January 2013 - galaxy-dev - lists.galaxyproject.org

Error downloading files from Galaxy
by To Henry 02 Jan '13

02 Jan '13

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. Regards Henry This email (including any attachments or links) may contain confidential and/or legally privileged information and is intended only to be read or used by the addressee. If you are not the intended addressee, any use, distribution, disclosure or copying of this email is strictly prohibited. Confidentiality and legal privilege attached to this email (including any attachments) are not waived or lost by reason of its mistaken delivery to you. If you have received this email in error, please delete it and notify us immediately by telephone or email. Peter MacCallum Cancer Centre provides no guarantee that this transmission is free of virus or that it has not been intercepted or altered and will not be liable for any delay in its receipt.

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Very confused about workflow_step_connection table?
by Sachit Adhikari 02 Jan '13

02 Jan '13

Dear all, This is the content of my workflow_step_connection table: +----+----------------+---------------+-------------+------------+ | id | output_step_id | input_step_id|output_name|input_name | +----+----------------+---------------+-------------+------------+ | 1 | 1 | 2 | output | input_file | 2 | 3 | 4 | output | input_file | | 3 | 4 | 5 | output_file | input_file | | 4 | 7 | 6 | output_file | input_file | | 5 | 8 | 7 | output | input_file | | 6 | 6 | 9 | output_file | input_file | +----+----------------+---------------+-------------+------------+ How is output_step_id and input_step_id is assigned? Can someone explain me how's connection is build? Thanks

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What is the difference between the table stored_workflow and workflow in Galaxy?
by Sachit Adhikari 02 Jan '13

02 Jan '13

Greetings all, 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. Cheers, Sachit

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Import error : no module named ...
by julie dubois 02 Jan '13

02 Jan '13

Hi all, 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 the scripts. 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? Thanks. Julie

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Tool error occurred when adding my tool to galaxy
by Tan Jun 31 Dec '12

31 Dec '12

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

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