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" 
<sheldon.bri...@ssc-spc.gc.ca<mailto:sheldon.bri...@ssc-spc.gc.ca>> 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: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" 
<sheldon.bri...@ssc-spc.gc.ca<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" 
<sheldon.bri...@ssc-spc.gc.ca<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" 
<sheldon.bri...@ssc-spc.gc.ca<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" 
<sheldon.bri...@ssc-spc.gc.ca<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/

<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/

Reply via email to