Dear Galaxy Developers,
My user name is henry.to(a)petermac.org
I'm having issues downloading files (which is an issue I didn't used to have), particularly ones which have >50 columns. These can be uploaded, but then cannot be downloaded from the server.
I have attached an example txt file and can provide other examples (via a shared history) of files that I can no longer download.
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These are various tables related to workflow in Galaxy that I found in the
database. There are very similar tables like: workflow and stored_workflow,
workflow_step_tag_association, stored_workflow_tag_association etc. I want
to know what does specific table holds. What are the fundamental
differences between workflow and stored_workflow? Is there Galaxy
documentation available for it? If so, please provide me the link.
Happy new year!
I have western mysteries that I cannot resolve.
I have a local instance of galaxy and while this instance run correctly
since several hours or days, suddenly the jobs fail and this error appears :
Import error : no module named CistromeAP.jianlib.inout
CistromeAP is the name of my main directory for galaxy and it contains the
sub directory jianlib with the script inout.py.
Tha application which runs with this module runs correctly for several jobs
and for a mysterious reason, a next job don't run because it cannot find
This error appears with different applications and at different time of
using of galaxy.
Sometimes even, it appears just after the launching of galaxy!!!
Is it a problem with my server apache and why ?
Have you a test to know where come the problem from?
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:
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
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
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?
School of Computer Engineering and Science Shanghai University, Shanghai China