Tool error occurred when adding my tool to galaxy
Hi, all I'm new here. These days I'm trying to add a tool in Galaxy, as showed in screencast. I did the same thing with that in screencast. But an error occurred. The error says: tool error An error occurred running this job:failure preparing job The message in the terminal says: galaxy.jobs.handler DEBUG 2012-12-29 15:54:25,504 dispatching job 7 to local runner galaxy.jobs.handler INFO 2012-12-29 15:54:25,733 (7) Job dispatched galaxy.jobs.runners.local DEBUG 2012-12-29 15:54:25,818 Local runner: starting job 7 galaxy.jobs.runners.local ERROR 2012-12-29 15:54:26,061 failure running job 7 Traceback (most recent call last): File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/jobs/runners/local.py", line 72, in run_job job_wrapper.prepare() File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/jobs/__init__.py", line 180, in prepare config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/tools/__init__.py", line 2430, in build_config_files f.write( fill_template( template_text, context=param_dict ) ) File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1356767666_06_36079.py", line 149, in respond KeyError: 'thype' 127.0.0.1 - - [29/Dec/2012:15:54:27 +0800] "GET /api/histories/f597429621d6eb2b HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.19 (KHTML, like Gecko) Ubuntu/11.10 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19" 127.0.0.1 - - [29/Dec/2012:15:54:27 +0800] "GET /api/histories/f597429621d6eb2b/contents?ids=ebfb8f50c6abde6d HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.19 (KHTML, like Gecko) Ubuntu/11.10 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19" Could anybody help me? Thanks! =================================================== Regards! School of Computer Engineering and Science Shanghai University, Shanghai China Tan Jun 谭军
I'm sure you checked carefully before posting, but your traceback ends with KeyError: 'thype' suggesting maybe a simple syntax/spelling problem to me. On Sat, Dec 29, 2012 at 7:36 PM, Tan Jun <tanjun2525@gmail.com> wrote:
** Hi, all I'm new here. These days I'm trying to add a tool in Galaxy, as showed in screencast. I did the same thing with that in screencast. But an error occurred. The error says: tool error An error occurred running this job:failure preparing job
The message in the terminal says: galaxy.jobs.handler DEBUG 2012-12-29 15:54:25,504 dispatching job 7 to local runner galaxy.jobs.handler INFO 2012-12-29 15:54:25,733 (7) Job dispatched galaxy.jobs.runners.local DEBUG 2012-12-29 15:54:25,818 Local runner: starting job 7 galaxy.jobs.runners.local ERROR 2012-12-29 15:54:26,061 failure running job 7 Traceback (most recent call last): File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/jobs/runners/local.py", line 72, in run_job job_wrapper.prepare() File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/jobs/__init__.py", line 180, in prepare config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/tools/__init__.py", line 2430, in build_config_files f.write( fill_template( template_text, context=param_dict ) ) File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1356767666_06_36079.py", line 149, in respond KeyError: 'thype' 127.0.0.1 - - [29/Dec/2012:15:54:27 +0800] "GET /api/histories/f597429621d6eb2b HTTP/1.1" 200 - " http://localhost:8080/history" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.19 (KHTML, like Gecko) Ubuntu/11.10 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19" 127.0.0.1 - - [29/Dec/2012:15:54:27 +0800] "GET /api/histories/f597429621d6eb2b/contents?ids=ebfb8f50c6abde6d HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.19 (KHTML, like Gecko) Ubuntu/11.10 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19" Could anybody help me? Thanks!
Hi Tan, If you go into your tool xml file I think you will find a tag error the traceback. Something like type=select you may have put thype a simple typo. Happy Holidays James Boocock On Sat, 2012-12-29 at 16:36 +0800, Tan Jun wrote:
Hi, all I'm new here. These days I'm trying to add a tool in Galaxy, as showed in screencast. I did the same thing with that in screencast. But an error occurred. The error says: tool error An error occurred running this job:failure preparing job
The message in the terminal says: galaxy.jobs.handler DEBUG 2012-12-29 15:54:25,504 dispatching job 7 to local runner galaxy.jobs.handler INFO 2012-12-29 15:54:25,733 (7) Job dispatched galaxy.jobs.runners.local DEBUG 2012-12-29 15:54:25,818 Local runner: starting job 7 galaxy.jobs.runners.local ERROR 2012-12-29 15:54:26,061 failure running job 7 Traceback (most recent call last): File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/jobs/runners/local.py", line 72, in run_job job_wrapper.prepare() File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/jobs/__init__.py", line 180, in prepare config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/tools/__init__.py", line 2430, in build_config_files f.write( fill_template( template_text, context=param_dict ) ) File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1356767666_06_36079.py", line 149, in respond KeyError: 'thype' 127.0.0.1 - - [29/Dec/2012:15:54:27 +0800] "GET /api/histories/f597429621d6eb2b HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.19 (KHTML, like Gecko) Ubuntu/11.10 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19" 127.0.0.1 - - [29/Dec/2012:15:54:27 +0800] "GET /api/histories/f597429621d6eb2b/contents?ids=ebfb8f50c6abde6d HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.19 (KHTML, like Gecko) Ubuntu/11.10 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
Could anybody help me? Thanks!
______________________________________________________________________ =================================================== Regards! School of Computer Engineering and Science Shanghai University, Shanghai China Tan Jun 谭军 ___________________________________________________________ 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:
Hi Tan, If you go into your tool xml file I think you will find a tag error the traceback. Something like type=select you may have put thype a simple typo. Happy Holidays James Boocock On Sat, 2012-12-29 at 16:36 +0800, Tan Jun wrote:
Hi, all I'm new here. These days I'm trying to add a tool in Galaxy, as showed in screencast. I did the same thing with that in screencast. But an error occurred. The error says: tool error An error occurred running this job:failure preparing job
The message in the terminal says: galaxy.jobs.handler DEBUG 2012-12-29 15:54:25,504 dispatching job 7 to local runner galaxy.jobs.handler INFO 2012-12-29 15:54:25,733 (7) Job dispatched galaxy.jobs.runners.local DEBUG 2012-12-29 15:54:25,818 Local runner: starting job 7 galaxy.jobs.runners.local ERROR 2012-12-29 15:54:26,061 failure running job 7 Traceback (most recent call last): File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/jobs/runners/local.py", line 72, in run_job job_wrapper.prepare() File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/jobs/__init__.py", line 180, in prepare config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/tools/__init__.py", line 2430, in build_config_files f.write( fill_template( template_text, context=param_dict ) ) File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/tanjun/galaxy/galaxy-galaxy-dist-36ad8aa7b922/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1356767666_06_36079.py", line 149, in respond KeyError: 'thype' 127.0.0.1 - - [29/Dec/2012:15:54:27 +0800] "GET /api/histories/f597429621d6eb2b HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.19 (KHTML, like Gecko) Ubuntu/11.10 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19" 127.0.0.1 - - [29/Dec/2012:15:54:27 +0800] "GET /api/histories/f597429621d6eb2b/contents?ids=ebfb8f50c6abde6d HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/535.19 (KHTML, like Gecko) Ubuntu/11.10 Chromium/18.0.1025.168 Chrome/18.0.1025.168 Safari/535.19"
Could anybody help me? Thanks!
______________________________________________________________________ =================================================== Regards! School of Computer Engineering and Science Shanghai University, Shanghai China Tan Jun 谭军 ___________________________________________________________ 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:
participants (3)
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James Boocock -
Ross -
Tan Jun