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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 01 Jan '13

01 Jan '13

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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MySQL Returning Empty Set Result in Galaxy
by Sachit Adhikari 31 Dec '12

31 Dec '12

Hello all, *Happy New Year* * * I have configured MySQL in Galaxy. I have edited universe_wsgi.ini file: *database_connection = mysql://username:password@ /database_name?unix_socket=/var/run/mysqld/mysqld.sock * * * I restarted the galaxy and all the galaxy_tables has been created but all of those table returns empty sets. There are no data's on the table. I then created a new workflow and again saw the database. The workflow table was empty. The tables has been created but all the tables are empty. Am I missing something? Regards, Sachit

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Re: [galaxy-dev] expand disk size limit
by Dannon Baker 28 Dec '12

28 Dec '12

The maximum size of any EBS volume is 1TB (this is currently an Amazon limit, not Galaxy or Cloudman). We're hopeful that they'll eventually raise this, but for now we're planning on using S3 as a way around this for Galaxy. If the resize UI didn't indicate that your other entries were invalid, then that's a bug and I'll look into it. Lastly, please remember to email/cc the list so that others can benefit from questions like this. -Dannon On Dec 28, 2012, at 12:32 PM, "Sun, Wenping [USA]" <Sun_Wenping(a)bah.com> wrote: > Hi Donnon, > > I am working to try to expand the disk size on cloudman. I used the upper limit 1tb and there was no response from cloudman interface. However, when I changed to 800gb, it worked. Do you have any suggestion if I need the disk size more than 1tb? I may think to have at least 10tb as the start point if possible. > > Thank you in advance, > Kathryn

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Re: [galaxy-dev] Where is the workflow stored in Galaxy?
by Dannon Baker 28 Dec '12

28 Dec '12

Yes, there is a relationship - in the database there's also a WorkflowStepConnection table that relates inputs and outputs (WorkflowStep + i/o name) between steps. On Dec 28, 2012, at 8:33 AM, Sachit Adhikari <sachit.technerves(a)gmail.com> wrote: > Hi Dannon, > > Thank you for your answer. What I meant by the last question is that: > > When I create a workflow (tophat-bowtie-bowtie2). The input is first processed by tophat and the output of tophat is processed by bowtie and then the output of bowtie and processed by bowtie2 and that's the final output. There's some sort of relationship, right? Is this relationship stored in database? > > On Fri, Dec 28, 2012 at 7:34 AM, Dannon Baker <dannonbaker(a)me.com> wrote: > A workflow is just the definition of a particular process or set of steps. This information is stored in the database (see Workflow, StoredWorkflow, WorkflowStep tables). Running that workflow creates datasets in a history (datasets which are stored in database/files). > > And, I'm not sure exactly what you're asking in your last question, can you clarify? > > -Dannon > > > On Dec 28, 2012, at 2:16 AM, Sachit Adhikari <sachit.technerves(a)gmail.com> wrote: > > > I have searched the mailing list and found that the output, histories and workflows are stored in ~/database/files. To do a little experiment I deleted all the inside that directory. I then open my Galaxy and browse the workflow. But the workflow is still there. I was wondering where is the workflow stored in Galaxy? Also, if possible can I know how is the relationship specified by user while creating workflow is stored? > > > > Happy New year > > > > Regards, > > > > Sachit > > ___________________________________________________________ > > 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/ > >

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Where is the workflow stored in Galaxy?
by Sachit Adhikari 28 Dec '12

28 Dec '12

I have searched the mailing list and found that the output, histories and workflows are stored in ~/database/files. To do a little experiment I deleted all the inside that directory. I then open my Galaxy and browse the workflow. But the workflow is still there. I was wondering where is the workflow stored in Galaxy? Also, if possible can I know how is the relationship specified by user while creating workflow is stored? *Happy New year* Regards, Sachit

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Tophat issue
by Luciano Cosme 28 Dec '12

28 Dec '12

Howdy, I am getting the following error with tophat: Error in tophat: [2012-12-27 15:08:40] Beginning TopHat run (v2.0.5) ----------------------------------------------- [2012-12-27 15:08:40] Checking for Bowtie Traceback (most recent call last): File "/usr/bin/tophat", line 4035, in <module> sys.exit(main()) File "/usr/bin/tophat", line 3836, in main check_bowtie(params) File "/usr/bin/tophat", line 1473, in check_bowtie bowtie_version = get_bowtie_version(params.bowtie2) File "/usr/bin/tophat", line 1351, in get_bowtie_version bowtie_version = [int(x) for x in ver_numbers[:3]] + [int(ver_numbers[3][4:])] IndexError: list index out of range I tried Tophat and Tophat2 a couple times and always giving me the same error. The reads I am trying to map are from small RNA sequencing project. I am trying to map the unannotated reads back to the genome. I am not sure what is causing this problem, any help will be appreciated. Thank you. Luciano

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Where is the output of tools stored in Galaxy?
by Sachit Adhikari 27 Dec '12

27 Dec '12

Hello Everyone, *Merry Christmas and Happy New Year* * * I was wondering where are the output of the tools stored in the machine where the galaxy is hosted? And, can I change the path of the output of the tools? Thanks, Sachit

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How to refresh the tool panel in Galaxy?
by Huayan Gao 27 Dec '12

27 Dec '12

Hi, I am trying to add a tool into Galaxy. So far everything is ok except that I need to restart the server to make the tool showing up in the tool panel. So my question is that how to refresh the tool panel without restarting the server? After I install a tool from toolshed, I can see the tool immediately from the tool panel. This is exactly the function I want to implement in python. I was reading the code but too complicated. Could you point me the right place(code)? Thanks a lot. Best, Huayan

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