[galaxy-dev] (no subject)
Hello all, A lot is happening in in the Galaxy in November, and a lot of good stuff happened in October too. Take a look at the November 2014 Galaxy Newsletter https://wiki.galaxyproject.org/GalaxyUpdates/2014_11 for the complete story, but here are some highlights: - *IRC Channel is Now Publicly Archived https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#IRC_Channel_is_Now_Publicly_Archived* - Galaxy Training Network Launched https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#Galaxy_Training_Network = find a trainer near you (and sign up if you do training) - Galaxy Days: 2-3 December, Paris https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#Galaxy_Days:_2-3_December.2C_Paris - Swiss German Galaxy Tour 2014 Report https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#Swiss_German_Galaxy_Tour_2014_Report - Fall 2014 GUGGO Events Report https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#Fall_2014_GUGGO_Events_Report - and 11 other events between now and the end of the year https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#Other_Events - 38 new papers https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#New_Papers, including 3 featured papers - Who's Hiring https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#Who.27s_Hiring - Two new public Galaxy Servers https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#New_Public_Servers - 35 new ToolShed repos https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#ToolShed_Contributions - And a smattering of other news https://wiki.galaxyproject.org/GalaxyUpdates/2014_11#Other_News too Dave Clements and the Galaxy Team https://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/ ___ 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/
[galaxy-dev] (no subject)
Hello, Galaxy will not load my histories and as a result I can not run the analysis that I need to run. I have tried repeatedly since 7:00 AM EST to load them with no luck. I worked on this history yesterday and everything was fine. Maria ___ 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/
[galaxy-dev] (no subject)
Hello dev-team,
I have updated
code repository
of our production instance https://galaxy.cbio.mskcc.org to the recent
galaxy-dist (10216:ebe87051fadf), now the instance page it is not rendering
in a proper way.
The error message I can see from the log file as follows:
--
x.x.x.x - - [08/Aug/2013:15:00:49 -0400] GET / HTTP/1.1 200 - -
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.31 (KHTML, like Gecko)
Chrome/26.0.1410.63 Safari/537.31
x.x.x.x - - [08/Aug/2013:15:00:50 -0400] GET /root/tool_menu HTTP/1.1 404
- https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (X11; Linux x86_64)
AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31
x.x.x.x - - [08/Aug/2013:15:00:50 -0400] GET /history HTTP/1.1 200 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (X11; Linux x86_64)
AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31
x.x.x.x - - [08/Aug/2013:15:00:50 -0400] GET /history HTTP/1.1 500 -
https://galaxy.cbio.mskcc.org/; Mozilla/5.0 (X11; Linux x86_64)
AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.63 Safari/537.31
Exception happened during processing of request from ('127.0.0.1', 42042)
Traceback (most recent call last):
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
1068, in process_request_in_thread
self.finish_request(request, client_address)
File /usr/lib64/python2.6/SocketServer.py, line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File /usr/lib64/python2.6/SocketServer.py, line 617, in __init__
self.handle()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
442, in handle
BaseHTTPRequestHandler.handle(self)
File /usr/lib64/python2.6/BaseHTTPServer.py, line 329, in handle
self.handle_one_request()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
437, in handle_one_request
self.wsgi_execute()
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py, line
287, in wsgi_execute
self.wsgi_start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/urlmap.py, line 203,
in __call__
return app(environ, start_response)
File /codebase/lib/galaxy/web/framework/middleware/request_id.py, line
12, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/xforwardedhost.py,
line 21, in __call__
return self.app( environ, start_response )
File /codebase/lib/galaxy/web/framework/middleware/translogger.py, line
68, in __call__
return self.application(environ, replacement_start_response)
File /codebase/lib/galaxy/web/framework/middleware/error.py, line 159,
in __call__
exc_info)
File /codebase/lib/galaxy/web/framework/middleware/translogger.py, line
67, in replacement_start_response
return start_response( status, headers, exc_info )
File /codebase/lib/galaxy/web/framework/middleware/error.py, line 149,
in __call__
app_iter = self.application(environ, sr_checker)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py, line
84, in __call__
return self.application(environ, start_response)
File /codebase/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py,
line 633, in __call__
return self.application(environ, start_response)
File /codebase/lib/galaxy/web/framework/base.py, line 132, in __call__
return self.handle_request( environ, start_response )
File /codebase/lib/galaxy/web/framework/base.py, line 199, in
handle_request
return body( environ, start_response )
File /codebase/lib/galaxy/web/framework/__init__.py, line 985, in render
template.render_context( context )
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/template.py, line 319, in
render_context
**kwargs)
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py, line 692, in
_render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File /codebase/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py, line 718, in
_exec_template
callable_(context, *args, **kwargs)
File /codebase/database/compiled_templates/root/history.mako.py, line
73, in render_body
if bool( [ data for data in history.active_datasets if data.state in
['running', 'queued', '', None ] ] ):
AttributeError: 'Undefined' object has no attribute 'active_datasets'
Could you point me where I have to look to fix this issue.
thanks in advance,
--/Vipin
___
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/
[galaxy-dev] (no subject)
Hello all, The July 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07 . *Highlights:* - *GCC2013 http://wiki.galaxyproject.org/Events/GCC2013* starts *today*in Oslo, Norway. - Four new public servershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#New_Public_Servers - A record 53 new papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#New_Papers - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#Who.27s_Hiring at five different organizations - Galaxy @ ISMBhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#ISMB_.2F_ECCB_.2F_BOSC_.2F_MS_SIG_2013 - Other Upcoming Eventshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#Other_Upcoming_Events - New distributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#Galaxy_Distributions - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_07#Other_News If you have anything you would like to see in the August *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Dave Clements and the Galaxy Team -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] (no subject)
HI, Thanks for the reply. actually my server is not connected with the internet. Previously i downloaded in another system with internet connection and installed to server. now i gave internet connection to the server now i could connect to it and download the python eggs. Thanks Sridhar On Sat, May 4, 2013 at 12:36 AM, Adam Brenner aebre...@uci.edu wrote: What version of Python are you using? I believe Python 2.7 is the recommend version. I suggest you grab a fresh copy of galaxy from the stable branch and try again. -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ http://www.ics.uci.edu/%7Eaebrenne/ aebre...@uci.edu On Fri, May 3, 2013 at 12:24 AM, sridhar srinivasan sridhar2bioi...@gmail.com wrote: Dear All, i am installing galaxy first time. i face problem while installing the python eggs. while running the Run.sh command it gives as /home/sbsuser/.python-eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg-tmp/csamtools.so:6: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility � b �n 64 0� c � � � �� ? �� � ��U �#k � ! \ j Z o� [ � � � [ � � �9 - �� ra # ��� �� 8n � �C �U�; B � S l K (p� �� U � � P w 5 ≠ ' H š è π ø * ─ ␋ Ð Ä @ ê i couldn't read the message and also i couldn't open the galaxy page http://localhost:8080 Could you please suggest tth epossibilities to install. Thanks in advance Regards Sridhar ___ 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/
[galaxy-dev] (no subject)
Dear All, i am installing galaxy first time. i face problem while installing the python eggs. while running the Run.sh command it gives as /home/sbsuser/.python-eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg-tmp/csamtools.so:6: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility �b�n 640�c�����?�����U�#k�!\jZo�[� ��[���9-��ra#����� 8n��C�U�;B�SlK(p���U��P w 5 ≠ ' H è π ø * ─ ␋ Ð Ä @ ê i couldn't read the message and also i couldn't open the galaxy page http://localhost:8080 Could you please suggest tth epossibilities to install. Thanks in advance Regards Sridhar ___ 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] (no subject)
What version of Python are you using? I believe Python 2.7 is the recommend version. I suggest you grab a fresh copy of galaxy from the stable branch and try again. -- Adam Brenner Computer Science, Undergraduate Student Donald Bren School of Information and Computer Sciences Research Computing Support Office of Information Technology http://www.oit.uci.edu/rcs/ University of California, Irvine www.ics.uci.edu/~aebrenne/ aebre...@uci.edu On Fri, May 3, 2013 at 12:24 AM, sridhar srinivasan sridhar2bioi...@gmail.com wrote: Dear All, i am installing galaxy first time. i face problem while installing the python eggs. while running the Run.sh command it gives as /home/sbsuser/.python-eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg-tmp/csamtools.so:6: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility � b �n 64 0� c � � � �� ? �� � ��U �#k � ! \ j Z o� [ � � � [ � � �9 - �� ra # ��� �� 8n � �C �U�; B � S l K (p� �� U � � P w 5 ≠ ' H š è π ø * ─ ␋ Ð Ä @ ê i couldn't read the message and also i couldn't open the galaxy page http://localhost:8080 Could you please suggest tth epossibilities to install. Thanks in advance Regards Sridhar ___ 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] (no subject)
David, Thank you for reporting this error, which was due to a new tool shed feature being introduced in -central, which had not yet been wrapped in a backwards compatibility layer for -dist. As of 9440:bbb229927c68, the issue should be resolved. --Dave B. On 4/11/13 12:51:03.000, David Bonsall wrote: Dear Galaxy team, I'm trying to install NCBI + tools on a local instance of galaxy (rep: 8.1546099212f), but I get the following error, which I do not get when trying to install other tools. Thank you for all your hard work. It's all much appreciated David Error Traceback: View as: Interactive | Text | XML (full) ⇝ HTTPError: HTTP Error 500: Internal Server Error URL: http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1d92ebdf7e8d466cchangeset_revisions=1f546099212f Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:125 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:182 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:228 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:894 in prepare_for_install view common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) Module tool_shed.util.common_install_util:90 in get_dependencies_for_repository view required_repo_info_dicts = get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) ) Module tool_shed.util.common_install_util:283 in get_required_repo_info_dicts view response = urllib2.urlopen( url ) Module urllib2:126 in urlopen view return _opener.open(url, data, timeout) Module urllib2:400 in open view response = meth(req, response) Module urllib2:513 in http_response view 'http', request, response, code, msg, hdrs) Module urllib2:438 in error view return self._call_chain(*args) Module urllib2:372 in _call_chain view result = func(*args) Module urllib2:521 in http_error_default view raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error ___ 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] (no subject)
David, The reason shed_tools should be outside the Galaxy path is that tool shed mercurial repositories can interfere with the Galaxy mercurial repository, since mercurial will find more than one .hg directory. As long as the data you want to store is not a mercurial repository, you should be safe, but my advice would still be to locate it outside the Galaxy path to avoid any possibility of conflicts. --Dave B. On 4/16/13 16:28:01.000, David Bonsall wrote: Thanks Dave A quick update from /galaxy-dist % hg update stable .did the trick! Btw, I have another question I have since added sub-directories to /galaxy-dist to store blast databases etc. Is this bad? Will mercurial be able to update. I remember a warning to not install shed-tools directory in the main galaxy stem for this reason. Does this rule apply to all directories? Best Wishes David On Tue, Apr 16, 2013 at 9:16 PM, Dave Bouvier d...@bx.psu.edu mailto:d...@bx.psu.edu wrote: David, Thank you for reporting this error, which was due to a new tool shed feature being introduced in -central, which had not yet been wrapped in a backwards compatibility layer for -dist. As of 9440:bbb229927c68, the issue should be resolved. --Dave B. On 4/11/13 12:51:03.000, David Bonsall wrote: Dear Galaxy team, I'm trying to install NCBI + tools on a local instance of galaxy (rep: 8.1546099212f), but I get the following error, which I do not get when trying to install other tools. Thank you for all your hard work. It's all much appreciated David Error Traceback: View as: Interactive | Text | XML (full) ⇝ HTTPError: HTTP Error 500: Internal Server Error URL: http://127.0.0.1:8080/admin___toolshed/prepare_for_install?__tool_shed_url=http://toolshed.__g2.bx.psu.edu/repository_ids=__1d92ebdf7e8d466cchangeset___revisions=1f546099212f http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1d92ebdf7e8d466cchangeset_revisions=1f546099212f Module weberror.evalexception.__middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:125 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:182 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:228 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.__controllers.admin_toolshed:894 in prepare_for_install view common_install_util.get___dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) Module tool_shed.util.common_install___util:90 in get_dependencies_for___repository view required_repo_info_dicts = get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) ) Module tool_shed.util.common_install___util:283 in get_required_repo_info_dicts view response = urllib2.urlopen( url ) Module urllib2:126 in urlopen view return _opener.open(url, data, timeout) Module urllib2:400 in open view response = meth(req, response) Module urllib2:513 in http_response view 'http', request, response, code, msg, hdrs) Module urllib2:438 in error view return self._call_chain(*args) Module urllib2:372 in _call_chain view result = func(*args) Module urllib2:521 in http_error_default view raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error _ 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/ 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:
Re: [galaxy-dev] (no subject)
David, While I look into the cause of this error, could you tell me which revision of Galaxy you're running? --Dave B. On 4/11/13 12:51:03.000, David Bonsall wrote: Dear Galaxy team, I'm trying to install NCBI + tools on a local instance of galaxy (rep: 8.1546099212f), but I get the following error, which I do not get when trying to install other tools. Thank you for all your hard work. It's all much appreciated David Error Traceback: View as: Interactive | Text | XML (full) ⇝ HTTPError: HTTP Error 500: Internal Server Error URL: http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1d92ebdf7e8d466cchangeset_revisions=1f546099212f Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:125 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:182 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:228 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:894 in prepare_for_install view common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) Module tool_shed.util.common_install_util:90 in get_dependencies_for_repository view required_repo_info_dicts = get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) ) Module tool_shed.util.common_install_util:283 in get_required_repo_info_dicts view response = urllib2.urlopen( url ) Module urllib2:126 in urlopen view return _opener.open(url, data, timeout) Module urllib2:400 in open view response = meth(req, response) Module urllib2:513 in http_response view 'http', request, response, code, msg, hdrs) Module urllib2:438 in error view return self._call_chain(*args) Module urllib2:372 in _call_chain view result = func(*args) Module urllib2:521 in http_error_default view raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error ___ 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/
[galaxy-dev] (no subject)
Dear Galaxy team, I'm trying to install NCBI + tools on a local instance of galaxy (rep: 8.1546099212f), but I get the following error, which I do not get when trying to install other tools. Thank you for all your hard work. It's all much appreciated David Error Traceback: View as: Interactive | Text | XML (full) ⇝ HTTPError: HTTP Error 500: Internal Server Error URL: http://127.0.0.1:8080/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1d92ebdf7e8d466cchangeset_revisions=1f546099212f Module weberror.evalexception.middleware:364 in respond view app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:633 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:125 in __call__ view return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:182 in handle_request view body = method( trans, **kwargs ) Module galaxy.web.framework:228 in decorator view return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:894 in prepare_for_install view common_install_util.get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ) Module tool_shed.util.common_install_util:90 in get_dependencies_for_repository view required_repo_info_dicts = get_required_repo_info_dicts( tool_shed_url, util.listify( repo_info_dict ) ) Module tool_shed.util.common_install_util:283 in get_required_repo_info_dicts view response = urllib2.urlopen( url ) Module urllib2:126 in urlopen view return _opener.open(url, data, timeout) Module urllib2:400 in open view response = meth(req, response) Module urllib2:513 in http_response view 'http', request, response, code, msg, hdrs) Module urllib2:438 in error view return self._call_chain(*args) Module urllib2:372 in _call_chain view result = func(*args) Module urllib2:521 in http_error_default view raise HTTPError(req.get_full_url(), code, msg, hdrs, fp) HTTPError: HTTP Error 500: Internal Server Error ___ 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/
[galaxy-dev] (no subject)
Dear Galaxy manager, I'm using the GATK beta version on your Galaxy website. I'm little bit concerned by the fact that i cannot choose my reference genome, either in the depth of coverage or in the realigner target creator. I want to use the Hg19 genome, but i do not know how to load it. Can you help me please? Thanks -- *AUGUSTE Aurélie* Post doctorante Génétique et génomique du développement gonadique Université Paris-Diderot/Paris 7 Institut Jacques Monod CNRS-UMR 7592 555B - Bâtiment Buffon 15 Rue Hélène Brion Paris Cedex 13 France. Phone: 0033 1 57 27 81 17 ___ 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] (no subject)
Security warning: DO NOT CLICK on the link in this thread. Rehan Saleem - it is likely that your original sending hotmail email account has been compromised. We have removed it from the galaxy-...@bx.psu.edu mailing list to prevent further unmoderated posts until the problem is cleared. Contacting your local system administrator for help is one place to start. Anyone who did click on the link already should do the same, as this is usually how such viruses spread, although much depends on OS and other factors. Good luck! Jen Galaxy team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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] (no subject)
Hi, We are having problems fetching sequences from our mysql database to galaxy. Does anyone know how to do so? Thank you for your help. --Ricardo Perez. ___ 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] (no subject)
Hello Everyone, I am about to write a syncing tool for Galaxy like Dropbox using Python with the progress bar. How do I integrate it with galaxy? It would be easy for client to upload files using the syncing tool. Are there any syncing tools available for Galaxy? Thanks ___ 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] (no subject)
Hello everyone. Personnel of aid to put my galaxy that is place to be accessed by other machines already setup apache as the galaxy is on wiki, but I'm not getting access to another computer on my network. Does anyone know how to configure Apache to let the galaxy accessible to other machines? Thank you. -- *Alfredo Guilherme* * * ___ 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] (no subject)
Hello Alfredo, Setting up Galaxy as a production server has many components, so it is difficult to know exactly what the issue may be, especially if you have already followed the instructions on the wiki. For example, if Galaxy just not showing up on your intranet or are you having trouble logging in as non-administrator? Or perhaps you are asking where to look in the wiki? All of these topics are covered in the wiki. This is where to start: http://getgalaxy.org Follow the instructions for 'Advanced Configuration' that begin at the bottom of the primary wiki above, to find this areas: Running Galaxy in a production environment: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server Under the section Using a proxy server find specific instructions for Apache: http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy All Administrative resources can be found under: http://wiki.g2.bx.psu.edu/Admin This should help you or your administrator to get things going. If you get stuck at a particular spot, first check to see if it is a network configuration issue local to our site and resolve that as a first step. If it still seems to be a Galaxy configuration issue, then please provide more details. Be sure to keep the galaxy-...@bx.psu.edu mailing list on the cc list - we will want the developer's and community's support in helping to troubleshoot issues. Hopefully this helps, Jen Galaxy team On 10/4/12 8:28 AM, Alfredo Guilherme Silva Souza wrote: Hello everyone. Personnel of aid to put my galaxy that is place to be accessed by other machines already setup apache as the galaxy is on wiki, but I'm not getting access to another computer on my network. Does anyone know how to configure Apache to let the galaxy accessible to other machines? Thank you. -- /*Alfredo Guilherme*/ /* */ ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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] (no subject)
Hello Jean! I am using the galaxy in my project CBT (Work Completion of course), I am student of Computer Science. I'll put my project to run on a server of a university to make the presentation, only for this first'm running and configuring everything in my notebook (locally), I followed all the steps to configure apache, just that I can only access the galaxy by the address that I put in the galaxy, if I access my apache can not view the project as configured galaxy. Sorry about my doubts, I think someone may have already gone through it and maybe you can help me. Hugs. 2012/10/4 Jennifer Jackson j...@bx.psu.edu Hello Alfredo, Setting up Galaxy as a production server has many components, so it is difficult to know exactly what the issue may be, especially if you have already followed the instructions on the wiki. For example, if Galaxy just not showing up on your intranet or are you having trouble logging in as non-administrator? Or perhaps you are asking where to look in the wiki? All of these topics are covered in the wiki. This is where to start: http://getgalaxy.org Follow the instructions for 'Advanced Configuration' that begin at the bottom of the primary wiki above, to find this areas: Running Galaxy in a production environment: http://wiki.g2.bx.psu.edu/**Admin/Config/Performance/**Production%20Serverhttp://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server Under the section Using a proxy server find specific instructions for Apache: http://wiki.g2.bx.psu.edu/**Admin/Config/Apache%20Proxyhttp://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy All Administrative resources can be found under: http://wiki.g2.bx.psu.edu/**Admin http://wiki.g2.bx.psu.edu/Admin This should help you or your administrator to get things going. If you get stuck at a particular spot, first check to see if it is a network configuration issue local to our site and resolve that as a first step. If it still seems to be a Galaxy configuration issue, then please provide more details. Be sure to keep the galaxy-...@bx.psu.edu mailing list on the cc list - we will want the developer's and community's support in helping to troubleshoot issues. Hopefully this helps, Jen Galaxy team On 10/4/12 8:28 AM, Alfredo Guilherme Silva Souza wrote: Hello everyone. Personnel of aid to put my galaxy that is place to be accessed by other machines already setup apache as the galaxy is on wiki, but I'm not getting access to another computer on my network. Does anyone know how to configure Apache to let the galaxy accessible to other machines? Thank you. -- /*Alfredo Guilherme*/ /* */ __**_ 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/ -- Jennifer Jackson http://galaxyproject.org -- *Alfredo Guilherme* * * ___ 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] (no subject)
MY Y Sent from my iPhone ___ 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] (no subject)
To: From: James Taylor ja...@jamestaylor.org Subject: Re: [galaxy-dev] List of browsers which supports galaxy Quoting Nate Coraor (2012-07-13 17:22:22) We don't maintain an official list except with Internet Explorer, for which support was dropped recently, as Peter noted above. We do attempt to continue to support IE9. It is no longer possible for us to support earlier versions of IE. IE is the most difficult browser for us to deal with because of its many issues, bug reports or patches for IE9+ support are welcome. Thanks. ___ 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] (no subject)
Hello Susan, Are you still having problem with registration? Please try again, doing the following to register at the Galaxy main public instance. - Start at: http://usegalaxy.org/ - This will take you to: https://main.g2.bx.psu.edu/ - On the top menu, far right, is the User menu. Click on this, there are two options, register is the second. Best, Jen Galaxy team On 6/28/12 1:51 PM, Susan Hester wrote: Hi, I'm trying to register in Galaxy on the public server and under the user tab register is greyed out? How do I register? Susan Hester, Ph.D. Research Biologist Systems Biology Branch Integrated Systems Toxicology Division (ISTD) National Health and Environmental Effects Research Lab US Environmental Protection Agency 109 T.W. Alexander Dr. MD-B143-06 Research Triangle Park, NC 27711 hester.su...@epa.gov ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ 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] (no subject)
Hello, I have never used this support route before however I have a question about a Galaxy wrapper that I made for a python tool. I have a text input box connected to a $command_line_spot in an attempt to run a string such as IN[4]=='gene' on the command line (quotations included) through text box input. When I put IN[4]=='gene' directly in the command line it runs fine, however when I put it through my text box it puts the string on the command line as __dq__IN__ob__4__cb__==__sq__gene__sqdq__ IN[4]=='gene' instead of just IN[4]=='gene'. Sorry if this email makes no sense whatsoever, it is very out of context but I thought I'd ask. Note: I am running the latest release of galaxy which I pulled from mercurial. Thanks, Carlos The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___ 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] (no subject)
Hi Carlos See: galaxy_dist/lib/galaxy/util/__init__.py for characters that are allowed but need to be escaped Regards, Hans On 06/28/2012 03:14 PM, Carlos Reyes wrote: Hello, I have never used this support route before however I have a question about a Galaxy wrapper that I made for a python tool. I have a text input box connected to a $command_line_spot in an attempt to run a string such as IN[4]=='gene' on the command line (quotations included) through text box input. When I put IN[4]=='gene' directly in the command line it runs fine, however when I put it through my text box it puts the string on the command line as __dq__IN__ob__4__cb__==__sq__gene__sqdq__ IN[4]=='gene' instead of just IN[4]=='gene'. Sorry if this email makes no sense whatsoever, it is very out of context but I thought I'd ask. Note: I am running the latest release of galaxy which I pulled from mercurial. Thanks, Carlos The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. ___ 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] (no subject)
Hi, I'm trying to register in Galaxy on the public server and under the user tab register is greyed out? How do I register? Susan Hester, Ph.D. Research Biologist Systems Biology Branch Integrated Systems Toxicology Division (ISTD) National Health and Environmental Effects Research Lab US Environmental Protection Agency 109 T.W. Alexander Dr. MD-B143-06 Research Triangle Park, NC 27711 hester.su...@epa.gov___ 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] (no subject)
On 01/24/2012 06:19 AM, Vidya .H.K wrote: Hi, Actually I am not computer expert as well. I have just started to work in this area. so I am not able to figure out how to solve this problem. I request you to elaborate on what you meant in your previous mail. by simulating a complete command line I meant the following: You look how macs_wrapper.py is called by galaxy. This is written in the macs_wrapper.xml and then you execute the same command line. But I just realize, you have re-submitted the same question in a different e-mail thread again (unfortunately, again without a subject line). Thanks in advance As I wrote in my previous e-mail: Please send all follow-up with a cc to the mailing list (reply-all). In order to debug you situation you need to simulate a complete commandline, the same Galaxy is doing. Regards, Hans On 01/23/2012 05:35 AM, Vidya .H.K wrote: Hi, Sorry for delayed reply. When I execute macs_wrapper.py on command line, I get the following error. python macs_wrapper.py File stdin, line 1 python macs_wrapper.py Thanks in advance On 01/10/2012 06:31 AM, Vidya .H.K wrote: Hi, I think macs is exceutable with galaxy user. what happens if you execute macs_wrapper.py on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list (reply-all). On 01/09/2012 05:04 AM, Vidya .H.K wrote: Hi, I am new user to galaxy. I have installed galaxy on the Linux local server for ChIP-seq analysis. While running MACS, an error is flagged An error occurred running this job: /bin/sh: macs: not found . I have set the path for macs in /bin. But still the error persists. It would be great if any one help me resolve this problem. Hi Vidya Is macs executable for the galaxy user (ie the user the galaxy server is running as) ? Regards, Hans Thanks in advance. Regards vidya ___ 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] (no subject)
Hi, I have locally installed galaxy on a linux(ubuntu) machine. I have not installed all the tools on the local galaxy server. I am not able to integrate MACS peak calling tool with galaxy. I have followed all the instructions for installation of MACS and it is running fine on the commandline(standalone is fine).But with galaxy it is giving the following error: An error occurred running this job: /bin/sh: macs: not found I have tried executing the macs_wrapper.py in the commandline and I have got the following error: Traceback (most recent call last): File macs_wrapper.py, line 135, in module if __name__ == __main__: main() File macs_wrapper.py, line 45, in main options = simplejson.load( open( sys.argv[1] ) ) IndexError: list index out of range I have set the PYTHONPATH(i.e PYTHONPATH=~/galaxy-dist/lib) and I have macs in PATH. I am not a technical/computer expert as well, hence I would appreciate if any one could help me resolve this problem tell me where I am going wrong Thanks in advance Regards ___ 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] (no subject)
Hi, Actually I am not computer expert as well. I have just started to work in this area. so I am not able to figure out how to solve this problem. I request you to elaborate on what you meant in your previous mail. Thanks in advance As I wrote in my previous e-mail: Please send all follow-up with a cc to the mailing list (reply-all). In order to debug you situation you need to simulate a complete commandline, the same Galaxy is doing. Regards, Hans On 01/23/2012 05:35 AM, Vidya .H.K wrote: Hi, Sorry for delayed reply. When I execute macs_wrapper.py on command line, I get the following error. python macs_wrapper.py File stdin, line 1 python macs_wrapper.py Thanks in advance On 01/10/2012 06:31 AM, Vidya .H.K wrote: Hi, I think macs is exceutable with galaxy user. what happens if you execute macs_wrapper.py on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list (reply-all). On 01/09/2012 05:04 AM, Vidya .H.K wrote: Hi, I am new user to galaxy. I have installed galaxy on the Linux local server for ChIP-seq analysis. While running MACS, an error is flagged An error occurred running this job: /bin/sh: macs: not found . I have set the path for macs in /bin. But still the error persists. It would be great if any one help me resolve this problem. Hi Vidya Is macs executable for the galaxy user (ie the user the galaxy server is running as) ? Regards, Hans Thanks in advance. Regards vidya ___ 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/
Re: [galaxy-dev] (no subject)
As I wrote in my previous e-mail: Please send all follow-up with a cc to the mailing list (reply-all). In order to debug you situation you need to simulate a complete commandline, the same Galaxy is doing. Regards, Hans On 01/23/2012 05:35 AM, Vidya .H.K wrote: Hi, Sorry for delayed reply. When I execute macs_wrapper.py on command line, I get the following error. python macs_wrapper.py File stdin, line 1 python macs_wrapper.py Thanks in advance On 01/10/2012 06:31 AM, Vidya .H.K wrote: Hi, I think macs is exceutable with galaxy user. what happens if you execute macs_wrapper.py on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list (reply-all). On 01/09/2012 05:04 AM, Vidya .H.K wrote: Hi, I am new user to galaxy. I have installed galaxy on the Linux local server for ChIP-seq analysis. While running MACS, an error is flagged An error occurred running this job: /bin/sh: macs: not found . I have set the path for macs in /bin. But still the error persists. It would be great if any one help me resolve this problem. Hi Vidya Is macs executable for the galaxy user (ie the user the galaxy server is running as) ? Regards, Hans Thanks in advance. Regards vidya ___ 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/ Regards H.K.VIDYA - Institute of Bioinformatics and Applied Biotechnology, Bangalore ___ 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] (no subject)
On 01/10/2012 06:31 AM, Vidya .H.K wrote: Hi, I think macs is exceutable with galaxy user. what happens if you execute macs_wrapper.py on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list (reply-all). On 01/09/2012 05:04 AM, Vidya .H.K wrote: Hi, I am new user to galaxy. I have installed galaxy on the Linux local server for ChIP-seq analysis. While running MACS, an error is flagged An error occurred running this job: /bin/sh: macs: not found . I have set the path for macs in /bin. But still the error persists. It would be great if any one help me resolve this problem. Hi Vidya Is macs executable for the galaxy user (ie the user the galaxy server is running as) ? Regards, Hans Thanks in advance. Regards vidya ___ 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/ Regards H.K.VIDYA PGDB-10-10-33 - Institute of Bioinformatics and Applied Biotechnology, Bangalore ___ 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] (no subject)
Hi, I am new user to galaxy. I have installed galaxy on the Linux local server for ChIP-seq analysis. While running MACS, an error is flagged An error occurred running this job: /bin/sh: macs: not found . I have set the path for macs in /bin. But still the error persists. It would be great if any one help me resolve this problem. Thanks in advance. Regards vidya ___ 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] (no subject)
On 01/09/2012 05:04 AM, Vidya .H.K wrote: Hi, I am new user to galaxy. I have installed galaxy on the Linux local server for ChIP-seq analysis. While running MACS, an error is flagged An error occurred running this job: /bin/sh: macs: not found . I have set the path for macs in /bin. But still the error persists. It would be great if any one help me resolve this problem. Hi Vidya Is macs executable for the galaxy user (ie the user the galaxy server is running as) ? Regards, Hans Thanks in advance. Regards vidya ___ 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/
Re: [galaxy-dev] (no subject)
Kristen Eisenberg wrote: [galaxy-dev] Failure to prepare job error Hello, I'm running a Python/R tool from my Amazon Galaxy instance. To use R, I import a package I've installed called PypeR. My tool works fine from the command line, but when I try to run it on my Amazon instance, it gives me this error: Traceback (most recent call last): File /nfs/software/galaxy/lib/galaxy/jobs/runners/local.py, line 61, in run_job job_wrapper.prepare() File /nfs/software/galaxy/lib/galaxy/jobs/__init__.py, line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File /nfs/software/galaxy/lib/galaxy/tools/__init__.py, line 1543, in build_command_line command_line = fill_template( self.command, context=param_dict ) File /nfs/software/galaxy/lib/galaxy/util/template.py, line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File /nfs/software/galaxy/eggs/Cheetah-2.2.2-py2.6-linux-i686-ucs4.egg/Cheetah/Template.py, line 1004, in __str__ return getattr(self, mainMethName)() File cheetah_DynamicallyCompiledCheetahTemplate_1311891781_86_41894.py, line 83, in respond EOFError: EOF when reading a line With the additional caption failure to prepare job. I've been struggling with this for days, and I'm pretty sure I don't have a typo in my .xml file. How can I solve this? Hi Kristen, Could you post the relevant XML file to the list? The error unfortunately indicates a syntax error or typo. --nate Kristen Eisenberg Billige Flüge Marketing GmbH Emanuelstr. 3, 10317 Berlin Deutschland Telefon: +49 (33) 5310967 Email: utebachmeier at gmail.com Site: http://flug.airego.de - Billige Flüge vergleichen ___ 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/
