September 2012 - galaxy-dev - lists.galaxyproject.org

Galaxy September 20, 2012 Distribution & News Brief
by Jennifer Jackson 21 Sep '12

21 Sep '12

*Galaxy September 20, 2012 Distribution & News Brief* http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_09_20 <http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_09_20> /*Highlights:* http://wiki.g2.bx.psu.edu/News <http://wiki.g2.bx.psu.edu/News>/ * A /*new Galaxy tool*/<http://wiki.g2.bx.psu.edu/DevNewsBriefs/2012_09_20#Galaxy_Tool_Factory> that writes other /*new Galaxy tools*/! The /*Tool Factory*/ is in the Galaxy's Main *Tool Shed* (*/toolfactory/*). Try it now! * Learn how to *display multiple versions of a tool* in the Galaxy tool panel. * *CloudLaunch Overhaul* includes Boto 2.5.2 and simplified instance selection and key generation. * Release also includes more *Tool Shed *updates, *Framework* and *API* updates, plus *Security* and *Bug* fixes. http://getgalaxy.org http://bitbucket.org/galaxy/galaxy-dist <http://bitbucket.org/galaxy/galaxy-dist> *new: * $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist* upgrade:* $ hg pull -u -r da9d740fce31 ** *Thanks for using Galaxy!* Jennifer Jackson & Galaxy Team http://galaxyproject.org

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zombie undeletable files in toolshed, and versioning question
by kevyin 20 Sep '12

20 Sep '12

Hi, I have a tool on the main galaxy toolshed called fastq_groomer_parallel. During an update, with a new tar.gz upload I accidentally included in an unrelated big folder of stuff under the folder build/ The upload failed (with no helpful error message, only to turn on debug mode) I went and browsed the files via the web interface and the folder is there, but when I tried to delete it it says "No changes to repository. " Everything is normal, ie I can install this from a galaxy instance and the build/ folder is not there. when I hg pull and push etc the folder is not there. I have another question with versioning. So far with my experimentation on the testtoolshed, The version is only bumped when I upload via an archive not when I push to the repo. Is this meant to be the case? Also "Get Updates" to a toolshed tool as a galaxy Admin. doesnt seem to work, I basically have to install a new instance again, is this normal? Regards, Kevin.

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Setting error levels in <stdio>
by Peter Cock 20 Sep '12

20 Sep '12

Hi all, Regarding https://bitbucket.org/galaxy/galaxy-central/issue/325 and the new <stdio> tag is described on the wiki here: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax The wiki text is unclear - it suggests square brackets might be needed, but the example lacks them: 1 <stdio> 2 <exit_code range="2" level="fatal" description="Out of Memory" /> 3 <exit_code range="3:5" level="warning" description="Low disk space" /> 4 <exit_code range="6:" level="fatal" description="Bad input dataset" /> 5 </stdio> In particular the less-than syntax might be being miss-rendered by the wiki. I've tried this as a way to say non-zero (i.e. more than one, or less than zero), but had an error in the Galaxy log from this: <stdio> <exit_code range="1:" /> <exit_code range="://0" /> </stdio> Thanks, Peter

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single database connection and multiple Galaxy instance
by Vipin TS 20 Sep '12

20 Sep '12

Hi Galaxy team, Can I use a single database connection to serve multiple Galaxy instance ? thanks, --Vipin

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Do ToolShed updates cope with renaming files?
by Peter Cock 20 Sep '12

20 Sep '12

Hi all, I'd like to check (before I try this), if is this expected to work or not? For the normal tool wrappers, is it possible to rename the XML file (but leave the tool ID inside the XML file unchanged), and have this *just work* (TM) when automatically updated via the ToolShed? Similarly, for the new 'blast_datatypes' Tool Shed entry, can I rename xml.py which defines the file format(s) to something like ncbi_blast.py (and update the datatypes_conf.xml ToolShed file to match)? My desire here is partly to avoid the current namespace clash with galaxy.datatypes.xml but also that I intend this to include other non-XML BLAST formats as well (e.g. BLAST database). Thanks, Peter

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Sanity testing of ToolShed uploads
by Peter Cock 20 Sep '12

20 Sep '12

Hi all, Having just accidental uploaded the wrong tar-ball to the ToolShed, I think it would be helpful to add some sanity testing to the ToolShed. I accidentally uploaded a tar-ball for the ncbi_blast_plus repository to the blast_datatypes repository instead. The two repositories a have no tools or file types in common. Something like the following check would catch this kind of (easily made) human error: Compare the incoming tool identifiers and file format extensions to those already defined, and raise an error if there is *no* overlap. This test would allow you to add/remove individual components. Another idea would be an "Are you sure?" prompt after processing the upload showing the diff against the current version. Regards, Peter

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Re: [galaxy-dev] Error when <param> has no value and type is float or integer
by Jim Johnson 20 Sep '12

20 Sep '12

I believe you have to tag with optional="true" when omitting the value: <param name="x" type="integer" optional="true" help="the x param"/> > Hi, > > If I have a tool wrapper with this: > > <param name="x" type="integer" help="the x param"/> > > I get an error when I start Galaxy: > > galaxy.tools ERROR 2012-09-19 12:09:08,056 Error reading tool from > path: RGalaxy_test_tool/foo.xml > Traceback (most recent call last): > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", > line 332, in load_tool_tag_set > tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", > line 450, in load_tool > return ToolClass( config_file, root, self.app, guid=guid ) > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", > line 788, in __init__ > self.parse( root, guid=guid ) > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", > line 959, in parse > self.parse_inputs( root ) > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", > line 1043, in parse_inputs > display, inputs = self.parse_input_page( page, enctypes ) > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", > line 1439, in parse_input_page > inputs = self.parse_input_elem( input_elem, enctypes ) > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", > line 1532, in parse_input_elem > param = self.parse_param_elem( elem, enctypes, context ) > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", > line 1544, in parse_param_elem > param = ToolParameter.build( self, input_elem ) > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/parameters/basic.py", > line 176, in build > return parameter_types[param_type]( tool, param ) > File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/parameters/basic.py", > line 228, in __init__ > raise ValueError( "The settings for the field named '%s' require a > 'value' setting and optionally a default value which must be an > integer" % self.name ) > ValueError: The settings for the field named 'x' require a 'value' > setting and optionally a default value which must be an integer > > However, according to the documentation: > http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cparam.3E_t… > > The "value" attribute to the param tag is not required. > > It's easy to work around this, by adding value="", but I'm wondering > if it's a bug, documentation or otherwise. > > Thanks, > Dan

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Error when <param> has no value and type is float or integer
by Dan Tenenbaum 19 Sep '12

19 Sep '12

Hi, If I have a tool wrapper with this: <param name="x" type="integer" help="the x param"/> I get an error when I start Galaxy: galaxy.tools ERROR 2012-09-19 12:09:08,056 Error reading tool from path: RGalaxy_test_tool/foo.xml Traceback (most recent call last): File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", line 332, in load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", line 450, in load_tool return ToolClass( config_file, root, self.app, guid=guid ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", line 788, in __init__ self.parse( root, guid=guid ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", line 959, in parse self.parse_inputs( root ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", line 1043, in parse_inputs display, inputs = self.parse_input_page( page, enctypes ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", line 1439, in parse_input_page inputs = self.parse_input_elem( input_elem, enctypes ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", line 1532, in parse_input_elem param = self.parse_param_elem( elem, enctypes, context ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/__init__.py", line 1544, in parse_param_elem param = ToolParameter.build( self, input_elem ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 176, in build return parameter_types[param_type]( tool, param ) File "/Users/dtenenba/dev/galaxy-dist/lib/galaxy/tools/parameters/basic.py", line 228, in __init__ raise ValueError( "The settings for the field named '%s' require a 'value' setting and optionally a default value which must be an integer" % self.name ) ValueError: The settings for the field named 'x' require a 'value' setting and optionally a default value which must be an integer However, according to the documentation: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cparam.3E_t… The "value" attribute to the param tag is not required. It's easy to work around this, by adding value="", but I'm wondering if it's a bug, documentation or otherwise. Thanks, Dan

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concatenate datasets: how to fixate first dataset
by Marc Logghe 19 Sep '12

19 Sep '12

Hi, In a workflow the last step is 'concatenate datasets' where the results table (dataset 2) is concatenated to a table header (dataset 1). Issue is that whenever the workflow is run, the table header dataset is required input at runtime. Is there a way to fixate that e.g. making it the input not necessary at runtime but take it from shared datasets or something ? Btw: I did try to first publish dataset 1 hoping that this would solve the problem but unfortunately it does not. Or is there another way to add a header in such a way that the users should not be taking care of it themselves ? Regards, Marc ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx(a)ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________

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DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)
by Peter Cock 19 Sep '12

19 Sep '12

Hi all (and in particular, Scott), I've just updated my development server and found the following error when running jobs on our SGE cluster via DRMMA: galaxy.jobs.runners.drmaa ERROR 2012-09-18 09:43:20,698 Job wrapper finish method failed Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", line 371, in finish_job drm_job_state.job_wrapper.finish( stdout, stderr, exit_code ) File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py", line 1048, in finish if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): TypeError: check_tool_output() takes exactly 5 arguments (4 given) This looks to have been introduced in this commit: https://bitbucket.org/galaxy/galaxy-central/changeset/f557b7b05fdd701cbf99e… There should be an additional jobs argument, proposed fix: $ hg diff lib/galaxy/jobs/__init__.py diff -r 4007494e37e1 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Sep 18 09:40:19 2012 +0100 +++ b/lib/galaxy/jobs/__init__.py Tue Sep 18 10:06:44 2012 +0100 @@ -1045,7 +1045,8 @@ # Check what the tool returned. If the stdout or stderr matched # regular expressions that indicate errors, then set an error. # The same goes if the tool's exit code was in a given range. - if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): + job = self.get_job() + if ( self.check_tool_output( stdout, stderr, tool_exit_code, job ) ): task.state = task.states.OK else: task.state = task.states.ERROR (Let me know if you want this as a pull request - it seems a lot of effort for a tiny change.) Regards, Peter

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