Re: [galaxy-dev] Can't get automatic toolshed installation to work....
Hello Fab, What version of Galaxy are you running? Did you install it from the galaxy-dist repo on bitbucket? Am I understaning correctly that you are using a symbolic link to point your installation directory to /var/lib/galaxy-server/shed_tools? If so, why not just set the config setting to that path? From your paster log, it looks like that directory is not being used: > IOError: [Errno 2] No such file or directory: > u'shed_tools/shed_tools/toolshed.g2.bx.psu.edu/repos/malex/beast/677344fb75c1 > /beast/beast/beast.xml' See my inline comments for your 3 questions. On Nov 27, 2012, at 4:10 AM, fab wrote: > Dear Greg and Nikhil, > > We just installed a local instance of galaxy and encountered the same problem > as > Nikhil for the tools we tried to install from toolshed. Unfortunately I am not > skilled as you are and didn't manage to solve the problem from the information > in your posts. > > In my case I have in the univers_wgi.ini file: tool_config_file = > tool_conf.xml,shed_tool_conf.xml > ... with, in my main galaxy installation directory, a shed_tools link to the > directory /var/lib/galaxy-server/shed_tools > > The problem is that when I try to install a tool from toolshed, it shows me > the > popup with "Initializing repository installation failed" and after that the > tool > stays in the cloning state for ever. > When I try to uninstall it shows me the following message with traceback: > AttributeError: 'NoneType' object has no attribute 'startswith' > The entire stack trace for the exception I get just after the popup is as > follow: > > Error Traceback: > View as: Interactive | Text | XML (full) > ⇝ IOError: [Errno 2] No such file or directory: > u'shed_tools/shed_tools/toolshed.g2.bx.psu.edu/repos/malex/beast/677344fb75c1 > /beast/beast/beast.xml' > URL: http://192.167.142.244:8080/admin_toolshed/manage_repositories > File > '/usr/lib/galaxy-server/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception > /middleware.py', > line 364 in respond > app_iter = self.application(environ, detect_start_response) > File '/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', > line 98 in __call__ > environ, self.app) > File '/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line > 539 in intercept_output > app_iter = application(environ, replacement_start_response) > File '/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', > line > 80 in __call__ > return self.application(environ, start_response) > File > '/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', > line 632 in __call__ > return self.application(environ, start_response) > File '/usr/lib/galaxy-server/lib/galaxy/web/framework/base.py', line 160 in > __call__ > body = method( trans, **kwargs ) > File '/usr/lib/galaxy-server/lib/galaxy/web/framework/__init__.py', line 184 > in > decorator > return func( self, trans, *args, **kwargs ) > File '/usr/lib/galaxy-server/lib/galaxy/web/controllers/admin_toolshed.py', > line > 846 in manage_repositories > self.install_tool_shed_repositories( trans, repositories_for_installation, > reinstalling=reinstalling, **decoded_kwd ) > File '/usr/lib/galaxy-server/lib/galaxy/web/framework/__init__.py', line 184 > in > decorator > return func( self, trans, *args, **kwargs ) > File '/usr/lib/galaxy-server/lib/galaxy/web/controllers/admin_toolshed.py', > line > 634 in install_tool_shed_repositories > reinstalling=reinstalling ) > File '/usr/lib/galaxy-server/lib/galaxy/web/controllers/admin_toolshed.py', > line > 707 in handle_repository_contents > repository_tools_tups, sample_files_copied = handle_missing_index_file( > trans.app, tool_path, sample_files, repository_tools_tups ) > File '/usr/lib/galaxy-server/lib/galaxy/util/shed_util.py', line 1180 in > handle_missing_index_file > repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), > guid=guid ) > File '/usr/lib/galaxy-server/lib/galaxy/tools/__init__.py', line 437 in > load_tool > tree = util.parse_xml( config_file ) > File '/usr/lib/galaxy-server/lib/galaxy/util/__init__.py', line 106 in > parse_xml > tree = ElementTree.parse(fname) > File > '/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree > /ElementTree.py', > line 859 in parse > File > '/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree > /ElementTree.py', > line 576 in parse > IOError: [Errno 2] No such file or directory: > u'shed_tools/shed_tools/toolshed.g2.bx.psu.edu/repos/malex/beast/677344fb75c1 > /beast/beast/beast.xml' > > I didn't manage to understand what is the original error to see if the problem > is the exact same as for Nikhil. Therefore I have three questions: > - how do I get in the database to run the following command: update > tool_shed_repository set status = 'New' where status = 'Cloning' It depends on the database you have configured in your community_wsgi.ini file. What database do you
Re: [galaxy-dev] Can't get automatic toolshed installation to work....
Dear Greg and Nikhil, We just installed a local instance of galaxy and encountered the same problem as Nikhil for the tools we tried to install from toolshed. Unfortunately I am not skilled as you are and didn't manage to solve the problem from the information in your posts. In my case I have in the univers_wgi.ini file: tool_config_file = tool_conf.xml,shed_tool_conf.xml ... with, in my main galaxy installation directory, a shed_tools link to the directory /var/lib/galaxy-server/shed_tools The problem is that when I try to install a tool from toolshed, it shows me the popup with "Initializing repository installation failed" and after that the tool stays in the cloning state for ever. When I try to uninstall it shows me the following message with traceback: AttributeError: 'NoneType' object has no attribute 'startswith' The entire stack trace for the exception I get just after the popup is as follow: Error Traceback: View as: Interactive | Text | XML (full) ⇝ IOError: [Errno 2] No such file or directory: u'shed_tools/shed_tools/toolshed.g2.bx.psu.edu/repos/malex/beast/677344fb75c1 /beast/beast/beast.xml' URL: http://192.167.142.244:8080/admin_toolshed/manage_repositories File '/usr/lib/galaxy-server/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception /middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/usr/lib/galaxy-server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/usr/lib/galaxy-server/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/usr/lib/galaxy-server/lib/galaxy/web/controllers/admin_toolshed.py', line 846 in manage_repositories self.install_tool_shed_repositories( trans, repositories_for_installation, reinstalling=reinstalling, **decoded_kwd ) File '/usr/lib/galaxy-server/lib/galaxy/web/framework/__init__.py', line 184 in decorator return func( self, trans, *args, **kwargs ) File '/usr/lib/galaxy-server/lib/galaxy/web/controllers/admin_toolshed.py', line 634 in install_tool_shed_repositories reinstalling=reinstalling ) File '/usr/lib/galaxy-server/lib/galaxy/web/controllers/admin_toolshed.py', line 707 in handle_repository_contents repository_tools_tups, sample_files_copied = handle_missing_index_file( trans.app, tool_path, sample_files, repository_tools_tups ) File '/usr/lib/galaxy-server/lib/galaxy/util/shed_util.py', line 1180 in handle_missing_index_file repository_tool = app.toolbox.load_tool( os.path.join( tool_path, tup_path ), guid=guid ) File '/usr/lib/galaxy-server/lib/galaxy/tools/__init__.py', line 437 in load_tool tree = util.parse_xml( config_file ) File '/usr/lib/galaxy-server/lib/galaxy/util/__init__.py', line 106 in parse_xml tree = ElementTree.parse(fname) File '/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree /ElementTree.py', line 859 in parse File '/usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree /ElementTree.py', line 576 in parse IOError: [Errno 2] No such file or directory: u'shed_tools/shed_tools/toolshed.g2.bx.psu.edu/repos/malex/beast/677344fb75c1 /beast/beast/beast.xml' I didn't manage to understand what is the original error to see if the problem is the exact same as for Nikhil. Therefore I have three questions: - how do I get in the database to run the following command: update tool_shed_repository set status = 'New' where status = 'Cloning' - how do I check for the problem that Nikhil underpinned (the python function with environment variable TMPDIR undefined)? - how do I implement the solution Nikhil gave in the case I see it is the same problem? Thank you very much in advance, best regards, fab. ___ 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/
Re: [galaxy-dev] Can't get automatic toolshed installation to work....
To get the repositories out of the limbo state, you'll have to get into your
database and run the following sql command. Doing this will allow you to
install those repositories that were in limbo. After they are installed, you
can uninstall them if you want to. The case on the Strings is necessary.
update tool_shed_repository set status = 'New' where status = 'Cloning';
It was great to talk with you at the conference as well!
Greg
On Aug 3, 2012, at 8:36 PM, Nikhil Joshi wrote:
> Hi Greg,
>
> So I looked at the the URL from the log file and it was trying to
> write to a tmp directory owned by root, so that was a problem. I
> traced the problem to a python function (make_tmp_directory) where it
> was using the environment variable "TMPDIR", which was not defined.
> So in our launch script we defined the variable and that seemed to
> work. However, the repositories that I installed before fixing this
> are in a limbo state. When I try to uninstall them I get that same
> AttributeError below. Any ideas on how I can reset my installed
> Galaxy toolshed repositories so that they are not in a limbo state?
> I've included the entire traceback below:
>
> Error Traceback:
> View as: Interactive | Text | XML (full)
> ⇝ AttributeError: 'NoneType' object has no attribute 'startswith'
> URL:
> http://optidavis.genomecenter.ucdavis.edu:8080/admin_toolshed/browse_repositories?operation=deactivate+or+uninstall&id=33b43b4e7093c91f
> Module weberror.evalexception.middleware:364 in respond view
>>> app_iter = self.application(environ, detect_start_response)
> Module paste.debug.prints:98 in __call__ view
>>> environ, self.app)
> Module paste.wsgilib:539 in intercept_output view
>>> app_iter = application(environ, replacement_start_response)
> Module paste.recursive:80 in __call__ view
>>> return self.application(environ, start_response)
> Module paste.httpexceptions:632 in __call__ view
>>> return self.application(environ, start_response)
> Module galaxy.web.framework.base:160 in __call__ view
>>> body = method( trans, **kwargs )
> Module galaxy.web.framework:184 in decorator view
>>> return func( self, trans, *args, **kwargs )
> Module galaxy.web.controllers.admin_toolshed:356 in
> browse_repositories view
>>> return self.deactivate_or_uninstall_repository( trans, **kwd )
> Module galaxy.web.framework:184 in decorator view
>>> return func( self, trans, *args, **kwargs )
> Module galaxy.web.controllers.admin_toolshed:408 in
> deactivate_or_uninstall_repository view
>>> repository_install_dir = os.path.abspath ( relative_install_dir )
> Module posixpath:343 in abspath view
>>> if not isabs(path):
> Module posixpath:53 in isabs view
>>> return s.startswith('/')
> AttributeError: 'NoneType' object has no attribute 'startswith'
>
> Any help is highly appreciated! BTW, it was really nice to get to
> talk to you at the conference. :)
>
> - Nik.
>
>
> On Fri, Aug 3, 2012 at 3:49 AM, Greg Von Kuster wrote:
>> Hello Nikhil,
>>
>>
>> On Aug 2, 2012, at 9:32 PM, Nikhil Joshi wrote:
>>
>>> Hi all,
>>>
>>> We just upgraded our local galaxy to the latest version and now I am
>>> trying to get automatic tool installation to work properly. I changed
>>> the universe_wsgi.ini file to enable the toolshed xml file,
>>
>> Regarding this, do you mean that you have something like the following
>> setting?
>>
>> tool_config_files = tool_conf.xml,shed_tool_conf.xml
>>
>>
>>> I created
>>> a "shed_tools" directory one above the galaxy install, and restarted
>>> galaxy. But when I try to install a repository, I get this error as a
>>> popup: "Initializing repository installation failed".
>>
>> From what tool shed are you trying to install Galaxy? When this pop-up is
>> displayed, the last line of your Galaxy paster log should be a url. If you
>> paste that url into a browser it will display a page that displays the
>> entire stack trace for the exception. We'll need to see this information in
>> order to determine the cause of the problem.
>>
>>
>>> I tried this
>>> with various repositories, but I get the same error. Then when I go
>>> to "Manage installed tool shed repositories", all of the repositories
>>> I tried to install are stuck in the "Cloning" state. Finally, if I
>>> try to uninstall any of them, I get this error, with a traceback:
>>>
>>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>>
>>> Any ideas?
>>>
>>> - Nik.
>>>
>>> --
>>> Nikhil Joshi
>>> Bioinformatics Analyst/Programmer
>>> UC Davis Bioinformatics Core
>>> http://bioinformatics.ucdavis.edu/
>>> najoshi -at- ucdavis -dot- edu
>>> 530.752.2698 (w)
>>> ___
>>> 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.
Re: [galaxy-dev] Can't get automatic toolshed installation to work....
Hi Greg,
So I looked at the the URL from the log file and it was trying to
write to a tmp directory owned by root, so that was a problem. I
traced the problem to a python function (make_tmp_directory) where it
was using the environment variable "TMPDIR", which was not defined.
So in our launch script we defined the variable and that seemed to
work. However, the repositories that I installed before fixing this
are in a limbo state. When I try to uninstall them I get that same
AttributeError below. Any ideas on how I can reset my installed
Galaxy toolshed repositories so that they are not in a limbo state?
I've included the entire traceback below:
Error Traceback:
View as: Interactive | Text | XML (full)
⇝ AttributeError: 'NoneType' object has no attribute 'startswith'
URL:
http://optidavis.genomecenter.ucdavis.edu:8080/admin_toolshed/browse_repositories?operation=deactivate+or+uninstall&id=33b43b4e7093c91f
Module weberror.evalexception.middleware:364 in respond view
>> app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
>> environ, self.app)
Module paste.wsgilib:539 in intercept_output view
>> app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
>> return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__ view
>> return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
>> body = method( trans, **kwargs )
Module galaxy.web.framework:184 in decorator view
>> return func( self, trans, *args, **kwargs )
Module galaxy.web.controllers.admin_toolshed:356 in
browse_repositories view
>> return self.deactivate_or_uninstall_repository( trans, **kwd )
Module galaxy.web.framework:184 in decorator view
>> return func( self, trans, *args, **kwargs )
Module galaxy.web.controllers.admin_toolshed:408 in
deactivate_or_uninstall_repository view
>> repository_install_dir = os.path.abspath ( relative_install_dir )
Module posixpath:343 in abspath view
>> if not isabs(path):
Module posixpath:53 in isabs view
>> return s.startswith('/')
AttributeError: 'NoneType' object has no attribute 'startswith'
Any help is highly appreciated! BTW, it was really nice to get to
talk to you at the conference. :)
- Nik.
On Fri, Aug 3, 2012 at 3:49 AM, Greg Von Kuster wrote:
> Hello Nikhil,
>
>
> On Aug 2, 2012, at 9:32 PM, Nikhil Joshi wrote:
>
>> Hi all,
>>
>> We just upgraded our local galaxy to the latest version and now I am
>> trying to get automatic tool installation to work properly. I changed
>> the universe_wsgi.ini file to enable the toolshed xml file,
>
> Regarding this, do you mean that you have something like the following
> setting?
>
> tool_config_files = tool_conf.xml,shed_tool_conf.xml
>
>
>> I created
>> a "shed_tools" directory one above the galaxy install, and restarted
>> galaxy. But when I try to install a repository, I get this error as a
>> popup: "Initializing repository installation failed".
>
> From what tool shed are you trying to install Galaxy? When this pop-up is
> displayed, the last line of your Galaxy paster log should be a url. If you
> paste that url into a browser it will display a page that displays the entire
> stack trace for the exception. We'll need to see this information in order
> to determine the cause of the problem.
>
>
>> I tried this
>> with various repositories, but I get the same error. Then when I go
>> to "Manage installed tool shed repositories", all of the repositories
>> I tried to install are stuck in the "Cloning" state. Finally, if I
>> try to uninstall any of them, I get this error, with a traceback:
>>
>> AttributeError: 'NoneType' object has no attribute 'startswith'
>>
>> Any ideas?
>>
>> - Nik.
>>
>> --
>> Nikhil Joshi
>> Bioinformatics Analyst/Programmer
>> UC Davis Bioinformatics Core
>> http://bioinformatics.ucdavis.edu/
>> najoshi -at- ucdavis -dot- edu
>> 530.752.2698 (w)
>> ___
>> 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/
>
--
Nikhil Joshi
Bioinformatics Analyst/Programmer
UC Davis Bioinformatics Core
http://bioinformatics.ucdavis.edu/
najoshi -at- ucdavis -dot- edu
530.752.2698 (w)
___
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/
Re: [galaxy-dev] Can't get automatic toolshed installation to work....
Hello Nikhil, On Aug 2, 2012, at 9:32 PM, Nikhil Joshi wrote: > Hi all, > > We just upgraded our local galaxy to the latest version and now I am > trying to get automatic tool installation to work properly. I changed > the universe_wsgi.ini file to enable the toolshed xml file, Regarding this, do you mean that you have something like the following setting? tool_config_files = tool_conf.xml,shed_tool_conf.xml > I created > a "shed_tools" directory one above the galaxy install, and restarted > galaxy. But when I try to install a repository, I get this error as a > popup: "Initializing repository installation failed". >From what tool shed are you trying to install Galaxy? When this pop-up is >displayed, the last line of your Galaxy paster log should be a url. If you >paste that url into a browser it will display a page that displays the entire >stack trace for the exception. We'll need to see this information in order to >determine the cause of the problem. > I tried this > with various repositories, but I get the same error. Then when I go > to "Manage installed tool shed repositories", all of the repositories > I tried to install are stuck in the "Cloning" state. Finally, if I > try to uninstall any of them, I get this error, with a traceback: > > AttributeError: 'NoneType' object has no attribute 'startswith' > > Any ideas? > > - Nik. > > -- > Nikhil Joshi > Bioinformatics Analyst/Programmer > UC Davis Bioinformatics Core > http://bioinformatics.ucdavis.edu/ > najoshi -at- ucdavis -dot- edu > 530.752.2698 (w) > ___ > 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/ ___ 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/
[galaxy-dev] Can't get automatic toolshed installation to work....
Hi all, We just upgraded our local galaxy to the latest version and now I am trying to get automatic tool installation to work properly. I changed the universe_wsgi.ini file to enable the toolshed xml file, I created a "shed_tools" directory one above the galaxy install, and restarted galaxy. But when I try to install a repository, I get this error as a popup: "Initializing repository installation failed". I tried this with various repositories, but I get the same error. Then when I go to "Manage installed tool shed repositories", all of the repositories I tried to install are stuck in the "Cloning" state. Finally, if I try to uninstall any of them, I get this error, with a traceback: AttributeError: 'NoneType' object has no attribute 'startswith' Any ideas? - Nik. -- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w) ___ 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/
