August 2011 - galaxy-dev - lists.galaxyproject.org

Workflow Bug?
by John Chilton 02 Aug '11

02 Aug '11

Hello Galaxy Developers, I have a user who noticed a potential bug when extracting workflows from histories on our local Galaxy server. I have recreated the bug on the public Galaxy server with a much smaller history. The history can be found here: http://main.g2.bx.psu.edu/u/jmchilton/h/column-join-workflow-bug Basically when creating workflows from such histories, the second input to "Column Join" never seems to be connected to the previous step the way I would expect it to be. In the workflow editor you can manually create this connection, but it is easy to miss this in a large worfklow and have incomplete results as a consequence. Am I missing something or is this a bug? Thanks for your time, -John

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Question on timing with API, running workflows, and setting metadata
by Duddy, John 02 Aug '11

02 Aug '11

I'd like to have an external program that registers a file by absolute path (link, not upload) in a data library, then immediately starts a workflow on it. My question is to whether or not that will work in the general case where: - The system is configured to set metadata externally - The compute grid is busy (so the set_meta call is queued for some time) In this case, will the workflow be queued and set idle, waiting for the set_meta() to complete? Or will the API call to register the data library block until the set_meta() is done? Thanks! John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jduddy(a)illumina.com<mailto:jduddy@illumina.com>

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Does Galaxy have a tool to run R script?
by liu bo 02 Aug '11

02 Aug '11

Dear all, I want to build a Galaxy tool to run R script. Do you know if there is already such tool or similar function? If you can share with me, I would very appreciate your help. Thank you, Bo Liu

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Nucleolar localization sequence Detector (NoD)
by Peter Cock 02 Aug '11

02 Aug '11

Dear all, I've just uploaded my Galaxy wrapper for command line NoD (clinod) to the Galaxy tool shed (under the Sequence Analysis category): http://usegalaxy.org/community NoD is from the Barton group at the University of Dundee, and does Nucleolar localization sequence (NoLS) prediction. There is also a web version: http://www.compbio.dundee.ac.uk/www-nod/ I promised this during my Galaxy Community Conference talk earlier in the year, and now that clinod v1.3 has been formally released I'm delighted to share this wrapper as well. My thanks to Peter Troshin and the rest of the NoD team for their help. Regards, Peter

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Re: [galaxy-dev] custom builds as tool in toolbox panel?
by Michal Stuglik 02 Aug '11

02 Aug '11

Dannon, "Extract Genomic DNA" tool demands that intervals had set genome build. In my case interval dataset is not persistent, I generate this in "meantime", so after generating this I set genome build to dataset by hand. It's not a problem if you do this in "history pane mode" but in workflow mode it is, basically because it is not possible to set custom genome build as a parameter (external?) for intervals ( can I ?). all the best, michal ps. Sorry for late answer, It's Summer time :) W dniu 13.07.2011 05:32, Dannon Baker pisze: > Could you elaborate on how you'd see this working, and perhaps give a use case? I'm not sure I follow what you mean. > > Thanks! > > -Dannon > > On Jul 7, 2011, at 3:57 AM, Michal Stuglik wrote: > >> hi, >> >> >> Would it be possible to build in a "Custom builds" form user menu to toolbox panel as a tool? >> Now it is not possible to use this feature in workflow ( as a part of pipeline)... >> >> >> all the best, >> michal >> >> ___________________________________________________________ >> 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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approximate line numbers shown in history items can be very imprecise
by Chaolin Zhang 02 Aug '11

02 Aug '11

Hi, I noticed that the current version of galaxy shows approximate number of lines for history items, when it is relatively big. I guess this is due to a consideration of performance, but it is quite annoying, because the exact line numbers provide a very easy way for users to get simple statistics. Sometimes the approximation can be really off. For instance, for one file with > 1 M lines, it shows ~850,000 lines. Any thought? Chaolin

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[API] Apache error?
by Louise-Amélie Schmitt 02 Aug '11

02 Aug '11

Hello everyone, I'm working on a script that uploads files and launchs workflows on them, but I keep getting errors that appear more or less randomly when the display() and submit() functions are called. In a nutshell, there is a 1/3 chance the calls fail this way. Nevertheless, the actions are properly triggered in Galaxy, surprisingly. Here is an example: When I launch a workflow, I get the following traceback even though the workflow is properly executed: http://localhost/galaxy-dev/api/workflows?key=273c7b4e3aaffd3884ef715aaf780… File "automated_preprocessing.py", line 61, in expandFile result = submit( api_key, api_url + 'workflows', wf_data, return_formatted=False) File "common.py", line 100, in submit r = post( api_key, url, data ) File "common.py", line 44, in post return simplejson.loads( urllib2.urlopen( req ).read() ) File "/g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/socket.py", line 329, in read data = self._sock.recv(rbufsize) File "/g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/httplib.py", line 518, in read return self._read_chunked(amt) File "/g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/httplib.py", line 561, in _read_chunked raise IncompleteRead(''.join(value)) Failed to expand file A: Type: <class 'httplib.IncompleteRead'> IncompleteRead(118 bytes read) Therefore, I cannot get the results within the script. Any idea? Best, L-A

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minor bug: double-quotes in dataset name
by Assaf Gordon 01 Aug '11

01 Aug '11

Hello, There's a small bug when entering a double-quote character in a dataset name: The double-quote confuses some later-on processing (templates and Display-Application XML), resulting in some problems. Example: This history has one BAM dataset with a name of: Hello "world" http://main.g2.bx.psu.edu/u/foobar/h/double-quotes-bug If you try to rename it (by clicking the "pencil" icon), you'll see only the "hello" part. If you try to load the BAM to the UCSC Genome browser, it will fail with this error message: Missing bigDataUrl setting from track of type=bam (Hello ) -gordon

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visual cue for <conditional> group parameters
by Assaf Gordon 01 Aug '11

01 Aug '11

Hi, The following tiny patch adds a light-gray visual cue in the html form, to give a better idea as to which parameters go together. It looks acceptable even with nested <conditional> parameters. See it in action here: http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_bowtie_pe1 http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_tophat_pe1 It might not be the prettiest thing, but it works nicely with minimal code changes. Patch is here: http://cancan.cshl.edu/labmembers/gordon/files/conditional-group-css2.patch Comments are welcomed, -gordon

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wrong static image URL when clicking re-run
by Assaf Gordon 01 Aug '11

01 Aug '11

Hi, A small bug: When clicking "re-run" to view a tool form, and the tool has embedded images, the URL of the images is not working. When viewing a tool that has embedded images, the relative <img> URL is "./static/images/histogram2.png". The tool's URL comes from: "http://main.g2.bx.psu.edu/tool_runner?tool_id=histogram_rpy" and so the absolute image URL becomes: "http://main.g2.bx.psu.edu/./static/images/histogram2.png" which works OK. But when viewing a tool by clicking "re-run", the tool's URL is: "http://main.g2.bx.psu.edu/galaxy/tool_runner/rerun?id=56" ("rerun" being a method in the "tool_runner" controller), which in turns makes the image absolute URL: "http://main.g2.bx.psu.edu/tool_runner/./static/images/XXXXX.png" - and it doesn't work. Note that the solution of changing all the images URLs in the XML files to start at the root (e.g. "/static/images/XXXX.png") is not optimal, because it will bypass the "prefix" URL that some people use (e.g. with "http://rave.cshl.edu/galaxy" instead of "http://rave.cshl.edu/"). a workaround (when using apache) is to add the following rewrite_rule: RewriteRule ^/tool_runner/static/(.*) /localdata1/galaxy/galaxy_prod/static/$1 [L] Or if using a "/galaxy" prefix: RewriteRule ^/galaxy/tool_runner/static/(.*) /localdata1/galaxy/galaxy_prod/static/$1 [L] -gordon

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