Re: [galaxy-dev] toolsectionlabel error (problem configuring toolshed hotplug?)
Hi Greg, When as admin I want to install a tool from main tool shed to local galaxy,I got this error. URL: http://128.146.132.147:1234/admin_toolshed/install_repository?tool_shed_url=http://toolshed.g2.bx.psu.edu/repo_info_dict=ae427cbeabf65b952fc515302aad902c2f9f0112:7b22686d6d6572223a205b22484d4d657220746f6f6c73222c2022687474703a2f2f746f6f6c736865642e67322e62782e7073752e6564752f7265706f732f6564776172642d6b6972746f6e2f686d6d657c2022363666383236326531363836225d7dincludes_tools=True File '/home/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 173 in decorator return func( self, trans, *args, **kwargs ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 322 in install_repository tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) File '/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/admin_toolshed.py', line 804 in build_tool_panel_section_select_field options.append( ( tool_section.name, tool_section.id ) ) AttributeError: 'ToolSectionLabel' object has no attribute 'name' Your help are absolutely appreciated. Liusong On Wed, Mar 7, 2012 at 9:58 AM, Greg Von Kuster g...@bx.psu.edu wrote: Hi Lisa, It looks like you are current with the tip from the galaxy-dist repository. What are you attempting to do, what exactly is the error you are seeing, and what is shown in your paster log? Thanks, Greg Von Kuster On Mar 6, 2012, at 9:08 PM, Lisa wrote: Hi Greg, I got the exactly same error today. I can install tools from main tool shed before without any problem. I tried hg incoming and hg pull -u to update my local instance. Here is the result for hg summary (galaxy_env)galaxy@osbc-147:~/galaxy-dist$ hg summary parent: 6621:26920e20157f tip Improve language in 'Import workflow' dialog. branch: default commit: 34 modified, 93 unknown update: (current) It looks like we are using diff branch (?) How could I apply your modification? Also I am not using local tool shed either. Thanks Lisa ___ 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] R scripts for DESeq
Just set up the email alert. Thanks. Lisa On Wed, Feb 22, 2012 at 9:27 PM, Greg Von Kuster g...@bx.psu.edu wrote: Lisa, In case you aren't aware, you can set your user preferences for your account in the tool shed to receive an email message when a new repository's first upload occurs. This would keep you from having to check the tool shed. Go to User - Preferences - Manage your email alerts and you'll see the following setting. On Feb 22, 2012, at 8:50 PM, Liusong Yang wrote: Hi Vipin, That is a wonderful news and I am eager to see it in tool shed. I am going to check tool shed frequently these days to get it asap. Thanks Lisa On Wed, Feb 22, 2012 at 4:07 PM, Vipin TS vipin...@gmail.com wrote: Hi, We have the recent release version of DESeq at our Galaxy instance, http://galaxy.tuebingen.mpg.de/tool_runner?tool_id=deseq I will add the Galaxy wrapper for DESeq in community tool shed in few days. regards, --Vipin Hi Lisa, I am going to send your question over to the galaxy-...@bx.psu.edu mailing list so that the development community can offer feedback. http://wiki.g2.bx.psu.edu/Support#Starting_a_technical.2C_local.2BAC8-cloud_instance.2C_or_development_thread Th galaxy-user list is primarily for tool/data usage on the Galaxy public server. http://wiki.g2.bx.psu.edu/Mailing%20Lists Thanks, Jen Galaxy team Original Message Subject: [galaxy-user] R scripts for DESeq Date: Tue, 21 Feb 2012 23:25:35 -0500 From: Liusong Yang liusongyang2...@gmail.com To: galaxy-u...@lists.bx.psu.edu Hello, I am planning to put DESeq into galaxy. I am a newcomer for both Galaxy and R. I have already read all of the related discussion in this group. I also noticed that there are r_wrapper.sh and DESeq.xml added into galaxy recently under the path of tools. These lines are from r_wrapper.sh. ### Run R providing the R script in $1 as standard input and passing ### the remaining arguments on the command line I guess this means we need to give the DESeq R script to the wrapper as standard input. My question is where or what is the DESeq R scripts? I installed R and DESeq package, but I can not fund anything like DESeq.R or something similar? I feel so confusing now. Any comments or suggestions would be absolutely appreciated! Thanks Lisa ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/ ___ 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/
