April 2010 - galaxy-user - lists.galaxyproject.org

Sending data to GBrowse
by Jelle Scholtalbers 13 Apr '10

13 Apr '10

Hi, I would like to be able to send data to my GBrowse2.0 instance. I have been trying some things based on the Epigraph tool but I can't seem to get it work. Below is a mail from Lincoln that was send to the GBrowse mailinglist about how to send data to GBrowse. If its possible, how should I configure the tool? Cheers, Jelle -------- In version 2.0 it is relatively easy. POST to the GBrowse URL (including the datasource part of the URL) with the following parameters: - action="upload_file" - file=<a multipart/form-encoded file upload> - upload_id=<any numeric id of your choosing> - id=<the id of the user that you are uploading to> Alternatively to providing the "file" argument you can provide a "data" argument with the uploaded data provided directly. The "id" argument indicates the id of the user that you are uploading for. You can get this ID by bookmarking a page -- the "id" parameter records the info. Alternatively, if you don't provide an ID, GBrowse will generate it for you and return the ID in the response cookie, in an argument called "gbrowse_sess". If you have administrator's mode enabled, then you can provide the ID of the administrator and the uploaded file will become part of the public set of tracks. Lincoln

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Sample management?
by Shawn Levy 13 Apr '10

13 Apr '10

I was at the recent ABRF meeting in Sacramento and one of the presentations from the Penn State core lab showed that Galaxy had a sample management/project management interface in development or possible available. I didn¹t see anything on the main pages or wiki and was wondering if Galaxy will be extended to include sample handling information. Thanks Shawn

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Problem w/Cheetah, repeating dataset input
by Jesse Erdmann 12 Apr '10

12 Apr '10

Hi all, I'm using the following XML: ... <inputs> <param type="data" format="txt" name="seqmeta" label="PAPS.seqmeta"/> <param type="data" format="txt" name="lib_info" label="Label Info"/> <repeat name="to_merge" title="Evaluation Inputs and Results"> <param type="select" name="pmm" label="Mismatch %" help="Maximum % of mismatch between the construct sequence and the comparison sequence."> <option value="10">10%</option> <option value="15">15%</option> <option value="20">20%</option> </param> <param type="text" name="max_length" label="Max Construct Length" value="25" /> <param format="fasta" name="fasta_in" type="data" label="FastA Output"/> <param format="txt" name="seq_stats" type="data" label="Sequence Stats"/> </repeat> </inputs> ... <configfiles> <configfile name="file_info"> #for $merge_set in enumerate( $to_merge ) #silent sys.stderr.write($merge_set.__str__() + "\n") #silent sys.stderr.write($merge_set.fasta_in.__str__()) #end for </configfile> </configfiles> ... And getting the resulting output: 127.0.0.1 - - [07/Apr/2010:15:31:50 -0500] "POST /admin/tool_reload HTTP/1.1" 200 - "http://localhost:8080/admin/reload_tool" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316 Firefox/3.6.2" 127.0.0.1 - - [07/Apr/2010:15:31:59 -0500] "POST /tool_runner/index HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316 Firefox/3.6.2" galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-04-07 15:32:03,765 RoundRobin queue: user/session did not exist, created new jobqueue for session = 6 galaxy.jobs DEBUG 2010-04-07 15:32:03,766 job 234 put in policy queue galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-04-07 15:32:03,766 RoundRobin queue: retrieving job from job queue for session = 6 galaxy.jobs DEBUG 2010-04-07 15:32:03,766 dispatching job 234 to local runner galaxy.jobs DEBUG 2010-04-07 15:32:05,423 job 234 dispatched (0, {'seq_stats': <galaxy.tools.DatasetFilenameWrapper object at 0x572b390>, '__index__': 0, 'max_length': <galaxy.tools.InputValueWrapper object at 0x572b8d0>, 'fasta_in': <galaxy.tools.DatasetFilenameWrapper object at 0x572b810>, 'pmm': <galaxy.tools.SelectToolParameterWrapper object at 0x572b290>}) 127.0.0.1 - - [07/Apr/2010:15:32:03 -0500] "GET /history HTTP/1.1" 200 - "http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316 Firefox/3.6.2" galaxy.jobs.runners.local ERROR 2010-04-07 15:32:07,356 failure running job 234 Traceback (most recent call last): File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/jobs/runners/local.py", line 55, in run_job job_wrapper.prepare() File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/jobs/__init__.py", line 386, in prepare config_filenames = self.tool.build_config_files( param_dict, self.working_directory ) File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/tools/__init__.py", line 1364, in build_config_files f.write( fill_template( template_text, context=param_dict ) ) File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/Users/jerdmann/Python/galaxy-central/eggs/Cheetah-2.2.2-py2.5-macosx-10.3-fat-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "cheetah_DynamicallyCompiledCheetahTemplate_1270672326_31_15888.py", line 86, in respond NotFound: cannot find 'fasta_in' while searching for 'merge_set.fasta_in' So, I'm printing the merge_set dictionary and seeing a fasta_in key, but when I try to use fasta_in it can not be found. I'm assuming this is probably a syntax oversight on my part, but I'm not seeing it. -- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann(a)umn.edu 612-626-3123 jesse(a)jesseerdmann.com Twitter: http://twitter.com/jesseerdmann

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where are my deleted datasets?
by Erick Antezana 12 Apr '10

12 Apr '10

Hi, I managed to enable the possibility to 'Add datasets' via the 'Upload directory of files' option for non-admin users. It works fine: I can import (as admin and non-admin user) specific datasets into my history (copy and/or no-copy) so that I could launch some tools over them, etc. However, if I delete a specific dataset (as admin) that was imported as non-admin and then login again as non-admin, I can still see the imported datasets in my history pane. Where is actually located the reference to the (deleted) dataset? I was able to find the copied files at .../database/files/000/* , these will be cleaned out (if deleted) by the purge scripts eventually... I am using SQLAlchemy with mysql for the DB connection. cheers, Erick

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Setting default access permission for datasets and histories
by H. Mei 12 Apr '10

12 Apr '10

Dear galaxy team, The possibility of setting default dataset/history permission (e.g. "Change default permissions for the current history") is mentioned in the page of http://bitbucket.org/galaxy/galaxy-central/wiki/SecurityFeatures. However I can't find it in the "Options" dropdown on Galaxy UI. Am I looking at a wrong place? The link http://www.bx.psu.edu/trac/local/manage_history_defaults.png is also broken. Best, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center (http://www.nbic.nl/) Skype: leon_mei Mobile: +31 6 41709231

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Sequence logo
by Erick Antezana 12 Apr '10

12 Apr '10

Hi, is there any Galaxy tool supporting the display of "sequence logos" (http://en.wikipedia.org/wiki/Sequence_logo) ? thanks, Erick

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Including mothur?
by Rohan Sachdeva 10 Apr '10

10 Apr '10

Hi All, I'm a microbial ecologist and use mothur a ton. It's a C++ commandline program that does lots of things that I think would work great in galaxy. Like trimming, barcode sorting, aligning, OTU calling, ecology stats, heatmap/diagram creation. Here's a link http://www.mothur.org/ Rohan

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how to turn on debug?
by Peter Andrews 09 Apr '10

09 Apr '10

I received a server error and would like to more detailed information Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) How do I 'turn debug on'?. I am using the public galaxy instance http://main.g2.bx.psu.edu/ Thanks, Peter Andrews -- -------------- Peter Andrews Programmer Computational Genetics Lab Dartmouth Hitchcock Medical Center (603) 653-9963

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Galaxy Instance
by Sonali Thakur 09 Apr '10

09 Apr '10

Could you please let me from where I can clone the latest galaxy? I tried cloning from below two and get the same revision. hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist hg clone https://bitbucket.org/galaxy/galaxy-dist/ I am not getting the one which we can see at http://main.g2.bx.psu.edu/root Please suggest. Regards -Sonali

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New select random lines tool available on test
by Kanwei Li 09 Apr '10

09 Apr '10

Dear users, I have created a new tool to randomly extract random lines from a dataset as some of you have requested it. It is now available in the repository and on our public test instance under "Text Manipulation". Any feedback is appreciated. Thanks, Kanwei

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