manually changing any database entries.  You should be able to install the repository and all of its dependencies using the Repair Repository feature.  See https://wiki.galaxyproject.org/RepairingInstalledRepositories
>
> Greg Von Kuster
>
> On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>
>
>
>
>
> Hi,
>
> Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven't had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!
> -Sheldon
>
> 1. Manually remove the installed repository subdirectory hierarchy from disk.
> 2. If the repository included any tools, manually remove entries for each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories )
> 3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required:
>
> The following assumes you're using postgres:
>
> update tool_shed_repository set deleted=True, uninstalled=True, status='Uninstalled', error_message=Null  where name = 'bcftools_view';
>
>
>
> From: Briand, Sheldon
> Sent: Wednesday, March 12, 2014 11:44 AM
> To: [hidden email]<mailto:[hidden email]>
> Subject: tophat2 install
>
> Hi,
>
> I ran into a problem installing tophat2 here:
> tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found
>
> I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.
>
> Repairing the repository doesn't make any difference.
>
> Thanks!
> -Sheldon
>
> Sheldon Briand
> NRC Research Computing Support Analyst
> Research Computing Support / Soutien Informartique a la Recherche
> Operations, Science Portfolio / Operations, Portefeuil des sciences
> SSC-NRC / SPC-CNRC
> Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
> Halifax, NS  B3H 3Z1
> 902 426-1677
> [hidden email]<mailto:[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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
> <Screenshot.png>
>
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
>
> 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:
>   http://lists.bx.psu.edu/
>
> 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:
>    http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Re: tophat2 install

Greg Von Kuster
Sorry, should have advised this:

> hg pull https://bitbucket.org/galaxy/galaxy-central#stable
> hg update stable

See the end ot this thread:

http://dev.list.galaxyproject.org/Persistent-jobs-in-cluster-queue-even-after-canceling-job-in-galaxy-td4663719.html




On Mar 20, 2014, at 1:51 PM, Björn Grüning <[hidden email]> wrote:

> Hi,
>
> you need to track galaxy-central to make use of the patches that are applied as bugfixes after the release. You can do that easily with changing the path in .hg/hgrc ... but I do not know if that is the right way to do ;) For me it worked.
>
> Cheers,
> Bjoern
>
> Am 20.03.2014 18:46, schrieb Briand, Sheldon:
>> pulling from https://bitbucket.org/galaxy/galaxy-dist
>> searching for changes
>> no changes found
>>
>> From: Greg Von Kuster [mailto:[hidden email]]
>> Sent: Thursday, March 20, 2014 2:36 PM
>> To: Briand, Sheldon
>> Cc: '[hidden email]'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> There have been several fixes released to the stable branch that you do not have in 12441.  I would recommend doing the following:
>>
>> hg pull
>> hg update stable
>>
>> Then uninstall the tophat2 repository and reinstall it.  See if that makes a difference.
>>
>>
>> On Mar 20, 2014, at 1:30 PM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>
>>
>> $ hg summary
>> parent: 12441:dc067a95261d
>>
>>> From the tool_dependencies.xml:
>>
>> <package name="tophat2" version="2.0.9">
>>       <repository changeset_revision="8549fd545473" name="package_tophat2_2_0_9" owner="devteam" prior_installation_required="False" toolshed
>> ="http://toolshed.g2.bx.psu.edu" />
>>
>>
>> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
>> Sent: Thursday, March 20, 2014 2:23 PM
>> To: Briand, Sheldon
>> Cc: '[hidden email]<mailto:[hidden email]>'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> What version of Galaxy are you running?  You want to look in the tophat2 repository directory, not its package dependency.  There should be a tool_dependencies.xml file in the tophat2's installation directory hierarchy somewhere.
>>
>> On Mar 20, 2014, at 1:12 PM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>
>>
>>
>> Hi,
>>
>> dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473
>> contains only:
>> env.sh
>>
>> If that isn't the right place to look let me know.
>>
>> -Sheldon
>>
>> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
>> Sent: Thursday, March 20, 2014 2:04 PM
>> To: Briand, Sheldon
>> Cc: '[hidden email]<mailto:[hidden email]>'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> It looks like your database and file system are out of sync.  Your database seems to think you have an installed repository but your file system does not seem to have the repository's installation directory.  Can you confirm that this is the case?
>>
>>
>> On Mar 20, 2014, at 11:53 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>
>>
>>
>>
>> Hi,
>>
>> Here is the error from the paster.log:
>>
>> Traceback (most recent call last):
>>   File "/BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", line 496, in handle_tool_dependencies
>>     from_install_manager=from_install_manager )
>>   File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 318, in install_package
>>     from_install_manager=from_install_manager )
>>   File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 245, in handle_complex_repository_d
>> ependency_for_package
>>     tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
>>   File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 126, in get_absolute_path_to_file_i
>> n_repository
>>     for root, dirs, files in os.walk( repo_files_dir ):
>>   File "/opt/local/python-2.7.5/lib/python2.7/os.py", line 276, in walk
>>     names = listdir(top)
>> TypeError: coercing to Unicode: need string or buffer, NoneType found
>>
>> -Sheldon
>>
>> From: [hidden email]<mailto:[hidden email]> [mailto:[hidden email]<mailto:[hidden email]>] On Behalf Of Briand, Sheldon
>> Sent: Thursday, March 20, 2014 10:52 AM
>> To: 'Greg Von Kuster'
>> Cc: '[hidden email]<mailto:[hidden email]>'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> Hi,
>>
>> Yes the error is:
>> Error installing tool dependency package tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found
>>
>> -Sheldon
>>
>> From: Greg Von Kuster [mailto:[hidden email]]
>> Sent: Thursday, March 20, 2014 10:49 AM
>> To: Briand, Sheldon
>> Cc: '[hidden email]<mailto:[hidden email]>'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> You should be able to click on the missing tool dependency and see its installation log.  It should show you whatever error is occuring that is not allowing successful installation.
>>
>> Greg Von Kuster
>>
>> On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>
>> Hi,
>>
>> The repair operation doesn't seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.
>>
>> -Sheldon
>>
>>
>> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
>> Sent: Thursday, March 20, 2014 10:26 AM
>> To: Briand, Sheldon
>> Cc: '[hidden email]<mailto:[hidden email]>'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> Hi Sheldon,
>>
>> I recommend not manually changing any database entries.  You should be able to install the repository and all of its dependencies using the Repair Repository feature.  See https://wiki.galaxyproject.org/RepairingInstalledRepositories
>>
>> Greg Von Kuster
>>
>> On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>
>>
>>
>>
>>
>> Hi,
>>
>> Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven't had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!
>> -Sheldon
>>
>> 1. Manually remove the installed repository subdirectory hierarchy from disk.
>> 2. If the repository included any tools, manually remove entries for each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories )
>> 3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required:
>>
>> The following assumes you're using postgres:
>>
>> update tool_shed_repository set deleted=True, uninstalled=True, status='Uninstalled', error_message=Null  where name = 'bcftools_view';
>>
>>
>>
>> From: Briand, Sheldon
>> Sent: Wednesday, March 12, 2014 11:44 AM
>> To: [hidden email]<mailto:[hidden email]>
>> Subject: tophat2 install
>>
>> Hi,
>>
>> I ran into a problem installing tophat2 here:
>> tophat2 version 2.0.9: coercing to Unicode: need string or buffer, NoneType found
>>
>> I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.
>>
>> Repairing the repository doesn't make any difference.
>>
>> Thanks!
>> -Sheldon
>>
>> Sheldon Briand
>> NRC Research Computing Support Analyst
>> Research Computing Support / Soutien Informartique a la Recherche
>> Operations, Science Portfolio / Operations, Portefeuil des sciences
>> SSC-NRC / SPC-CNRC
>> Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford
>> Halifax, NS  B3H 3Z1
>> 902 426-1677
>> [hidden email]<mailto:[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:
>>  http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>  http://galaxyproject.org/search/mailinglists/
>>
>> <Screenshot.png>
>>
>> ___________________________________________________________
>> 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:
>>  http://lists.bx.psu.edu/
>>
>> 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:
>>  http://lists.bx.psu.edu/
>>
>> 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:
>>   http://lists.bx.psu.edu/
>>
>> 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:
> http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: tophat2 install

Briand, Sheldon
No difference.  Same error

-----Original Message-----
From: Greg Von Kuster [mailto:[hidden email]]
Sent: Thursday, March 20, 2014 2:56 PM
To: Briand, Sheldon
Cc: [hidden email] Dev
Subject: Re: [galaxy-dev] tophat2 install

Sorry, should have advised this:

> hg pull https://bitbucket.org/galaxy/galaxy-central#stable
> hg update stable

See the end ot this thread:

http://dev.list.galaxyproject.org/Persistent-jobs-in-cluster-queue-even-after-canceling-job-in-galaxy-td4663719.html




On Mar 20, 2014, at 1:51 PM, Björn Grüning <[hidden email]> wrote:

> Hi,
>
> you need to track galaxy-central to make use of the patches that are applied as bugfixes after the release. You can do that easily with changing the path in .hg/hgrc ... but I do not know if that is the right way to do ;) For me it worked.
>
> Cheers,
> Bjoern
>
> Am 20.03.2014 18:46, schrieb Briand, Sheldon:
>> pulling from https://bitbucket.org/galaxy/galaxy-dist
>> searching for changes
>> no changes found
>>
>> From: Greg Von Kuster [mailto:[hidden email]]
>> Sent: Thursday, March 20, 2014 2:36 PM
>> To: Briand, Sheldon
>> Cc: '[hidden email]'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> There have been several fixes released to the stable branch that you do not have in 12441.  I would recommend doing the following:
>>
>> hg pull
>> hg update stable
>>
>> Then uninstall the tophat2 repository and reinstall it.  See if that makes a difference.
>>
>>
>> On Mar 20, 2014, at 1:30 PM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>
>>
>> $ hg summary
>> parent: 12441:dc067a95261d
>>
>>> From the tool_dependencies.xml:
>>
>> <package name="tophat2" version="2.0.9">
>>       <repository changeset_revision="8549fd545473"
>> name="package_tophat2_2_0_9" owner="devteam"
>> prior_installation_required="False" toolshed
>> ="http://toolshed.g2.bx.psu.edu" />
>>
>>
>> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
>> Sent: Thursday, March 20, 2014 2:23 PM
>> To: Briand, Sheldon
>> Cc: '[hidden email]<mailto:[hidden email]>'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> What version of Galaxy are you running?  You want to look in the tophat2 repository directory, not its package dependency.  There should be a tool_dependencies.xml file in the tophat2's installation directory hierarchy somewhere.
>>
>> On Mar 20, 2014, at 1:12 PM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>
>>
>>
>> Hi,
>>
>> dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473
>> contains only:
>> env.sh
>>
>> If that isn't the right place to look let me know.
>>
>> -Sheldon
>>
>> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
>> Sent: Thursday, March 20, 2014 2:04 PM
>> To: Briand, Sheldon
>> Cc: '[hidden email]<mailto:[hidden email]>'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> It looks like your database and file system are out of sync.  Your database seems to think you have an installed repository but your file system does not seem to have the repository's installation directory.  Can you confirm that this is the case?
>>
>>
>> On Mar 20, 2014, at 11:53 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>
>>
>>
>>
>> Hi,
>>
>> Here is the error from the paster.log:
>>
>> Traceback (most recent call last):
>>   File "/BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", line 496, in handle_tool_dependencies
>>     from_install_manager=from_install_manager )
>>   File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 318, in install_package
>>     from_install_manager=from_install_manager )
>>   File
>> "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 245, in handle_complex_repository_d ependency_for_package
>>     tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
>>   File
>> "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 126, in get_absolute_path_to_file_i n_repository
>>     for root, dirs, files in os.walk( repo_files_dir ):
>>   File "/opt/local/python-2.7.5/lib/python2.7/os.py", line 276, in walk
>>     names = listdir(top)
>> TypeError: coercing to Unicode: need string or buffer, NoneType found
>>
>> -Sheldon
>>
>> From:
>> [hidden email]<mailto:[hidden email]
>> x.psu.edu>
>> [mailto:[hidden email]<mailto:dev-bounces@lists.
>> bx.psu.edu>] On Behalf Of Briand, Sheldon
>> Sent: Thursday, March 20, 2014 10:52 AM
>> To: 'Greg Von Kuster'
>> Cc: '[hidden email]<mailto:[hidden email]>'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> Hi,
>>
>> Yes the error is:
>> Error installing tool dependency package tophat2 version 2.0.9:
>> coercing to Unicode: need string or buffer, NoneType found
>>
>> -Sheldon
>>
>> From: Greg Von Kuster [mailto:[hidden email]]
>> Sent: Thursday, March 20, 2014 10:49 AM
>> To: Briand, Sheldon
>> Cc: '[hidden email]<mailto:[hidden email]>'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> You should be able to click on the missing tool dependency and see its installation log.  It should show you whatever error is occuring that is not allowing successful installation.
>>
>> Greg Von Kuster
>>
>> On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>
>> Hi,
>>
>> The repair operation doesn't seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.
>>
>> -Sheldon
>>
>>
>> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
>> Sent: Thursday, March 20, 2014 10:26 AM
>> To: Briand, Sheldon
>> Cc: '[hidden email]<mailto:[hidden email]>'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> Hi Sheldon,
>>
>> I recommend not manually changing any database entries.  You should
>> be able to install the repository and all of its dependencies using
>> the Repair Repository feature.  See
>> https://wiki.galaxyproject.org/RepairingInstalledRepositories
>>
>> Greg Von Kuster
>>
>> On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>
>>
>>
>>
>>
>> Hi,
>>
>> Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven't had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!
>> -Sheldon
>>
>> 1. Manually remove the installed repository subdirectory hierarchy from disk.
>> 2. If the repository included any tools, manually remove entries for
>> each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories ) 3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required:
>>
>> The following assumes you're using postgres:
>>
>> update tool_shed_repository set deleted=True, uninstalled=True,
>> status='Uninstalled', error_message=Null  where name =
>> 'bcftools_view';
>>
>>
>>
>> From: Briand, Sheldon
>> Sent: Wednesday, March 12, 2014 11:44 AM
>> To: [hidden email]<mailto:[hidden email]>
>> Subject: tophat2 install
>>
>> Hi,
>>
>> I ran into a problem installing tophat2 here:
>> tophat2 version 2.0.9: coercing to Unicode: need string or buffer,
>> NoneType found
>>
>> I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.
>>
>> Repairing the repository doesn't make any difference.
>>
>> Thanks!
>> -Sheldon
>>
>> Sheldon Briand
>> NRC Research Computing Support Analyst Research Computing Support /
>> Soutien Informartique a la Recherche Operations, Science Portfolio /
>> Operations, Portefeuil des sciences SSC-NRC / SPC-CNRC Rm 329A, 1411
>> Oxford Street / Piece 329A, 1411 Rue Oxford Halifax, NS  B3H 3Z1
>> 902 426-1677
>> [hidden email]<mailto:[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:
>>  http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>  http://galaxyproject.org/search/mailinglists/
>>
>> <Screenshot.png>
>>
>> ___________________________________________________________
>> 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:
>>  http://lists.bx.psu.edu/
>>
>> 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:
>>  http://lists.bx.psu.edu/
>>
>> 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:
>>   http://lists.bx.psu.edu/
>>
>> 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:
> http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: tophat2 install

Briand, Sheldon
Hi,

Not sure if you saw my last email. Updating to the latest patch version doesn't seem to help.  I was wondering where I could get the galaxy package version of tophat2 and put it where it needs to be manually.  Then I could try the uninstall/install and see if that helps.

Thanks!
-Sheldon

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 3:11 PM
To: 'Greg Von Kuster'
Cc: [hidden email] Dev
Subject: Re: [galaxy-dev] tophat2 install

No difference.  Same error

-----Original Message-----
From: Greg Von Kuster [mailto:[hidden email]]
Sent: Thursday, March 20, 2014 2:56 PM
To: Briand, Sheldon
Cc: [hidden email] Dev
Subject: Re: [galaxy-dev] tophat2 install

Sorry, should have advised this:

> hg pull https://bitbucket.org/galaxy/galaxy-central#stable
> hg update stable

See the end ot this thread:

http://dev.list.galaxyproject.org/Persistent-jobs-in-cluster-queue-even-after-canceling-job-in-galaxy-td4663719.html




On Mar 20, 2014, at 1:51 PM, Björn Grüning <[hidden email]> wrote:

> Hi,
>
> you need to track galaxy-central to make use of the patches that are applied as bugfixes after the release. You can do that easily with changing the path in .hg/hgrc ... but I do not know if that is the right way to do ;) For me it worked.
>
> Cheers,
> Bjoern
>
> Am 20.03.2014 18:46, schrieb Briand, Sheldon:
>> pulling from https://bitbucket.org/galaxy/galaxy-dist
>> searching for changes
>> no changes found
>>
>> From: Greg Von Kuster [mailto:[hidden email]]
>> Sent: Thursday, March 20, 2014 2:36 PM
>> To: Briand, Sheldon
>> Cc: '[hidden email]'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> There have been several fixes released to the stable branch that you do not have in 12441.  I would recommend doing the following:
>>
>> hg pull
>> hg update stable
>>
>> Then uninstall the tophat2 repository and reinstall it.  See if that makes a difference.
>>
>>
>> On Mar 20, 2014, at 1:30 PM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>
>>
>> $ hg summary
>> parent: 12441:dc067a95261d
>>
>>> From the tool_dependencies.xml:
>>
>> <package name="tophat2" version="2.0.9">
>>       <repository changeset_revision="8549fd545473"
>> name="package_tophat2_2_0_9" owner="devteam"
>> prior_installation_required="False" toolshed
>> ="http://toolshed.g2.bx.psu.edu" />
>>
>>
>> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
>> Sent: Thursday, March 20, 2014 2:23 PM
>> To: Briand, Sheldon
>> Cc: '[hidden email]<mailto:[hidden email]>'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> What version of Galaxy are you running?  You want to look in the tophat2 repository directory, not its package dependency.  There should be a tool_dependencies.xml file in the tophat2's installation directory hierarchy somewhere.
>>
>> On Mar 20, 2014, at 1:12 PM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>
>>
>>
>> Hi,
>>
>> dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473
>> contains only:
>> env.sh
>>
>> If that isn't the right place to look let me know.
>>
>> -Sheldon
>>
>> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
>> Sent: Thursday, March 20, 2014 2:04 PM
>> To: Briand, Sheldon
>> Cc: '[hidden email]<mailto:[hidden email]>'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> It looks like your database and file system are out of sync.  Your database seems to think you have an installed repository but your file system does not seem to have the repository's installation directory.  Can you confirm that this is the case?
>>
>>
>> On Mar 20, 2014, at 11:53 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>
>>
>>
>>
>> Hi,
>>
>> Here is the error from the paster.log:
>>
>> Traceback (most recent call last):
>>   File "/BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", line 496, in handle_tool_dependencies
>>     from_install_manager=from_install_manager )
>>   File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 318, in install_package
>>     from_install_manager=from_install_manager )
>>   File
>> "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 245, in handle_complex_repository_d ependency_for_package
>>     tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
>>   File
>> "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 126, in get_absolute_path_to_file_i n_repository
>>     for root, dirs, files in os.walk( repo_files_dir ):
>>   File "/opt/local/python-2.7.5/lib/python2.7/os.py", line 276, in walk
>>     names = listdir(top)
>> TypeError: coercing to Unicode: need string or buffer, NoneType found
>>
>> -Sheldon
>>
>> From:
>> [hidden email]<mailto:[hidden email]
>> x.psu.edu>
>> [mailto:[hidden email]<mailto:dev-bounces@lists.
>> bx.psu.edu>] On Behalf Of Briand, Sheldon
>> Sent: Thursday, March 20, 2014 10:52 AM
>> To: 'Greg Von Kuster'
>> Cc: '[hidden email]<mailto:[hidden email]>'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> Hi,
>>
>> Yes the error is:
>> Error installing tool dependency package tophat2 version 2.0.9:
>> coercing to Unicode: need string or buffer, NoneType found
>>
>> -Sheldon
>>
>> From: Greg Von Kuster [mailto:[hidden email]]
>> Sent: Thursday, March 20, 2014 10:49 AM
>> To: Briand, Sheldon
>> Cc: '[hidden email]<mailto:[hidden email]>'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> You should be able to click on the missing tool dependency and see its installation log.  It should show you whatever error is occuring that is not allowing successful installation.
>>
>> Greg Von Kuster
>>
>> On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>
>> Hi,
>>
>> The repair operation doesn't seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.
>>
>> -Sheldon
>>
>>
>> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
>> Sent: Thursday, March 20, 2014 10:26 AM
>> To: Briand, Sheldon
>> Cc: '[hidden email]<mailto:[hidden email]>'
>> Subject: Re: [galaxy-dev] tophat2 install
>>
>> Hi Sheldon,
>>
>> I recommend not manually changing any database entries.  You should
>> be able to install the repository and all of its dependencies using
>> the Repair Repository feature.  See
>> https://wiki.galaxyproject.org/RepairingInstalledRepositories
>>
>> Greg Von Kuster
>>
>> On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>
>>
>>
>>
>>
>> Hi,
>>
>> Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven't had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!
>> -Sheldon
>>
>> 1. Manually remove the installed repository subdirectory hierarchy from disk.
>> 2. If the repository included any tools, manually remove entries for
>> each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories ) 3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required:
>>
>> The following assumes you're using postgres:
>>
>> update tool_shed_repository set deleted=True, uninstalled=True,
>> status='Uninstalled', error_message=Null  where name =
>> 'bcftools_view';
>>
>>
>>
>> From: Briand, Sheldon
>> Sent: Wednesday, March 12, 2014 11:44 AM
>> To: [hidden email]<mailto:[hidden email]>
>> Subject: tophat2 install
>>
>> Hi,
>>
>> I ran into a problem installing tophat2 here:
>> tophat2 version 2.0.9: coercing to Unicode: need string or buffer,
>> NoneType found
>>
>> I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.
>>
>> Repairing the repository doesn't make any difference.
>>
>> Thanks!
>> -Sheldon
>>
>> Sheldon Briand
>> NRC Research Computing Support Analyst Research Computing Support /
>> Soutien Informartique a la Recherche Operations, Science Portfolio /
>> Operations, Portefeuil des sciences SSC-NRC / SPC-CNRC Rm 329A, 1411
>> Oxford Street / Piece 329A, 1411 Rue Oxford Halifax, NS  B3H 3Z1
>> 902 426-1677
>> [hidden email]<mailto:[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:
>>  http://lists.bx.psu.edu/
>>
>> To search Galaxy mailing lists use the unified search at:
>>  http://galaxyproject.org/search/mailinglists/
>>
>> <Screenshot.png>
>>
>> ___________________________________________________________
>> 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:
>>  http://lists.bx.psu.edu/
>>
>> 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:
>>  http://lists.bx.psu.edu/
>>
>> 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:
>>   http://lists.bx.psu.edu/
>>
>> 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:
> http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: tophat2 install

Greg Von Kuster
If you installe dit from the main Tool Shed, then this repository has the recipe for installing the package.

http://toolshed.g2.bx.psu.edu/view/devteam/package_tophat2_2_0_9 

Greg Von Kuster
             
On Mar 25, 2014, at 9:25 AM, "Briand, Sheldon" <[hidden email]> wrote:

> Hi,
>
> Not sure if you saw my last email. Updating to the latest patch version doesn't seem to help.  I was wondering where I could get the galaxy package version of tophat2 and put it where it needs to be manually.  Then I could try the uninstall/install and see if that helps.
>
> Thanks!
> -Sheldon
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Briand, Sheldon
> Sent: Thursday, March 20, 2014 3:11 PM
> To: 'Greg Von Kuster'
> Cc: [hidden email] Dev
> Subject: Re: [galaxy-dev] tophat2 install
>
> No difference.  Same error
>
> -----Original Message-----
> From: Greg Von Kuster [mailto:[hidden email]]
> Sent: Thursday, March 20, 2014 2:56 PM
> To: Briand, Sheldon
> Cc: [hidden email] Dev
> Subject: Re: [galaxy-dev] tophat2 install
>
> Sorry, should have advised this:
>
>> hg pull https://bitbucket.org/galaxy/galaxy-central#stable
>> hg update stable
>
> See the end ot this thread:
>
> http://dev.list.galaxyproject.org/Persistent-jobs-in-cluster-queue-even-after-canceling-job-in-galaxy-td4663719.html
>
>
>
>
> On Mar 20, 2014, at 1:51 PM, Björn Grüning <[hidden email]> wrote:
>
>> Hi,
>>
>> you need to track galaxy-central to make use of the patches that are applied as bugfixes after the release. You can do that easily with changing the path in .hg/hgrc ... but I do not know if that is the right way to do ;) For me it worked.
>>
>> Cheers,
>> Bjoern
>>
>> Am 20.03.2014 18:46, schrieb Briand, Sheldon:
>>> pulling from https://bitbucket.org/galaxy/galaxy-dist
>>> searching for changes
>>> no changes found
>>>
>>> From: Greg Von Kuster [mailto:[hidden email]]
>>> Sent: Thursday, March 20, 2014 2:36 PM
>>> To: Briand, Sheldon
>>> Cc: '[hidden email]'
>>> Subject: Re: [galaxy-dev] tophat2 install
>>>
>>> There have been several fixes released to the stable branch that you do not have in 12441.  I would recommend doing the following:
>>>
>>> hg pull
>>> hg update stable
>>>
>>> Then uninstall the tophat2 repository and reinstall it.  See if that makes a difference.
>>>
>>>
>>> On Mar 20, 2014, at 1:30 PM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>>
>>> $ hg summary
>>> parent: 12441:dc067a95261d
>>>
>>>> From the tool_dependencies.xml:
>>>
>>> <package name="tophat2" version="2.0.9">
>>>      <repository changeset_revision="8549fd545473"
>>> name="package_tophat2_2_0_9" owner="devteam"
>>> prior_installation_required="False" toolshed
>>> ="http://toolshed.g2.bx.psu.edu" />
>>>
>>>
>>> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
>>> Sent: Thursday, March 20, 2014 2:23 PM
>>> To: Briand, Sheldon
>>> Cc: '[hidden email]<mailto:[hidden email]>'
>>> Subject: Re: [galaxy-dev] tophat2 install
>>>
>>> What version of Galaxy are you running?  You want to look in the tophat2 repository directory, not its package dependency.  There should be a tool_dependencies.xml file in the tophat2's installation directory hierarchy somewhere.
>>>
>>> On Mar 20, 2014, at 1:12 PM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>>
>>>
>>> Hi,
>>>
>>> dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd545473
>>> contains only:
>>> env.sh
>>>
>>> If that isn't the right place to look let me know.
>>>
>>> -Sheldon
>>>
>>> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
>>> Sent: Thursday, March 20, 2014 2:04 PM
>>> To: Briand, Sheldon
>>> Cc: '[hidden email]<mailto:[hidden email]>'
>>> Subject: Re: [galaxy-dev] tophat2 install
>>>
>>> It looks like your database and file system are out of sync.  Your database seems to think you have an installed repository but your file system does not seem to have the repository's installation directory.  Can you confirm that this is the case?
>>>
>>>
>>> On Mar 20, 2014, at 11:53 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>>
>>>
>>>
>>> Hi,
>>>
>>> Here is the error from the paster.log:
>>>
>>> Traceback (most recent call last):
>>>  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", line 496, in handle_tool_dependencies
>>>    from_install_manager=from_install_manager )
>>>  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 318, in install_package
>>>    from_install_manager=from_install_manager )
>>>  File
>>> "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 245, in handle_complex_repository_d ependency_for_package
>>>    tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
>>>  File
>>> "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 126, in get_absolute_path_to_file_i n_repository
>>>    for root, dirs, files in os.walk( repo_files_dir ):
>>>  File "/opt/local/python-2.7.5/lib/python2.7/os.py", line 276, in walk
>>>    names = listdir(top)
>>> TypeError: coercing to Unicode: need string or buffer, NoneType found
>>>
>>> -Sheldon
>>>
>>> From:
>>> [hidden email]<mailto:[hidden email]
>>> x.psu.edu>
>>> [mailto:[hidden email]<mailto:dev-bounces@lists.
>>> bx.psu.edu>] On Behalf Of Briand, Sheldon
>>> Sent: Thursday, March 20, 2014 10:52 AM
>>> To: 'Greg Von Kuster'
>>> Cc: '[hidden email]<mailto:[hidden email]>'
>>> Subject: Re: [galaxy-dev] tophat2 install
>>>
>>> Hi,
>>>
>>> Yes the error is:
>>> Error installing tool dependency package tophat2 version 2.0.9:
>>> coercing to Unicode: need string or buffer, NoneType found
>>>
>>> -Sheldon
>>>
>>> From: Greg Von Kuster [mailto:[hidden email]]
>>> Sent: Thursday, March 20, 2014 10:49 AM
>>> To: Briand, Sheldon
>>> Cc: '[hidden email]<mailto:[hidden email]>'
>>> Subject: Re: [galaxy-dev] tophat2 install
>>>
>>> You should be able to click on the missing tool dependency and see its installation log.  It should show you whatever error is occuring that is not allowing successful installation.
>>>
>>> Greg Von Kuster
>>>
>>> On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>> Hi,
>>>
>>> The repair operation doesn't seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.
>>>
>>> -Sheldon
>>>
>>>
>>> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
>>> Sent: Thursday, March 20, 2014 10:26 AM
>>> To: Briand, Sheldon
>>> Cc: '[hidden email]<mailto:[hidden email]>'
>>> Subject: Re: [galaxy-dev] tophat2 install
>>>
>>> Hi Sheldon,
>>>
>>> I recommend not manually changing any database entries.  You should
>>> be able to install the repository and all of its dependencies using
>>> the Repair Repository feature.  See
>>> https://wiki.galaxyproject.org/RepairingInstalledRepositories
>>>
>>> Greg Von Kuster
>>>
>>> On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>>
>>>
>>>
>>>
>>> Hi,
>>>
>>> Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven't had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!
>>> -Sheldon
>>>
>>> 1. Manually remove the installed repository subdirectory hierarchy from disk.
>>> 2. If the repository included any tools, manually remove entries for
>>> each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories ) 3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required:
>>>
>>> The following assumes you're using postgres:
>>>
>>> update tool_shed_repository set deleted=True, uninstalled=True,
>>> status='Uninstalled', error_message=Null  where name =
>>> 'bcftools_view';
>>>
>>>
>>>
>>> From: Briand, Sheldon
>>> Sent: Wednesday, March 12, 2014 11:44 AM
>>> To: [hidden email]<mailto:[hidden email]>
>>> Subject: tophat2 install
>>>
>>> Hi,
>>>
>>> I ran into a problem installing tophat2 here:
>>> tophat2 version 2.0.9: coercing to Unicode: need string or buffer,
>>> NoneType found
>>>
>>> I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.
>>>
>>> Repairing the repository doesn't make any difference.
>>>
>>> Thanks!
>>> -Sheldon
>>>
>>> Sheldon Briand
>>> NRC Research Computing Support Analyst Research Computing Support /
>>> Soutien Informartique a la Recherche Operations, Science Portfolio /
>>> Operations, Portefeuil des sciences SSC-NRC / SPC-CNRC Rm 329A, 1411
>>> Oxford Street / Piece 329A, 1411 Rue Oxford Halifax, NS  B3H 3Z1
>>> 902 426-1677
>>> [hidden email]<mailto:[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:
>>> http://lists.bx.psu.edu/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/mailinglists/
>>>
>>> <Screenshot.png>
>>>
>>> ___________________________________________________________
>>> 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:
>>> http://lists.bx.psu.edu/
>>>
>>> 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:
>>> http://lists.bx.psu.edu/
>>>
>>> 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:
>>>  http://lists.bx.psu.edu/
>>>
>>> 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:
>> http://lists.bx.psu.edu/
>>
>> 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:
>  http://lists.bx.psu.edu/
>
> 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:
  http://lists.bx.psu.edu/

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: tophat2 install

Briand, Sheldon
Hi,

Just wanted to let you know that my tophat2 install is working now.  In case it helps someone else in the future: Manually placing tool_dependencies.xml in the correct shed_tools directory, placing the tool dependency package in the correct dependencies directory, and uninstalling and then installing the tool dependency package worked.

Thanks for the advice.

-Sheldon

-----Original Message-----
From: Greg Von Kuster [mailto:[hidden email]]
Sent: Tuesday, March 25, 2014 10:34 AM
To: Briand, Sheldon
Cc: [hidden email] Dev
Subject: Re: [galaxy-dev] tophat2 install

If you installe dit from the main Tool Shed, then this repository has the recipe for installing the package.

http://toolshed.g2.bx.psu.edu/view/devteam/package_tophat2_2_0_9 

Greg Von Kuster
             
On Mar 25, 2014, at 9:25 AM, "Briand, Sheldon" <[hidden email]> wrote:

> Hi,
>
> Not sure if you saw my last email. Updating to the latest patch version doesn't seem to help.  I was wondering where I could get the galaxy package version of tophat2 and put it where it needs to be manually.  Then I could try the uninstall/install and see if that helps.
>
> Thanks!
> -Sheldon
>
> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Briand,
> Sheldon
> Sent: Thursday, March 20, 2014 3:11 PM
> To: 'Greg Von Kuster'
> Cc: [hidden email] Dev
> Subject: Re: [galaxy-dev] tophat2 install
>
> No difference.  Same error
>
> -----Original Message-----
> From: Greg Von Kuster [mailto:[hidden email]]
> Sent: Thursday, March 20, 2014 2:56 PM
> To: Briand, Sheldon
> Cc: [hidden email] Dev
> Subject: Re: [galaxy-dev] tophat2 install
>
> Sorry, should have advised this:
>
>> hg pull https://bitbucket.org/galaxy/galaxy-central#stable
>> hg update stable
>
> See the end ot this thread:
>
> http://dev.list.galaxyproject.org/Persistent-jobs-in-cluster-queue-eve
> n-after-canceling-job-in-galaxy-td4663719.html
>
>
>
>
> On Mar 20, 2014, at 1:51 PM, Björn Grüning <[hidden email]> wrote:
>
>> Hi,
>>
>> you need to track galaxy-central to make use of the patches that are applied as bugfixes after the release. You can do that easily with changing the path in .hg/hgrc ... but I do not know if that is the right way to do ;) For me it worked.
>>
>> Cheers,
>> Bjoern
>>
>> Am 20.03.2014 18:46, schrieb Briand, Sheldon:
>>> pulling from https://bitbucket.org/galaxy/galaxy-dist
>>> searching for changes
>>> no changes found
>>>
>>> From: Greg Von Kuster [mailto:[hidden email]]
>>> Sent: Thursday, March 20, 2014 2:36 PM
>>> To: Briand, Sheldon
>>> Cc: '[hidden email]'
>>> Subject: Re: [galaxy-dev] tophat2 install
>>>
>>> There have been several fixes released to the stable branch that you do not have in 12441.  I would recommend doing the following:
>>>
>>> hg pull
>>> hg update stable
>>>
>>> Then uninstall the tophat2 repository and reinstall it.  See if that makes a difference.
>>>
>>>
>>> On Mar 20, 2014, at 1:30 PM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>>
>>> $ hg summary
>>> parent: 12441:dc067a95261d
>>>
>>>> From the tool_dependencies.xml:
>>>
>>> <package name="tophat2" version="2.0.9">
>>>      <repository changeset_revision="8549fd545473"
>>> name="package_tophat2_2_0_9" owner="devteam"
>>> prior_installation_required="False" toolshed
>>> ="http://toolshed.g2.bx.psu.edu" />
>>>
>>>
>>> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
>>> Sent: Thursday, March 20, 2014 2:23 PM
>>> To: Briand, Sheldon
>>> Cc: '[hidden email]<mailto:[hidden email]>'
>>> Subject: Re: [galaxy-dev] tophat2 install
>>>
>>> What version of Galaxy are you running?  You want to look in the tophat2 repository directory, not its package dependency.  There should be a tool_dependencies.xml file in the tophat2's installation directory hierarchy somewhere.
>>>
>>> On Mar 20, 2014, at 1:12 PM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>>
>>>
>>> Hi,
>>>
>>> dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd54547
>>> 3
>>> contains only:
>>> env.sh
>>>
>>> If that isn't the right place to look let me know.
>>>
>>> -Sheldon
>>>
>>> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
>>> Sent: Thursday, March 20, 2014 2:04 PM
>>> To: Briand, Sheldon
>>> Cc: '[hidden email]<mailto:[hidden email]>'
>>> Subject: Re: [galaxy-dev] tophat2 install
>>>
>>> It looks like your database and file system are out of sync.  Your database seems to think you have an installed repository but your file system does not seem to have the repository's installation directory.  Can you confirm that this is the case?
>>>
>>>
>>> On Mar 20, 2014, at 11:53 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>>
>>>
>>>
>>> Hi,
>>>
>>> Here is the error from the paster.log:
>>>
>>> Traceback (most recent call last):
>>>  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/util/common_install_util.py", line 496, in handle_tool_dependencies
>>>    from_install_manager=from_install_manager )  File
>>> "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 318, in install_package
>>>    from_install_manager=from_install_manager )  File
>>> "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 245, in handle_complex_repository_d ependency_for_package
>>>    tool_dependencies_config =
>>> get_absolute_path_to_file_in_repository( repo_files_dir,
>>> 'tool_dependencies.xml' )  File "/BigData/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 126, in get_absolute_path_to_file_i n_repository
>>>    for root, dirs, files in os.walk( repo_files_dir ):
>>>  File "/opt/local/python-2.7.5/lib/python2.7/os.py", line 276, in walk
>>>    names = listdir(top)
>>> TypeError: coercing to Unicode: need string or buffer, NoneType
>>> found
>>>
>>> -Sheldon
>>>
>>> From:
>>> [hidden email]<mailto:galaxy-dev-bounces@lists.
>>> b
>>> x.psu.edu>
>>> [mailto:[hidden email]<mailto:dev-bounces@lists.
>>> bx.psu.edu>] On Behalf Of Briand, Sheldon
>>> Sent: Thursday, March 20, 2014 10:52 AM
>>> To: 'Greg Von Kuster'
>>> Cc: '[hidden email]<mailto:[hidden email]>'
>>> Subject: Re: [galaxy-dev] tophat2 install
>>>
>>> Hi,
>>>
>>> Yes the error is:
>>> Error installing tool dependency package tophat2 version 2.0.9:
>>> coercing to Unicode: need string or buffer, NoneType found
>>>
>>> -Sheldon
>>>
>>> From: Greg Von Kuster [mailto:[hidden email]]
>>> Sent: Thursday, March 20, 2014 10:49 AM
>>> To: Briand, Sheldon
>>> Cc: '[hidden email]<mailto:[hidden email]>'
>>> Subject: Re: [galaxy-dev] tophat2 install
>>>
>>> You should be able to click on the missing tool dependency and see its installation log.  It should show you whatever error is occuring that is not allowing successful installation.
>>>
>>> Greg Von Kuster
>>>
>>> On Mar 20, 2014, at 9:46 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>> Hi,
>>>
>>> The repair operation doesn't seem to make any difference (I already tried that before emailing).  Screenshot of the result attached.
>>>
>>> -Sheldon
>>>
>>>
>>> From: Greg Von Kuster [mailto:[hidden email]<http://bx.psu.edu>]
>>> Sent: Thursday, March 20, 2014 10:26 AM
>>> To: Briand, Sheldon
>>> Cc: '[hidden email]<mailto:[hidden email]>'
>>> Subject: Re: [galaxy-dev] tophat2 install
>>>
>>> Hi Sheldon,
>>>
>>> I recommend not manually changing any database entries.  You should
>>> be able to install the repository and all of its dependencies using
>>> the Repair Repository feature.  See
>>> https://wiki.galaxyproject.org/RepairingInstalledRepositories
>>>
>>> Greg Von Kuster
>>>
>>> On Mar 20, 2014, at 8:59 AM, "Briand, Sheldon" <[hidden email]<mailto:[hidden email]>> wrote:
>>>
>>>
>>>
>>>
>>>
>>> Hi,
>>>
>>> Just wondering if I can still use the following to fix up my messed up tophat2 install (the install had hung up on me, for 2 hours, and I tried to remove/repair it via the interface).  I haven't had problems installing any other tools or packages.  I am using postgres but this advice was given 2 years ago to another user and fields may have changed.  Thanks for any help!
>>> -Sheldon
>>>
>>> 1. Manually remove the installed repository subdirectory hierarchy from disk.
>>> 2. If the repository included any tools, manually remove entries for
>>> each of them from the shed_tool-conf.xml file ( or the equivalent file you have configured for handling installed repositories ) 3. Manually update the database using the following command (assuming your installed repository is named 'bcftools_view' and it is the only repository you have installed with that name) - letter capitalization is required:
>>>
>>> The following assumes you're using postgres:
>>>
>>> update tool_shed_repository set deleted=True, uninstalled=True,
>>> status='Uninstalled', error_message=Null  where name =
>>> 'bcftools_view';
>>>
>>>
>>>
>>> From: Briand, Sheldon
>>> Sent: Wednesday, March 12, 2014 11:44 AM
>>> To: [hidden email]<mailto:[hidden email]>
>>> Subject: tophat2 install
>>>
>>> Hi,
>>>
>>> I ran into a problem installing tophat2 here:
>>> tophat2 version 2.0.9: coercing to Unicode: need string or buffer,
>>> NoneType found
>>>
>>> I have only used the interface to do the installation (no manual deletes).  The rest of the dependencies for tophat2 installed just fine.
>>>
>>> Repairing the repository doesn't make any difference.
>>>
>>> Thanks!
>>> -Sheldon
>>>
>>> Sheldon Briand
>>> NRC Research Computing Support Analyst Research Computing Support /
>>> Soutien Informartique a la Recherche Operations, Science Portfolio /
>>> Operations, Portefeuil des sciences SSC-NRC / SPC-CNRC Rm 329A, 1411
>>> Oxford Street / Piece 329A, 1411 Rue Oxford Halifax, NS  B3H 3Z1
>>> 902 426-1677
>>> [hidden email]<mailto:[hidden email]>
>>>
>>> ___________________________________________________________
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>>>
>>> <Screenshot.png>
>>>
>>> ___________________________________________________________
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>>>
>>>
>>>
>>>
>>> ___________________________________________________________
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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:
>> http://lists.bx.psu.edu/
>>
>> 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:
>  http://lists.bx.psu.edu/
>
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>


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