Re: [galaxy-dev] tophat2 install

2014-03-28 Thread 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:g...@bx.psu.edu] 
Sent: Tuesday, March 25, 2014 10:34 AM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu 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"  
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: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, 
> Sheldon
> Sent: Thursday, March 20, 2014 3:11 PM
> To: 'Greg Von Kuster'
> Cc: galaxy-dev@lists.bx.psu.edu Dev
> Subject: Re: [galaxy-dev] tophat2 install
> 
> No difference.  Same error
> 
> -Original Message-
> From: Greg Von Kuster [mailto:g...@bx.psu.edu]
> Sent: Thursday, March 20, 2014 2:56 PM
> To: Briand, Sheldon
> Cc: galaxy-dev@lists.bx.psu.edu 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  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:g...@bx.psu.edu]
>>> Sent: Thursday, March 20, 2014 2:36 PM
>>> To: Briand, Sheldon
>>> Cc: 'galaxy-dev@lists.bx.psu.edu'
>>> 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" 
>>> mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote:
>>> 
>>> 
>>> $ hg summary
>>> parent: 12441:dc067a95261d
>>> 
>>>> From the tool_dependencies.xml:
>>> 
>>> 
>>>  >> name="package_tophat2_2_0_9" owner="devteam" 
>>> prior_installation_required="False" toolshed 
>>> ="http://toolshed.g2.bx.psu.edu"; />
>>> 
>>> 
>>> From: Greg Von Kuster [mailto:g...@bx.psu.edu<http://bx.psu.edu>]
>>> Sent: Thursday, March 20, 2014 2:23 PM
>>> To: Briand, Sheldon
>>> Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
>>> 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" 
>>> mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote:
>>> 
>>> 
>>> 
>>> Hi,
>>> 
>>> dependancies/tophat2/2.0.9/devteam/package_tophat2_2_0_9/8549fd54547
>>> 3
>>> contains on

Re: [galaxy-dev] tophat2 install

2014-03-25 Thread 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: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 3:11 PM
To: 'Greg Von Kuster'
Cc: galaxy-dev@lists.bx.psu.edu Dev
Subject: Re: [galaxy-dev] tophat2 install

No difference.  Same error

-Original Message-
From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 2:56 PM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu 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  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:g...@bx.psu.edu]
>> Sent: Thursday, March 20, 2014 2:36 PM
>> To: Briand, Sheldon
>> Cc: 'galaxy-dev@lists.bx.psu.edu'
>> 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" 
>> mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote:
>> 
>> 
>> $ hg summary
>> parent: 12441:dc067a95261d
>> 
>>> From the tool_dependencies.xml:
>> 
>> 
>>   > name="package_tophat2_2_0_9" owner="devteam" 
>> prior_installation_required="False" toolshed 
>> ="http://toolshed.g2.bx.psu.edu"; />
>> 
>> 
>> From: Greg Von Kuster [mailto:g...@bx.psu.edu<http://bx.psu.edu>]
>> Sent: Thursday, March 20, 2014 2:23 PM
>> To: Briand, Sheldon
>> Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
>> 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" 
>> mailto:sheldon.bri...@ssc-spc.gc.ca>> 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:g...@bx.psu.edu<http://bx.psu.edu>]
>> Sent: Thursday, March 20, 2014 2:04 PM
>> To: Briand, Sheldon
>> Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
>> 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" 
>> mailto:sheldon.bri...@ssc-spc.gc.ca>> 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_d

Re: [galaxy-dev] tophat2 install

2014-03-25 Thread 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"  
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: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
> Sent: Thursday, March 20, 2014 3:11 PM
> To: 'Greg Von Kuster'
> Cc: galaxy-dev@lists.bx.psu.edu Dev
> Subject: Re: [galaxy-dev] tophat2 install
> 
> No difference.  Same error
> 
> -Original Message-
> From: Greg Von Kuster [mailto:g...@bx.psu.edu]
> Sent: Thursday, March 20, 2014 2:56 PM
> To: Briand, Sheldon
> Cc: galaxy-dev@lists.bx.psu.edu 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  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:g...@bx.psu.edu]
>>> Sent: Thursday, March 20, 2014 2:36 PM
>>> To: Briand, Sheldon
>>> Cc: 'galaxy-dev@lists.bx.psu.edu'
>>> 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" 
>>> mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote:
>>> 
>>> 
>>> $ hg summary
>>> parent: 12441:dc067a95261d
>>> 
>>>> From the tool_dependencies.xml:
>>> 
>>> 
>>>  >> name="package_tophat2_2_0_9" owner="devteam" 
>>> prior_installation_required="False" toolshed 
>>> ="http://toolshed.g2.bx.psu.edu"; />
>>> 
>>> 
>>> From: Greg Von Kuster [mailto:g...@bx.psu.edu<http://bx.psu.edu>]
>>> Sent: Thursday, March 20, 2014 2:23 PM
>>> To: Briand, Sheldon
>>> Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
>>> 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" 
>>> mailto:sheldon.bri...@ssc-spc.gc.ca>> 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:g...@bx.psu.edu<http://bx.psu.edu>]
>>> Sent: Thursday, March 20, 2014 2:04 PM
>>> To: Briand, Sheldon
>>> Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
>>> Subject: Re: [galaxy-dev] tophat2 install
>>> 
>>> It looks like your database and file system are out of sync.  Your database 
>>> seems to

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Briand, Sheldon 
No difference.  Same error

-Original Message-
From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
Sent: Thursday, March 20, 2014 2:56 PM
To: Briand, Sheldon
Cc: galaxy-dev@lists.bx.psu.edu 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  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:g...@bx.psu.edu]
>> Sent: Thursday, March 20, 2014 2:36 PM
>> To: Briand, Sheldon
>> Cc: 'galaxy-dev@lists.bx.psu.edu'
>> 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" 
>> mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote:
>> 
>> 
>> $ hg summary
>> parent: 12441:dc067a95261d
>> 
>>> From the tool_dependencies.xml:
>> 
>> 
>>   > name="package_tophat2_2_0_9" owner="devteam" 
>> prior_installation_required="False" toolshed 
>> ="http://toolshed.g2.bx.psu.edu"; />
>> 
>> 
>> From: Greg Von Kuster [mailto:g...@bx.psu.edu<http://bx.psu.edu>]
>> Sent: Thursday, March 20, 2014 2:23 PM
>> To: Briand, Sheldon
>> Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
>> 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" 
>> mailto:sheldon.bri...@ssc-spc.gc.ca>> 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:g...@bx.psu.edu<http://bx.psu.edu>]
>> Sent: Thursday, March 20, 2014 2:04 PM
>> To: Briand, Sheldon
>> Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
>> 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" 
>> mailto:sheldon.bri...@ssc-spc.gc.ca>> 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

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread 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  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:g...@bx.psu.edu]
>> Sent: Thursday, March 20, 2014 2:36 PM
>> To: Briand, Sheldon
>> Cc: 'galaxy-dev@lists.bx.psu.edu'
>> 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" 
>> mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote:
>> 
>> 
>> $ hg summary
>> parent: 12441:dc067a95261d
>> 
>>> From the tool_dependencies.xml:
>> 
>> 
>>   > name="package_tophat2_2_0_9" owner="devteam" 
>> prior_installation_required="False" toolshed
>> ="http://toolshed.g2.bx.psu.edu"; />
>> 
>> 
>> From: Greg Von Kuster [mailto:g...@bx.psu.edu<http://bx.psu.edu>]
>> Sent: Thursday, March 20, 2014 2:23 PM
>> To: Briand, Sheldon
>> Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
>> 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" 
>> mailto:sheldon.bri...@ssc-spc.gc.ca>> 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:g...@bx.psu.edu<http://bx.psu.edu>]
>> Sent: Thursday, March 20, 2014 2:04 PM
>> To: Briand, Sheldon
>> Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
>> 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" 
>> mailto:sheldon.bri...@ssc-spc.gc.ca>> 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 27

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Björn Grüning 

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:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 2:36 PM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote:


$ hg summary
parent: 12441:dc067a95261d


From the tool_dependencies.xml:



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


From: Greg Von Kuster [mailto:g...@bx.psu.edu<http://bx.psu.edu>]
Sent: Thursday, March 20, 2014 2:23 PM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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:g...@bx.psu.edu<http://bx.psu.edu>]
Sent: Thursday, March 20, 2014 2:04 PM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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: galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu> 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu<mailto:dev-boun...@lists.bx.psu.edu>] On 
Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 10:52 AM
To: 'Greg Von Kuster'
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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:g...@bx.psu.edu<htt

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Briand, Sheldon 
pulling from https://bitbucket.org/galaxy/galaxy-dist
searching for changes
no changes found

From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 2:36 PM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> wrote:


$ hg summary
parent: 12441:dc067a95261d

>From the tool_dependencies.xml:


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


From: Greg Von Kuster [mailto:g...@bx.psu.edu<http://bx.psu.edu>]
Sent: Thursday, March 20, 2014 2:23 PM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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:g...@bx.psu.edu<http://bx.psu.edu>]
Sent: Thursday, March 20, 2014 2:04 PM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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: 
galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu> 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu<mailto:dev-boun...@lists.bx.psu.edu>]
 On Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 10:52 AM
To: 'Greg Von Kuster'
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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:g...@bx.psu.edu<http://bx.psu.edu>]
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
Subject: Re: [galaxy-dev] tophat2 install

Hi Sheldon,

I recommend not manually changing any database entries.  You should be able to 
install the repositor

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Greg Von Kuster 
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"  
wrote:

> $ hg summary
> parent: 12441:dc067a95261d
>  
> From the tool_dependencies.xml:
>  
> 
>name="package_tophat2_2_0_9" owner="devteam" 
> prior_installation_required="False" toolshed
> ="http://toolshed.g2.bx.psu.edu"; />
>  
>  
> From: Greg Von Kuster [mailto:g...@bx.psu.edu] 
> Sent: Thursday, March 20, 2014 2:23 PM
> To: Briand, Sheldon
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> 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"  
> 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:g...@bx.psu.edu] 
> Sent: Thursday, March 20, 2014 2:04 PM
> To: Briand, Sheldon
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> 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" 
>  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: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
> Sent: Thursday, March 20, 2014 10:52 AM
> To: 'Greg Von Kuster'
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> 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:g...@bx.psu.edu] 
> Sent: Thursday, March 20, 2014 10:49 AM
> To: Briand, Sheldon
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> 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"  
> 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:g...@bx.psu.edu] 
> Sent: Thursday, March 20, 2014 10:26 AM
> To: Briand, Sheldon
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> 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 dependencie

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Briand, Sheldon 
$ hg summary
parent: 12441:dc067a95261d

>From the tool_dependencies.xml:


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


From: Greg Von Kuster [mailto:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 2:23 PM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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:g...@bx.psu.edu<http://bx.psu.edu>]
Sent: Thursday, March 20, 2014 2:04 PM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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: 
galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu> 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu<mailto:dev-boun...@lists.bx.psu.edu>]
 On Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 10:52 AM
To: 'Greg Von Kuster'
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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:g...@bx.psu.edu<http://bx.psu.edu>]
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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 subdire

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Greg Von Kuster 
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"  
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:g...@bx.psu.edu] 
> Sent: Thursday, March 20, 2014 2:04 PM
> To: Briand, Sheldon
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> 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" 
>  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: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
> Sent: Thursday, March 20, 2014 10:52 AM
> To: 'Greg Von Kuster'
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> 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:g...@bx.psu.edu] 
> Sent: Thursday, March 20, 2014 10:49 AM
> To: Briand, Sheldon
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> 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"  
> 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:g...@bx.psu.edu] 
> Sent: Thursday, March 20, 2014 10:26 AM
> To: Briand, Sheldon
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> 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"  
> 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

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Briand, Sheldon 
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:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 2:04 PM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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: 
galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu> 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu<mailto:dev-boun...@lists.bx.psu.edu>]
 On Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 10:52 AM
To: 'Greg Von Kuster'
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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:g...@bx.psu.edu<http://bx.psu.edu>]
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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: galaxy

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Greg Von Kuster 
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"  
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: galaxy-dev-boun...@lists.bx.psu.edu 
> [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
> Sent: Thursday, March 20, 2014 10:52 AM
> To: 'Greg Von Kuster'
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> 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:g...@bx.psu.edu] 
> Sent: Thursday, March 20, 2014 10:49 AM
> To: Briand, Sheldon
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> 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"  
> 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:g...@bx.psu.edu] 
> Sent: Thursday, March 20, 2014 10:26 AM
> To: Briand, Sheldon
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> 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"  
> 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: galaxy-dev@lists.bx.psu.edu
> Subject: tophat2 install
>  
> Hi,
>  
> I ran into a problem installing tophat2 here:
&

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Briand, Sheldon 
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: galaxy-dev-boun...@lists.bx.psu.edu 
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Briand, Sheldon
Sent: Thursday, March 20, 2014 10:52 AM
To: 'Greg Von Kuster'
Cc: 'galaxy-dev@lists.bx.psu.edu'
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:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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:g...@bx.psu.edu<http://bx.psu.edu>]
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>
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
sheldon.bri...@ssc-spc.gc.ca<mailto:sheldon.bri...@ssc-spc.gc.ca>

___
Please keep all replies on t

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Briand, Sheldon 
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:g...@bx.psu.edu]
Sent: Thursday, March 20, 2014 10:49 AM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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:g...@bx.psu.edu<http://bx.psu.edu>]
Sent: Thursday, March 20, 2014 10:26 AM
To: Briand, Sheldon
Cc: 'galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>'
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" 
mailto:sheldon.bri...@ssc-spc.gc.ca>> 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: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu>
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
sheldon.bri...@ssc-spc.gc.ca<mailto:sheldon.bri...@ssc-spc.gc.ca>

___
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/

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Greg Von Kuster 
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"  
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:g...@bx.psu.edu] 
> Sent: Thursday, March 20, 2014 10:26 AM
> To: Briand, Sheldon
> Cc: 'galaxy-dev@lists.bx.psu.edu'
> 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"  
> 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: galaxy-dev@lists.bx.psu.edu
> 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
> sheldon.bri...@ssc-spc.gc.ca
>  
> ___
> 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/

Re: [galaxy-dev] tophat2 install

2014-03-20 Thread Greg Von Kuster 
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"  
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: galaxy-dev@lists.bx.psu.edu
> 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
> sheldon.bri...@ssc-spc.gc.ca
>  
> ___
> 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: [galaxy-dev] tophat2 install

2014-03-20 Thread 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: galaxy-dev@lists.bx.psu.edu
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
sheldon.bri...@ssc-spc.gc.ca

___
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/