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>
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<Screenshot.png>
___________________________________________________________
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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:
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/
