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

searching for changes

no changes found

From: Greg Von Kuster [mailto:greg@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.Briand@SSC-SPC.gc.ca> wrote:

$ hg summary

parent: 12441:dc067a95261d

From the tool_dependencies.xml:

<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:greg@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" <Sheldon.Briand@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:greg@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" <Sheldon.Briand@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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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:greg@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" <Sheldon.Briand@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:greg@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" <Sheldon.Briand@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
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.briand@ssc-spc.gc.ca

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