January 2015 - galaxy-dev - lists.galaxyproject.org

Tool param type "library_data"
by Dooley, Damion 19 Jan '15

19 Jan '15

I just discovered a scant reference to this on the ToolSyntax page, and tracked it down to something that looks like it was introduced around 2011: a "LibraryDatasetToolParameter" http://bitbucket.org/galaxy/galaxy-central/changeset/8553b02ce9ee/ changeset: 8553b02ce9ee user: kanwei date: 2011-07-19 03:56:23 summary: Tools: Add new LibraryDataset tool parameter to expose LDDAs to tools. Use trackster's modal popup interface for item selection. Add new InputWrapper that exposes LDDA templates as well. Now I can't quite fathom the syntax around this but it appears to be broken - python error displayed: TypeError: get_initial_value() got an unexpected keyword argument 'history' Which is because in the galaxy code the def get_initial_value( self, trans, context ) function is missing a "history=None" parameter like other types have?! But is this input type essentially discontinued (no other refs to it on the web) or is it supposed to be operational? I was hoping for a tool input that would list a particular libraries datasets, so that I could obtain their file paths for use in my tool. <param name="test" type="library_data" label="test" help="test help"/> <options library="Reference Bins"> </param> Regards, Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada

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galaxyp build for docker
by Evan Bollig PhD 19 Jan '15

19 Jan '15

Hey Bjoern, I'm playing with your docker recipes (https://github.com/bgruening/docker-recipes) today and I've been waiting for the galaxyp image build to complete for about 3 hours. For the majority of that time it has been stuck on RUN install-repository "--url http://testtoolshed.g2.bx.psu.edu/ -o bgruening --name package_openms_latest" What is the typical build time you experience? Any thoughts on how this could have gone wrong? Cheers, -Evan Bollig Research Associate | Application Developer | User Support Consultant Minnesota Supercomputing Institute 599 Walter Library 612 624 1447 evan(a)msi.umn.edu boll0107(a)umn.edu

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Unable to connect galaxy server after upgrade to latest version
by Ping Luo 19 Jan '15

19 Jan '15

I installed the latest galaxy server and started it without any change. The server stared on port 8080 and the log file looks fine. But when I typed http://localhost:8080, I got the error "Unable to connect". I had worked with version 2014_08_11 and had no problem at all. What could have been wrong?

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GCC2015 Training Day Topic Voting is open. Please vote!
by Dave Clements 19 Jan '15

19 Jan '15

Hello all,What topics should be offered at the GCC2015 Training Day <http://gcc2015.tsl.ac.uk/training-day/>? Topics <http://gcc2015.tsl.ac.uk/training-day/> for the GCC2015 Training Day <http://gcc2015.tsl.ac.uk/training-day/> are selected by you, the Galaxy Community. There are nominated topics <http://gcc2015.tsl.ac.uk/training-day/> spanning from basic usage to advanced deployment. No matter what you do with Galaxy, there are topics for you to choose from. Your vote will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters. *Topic voting closes 30 January.* The Training Day schedule, including instructors, will be published before early registration opens in February. *Vote Now <http://gcc2015.tsl.ac.uk/training-day/>* ------------------------------ *About the GCC2015 Training Day <http://gcc2015.tsl.ac.uk/training-day/>:* The 2015 Galaxy Community Conference (GCC2015) <http://gcc2015.tsl.ac.uk/> will start on 6 July with a Training Day <http://gcc2015.tsl.ac.uk/training-day/> featuring parallel tracks, each with several multi-hour workshops. There will be at least one complete track about using Galaxy for biological research, and at least one full track on deploying and managing Galaxy instances. As always, please let us know if you have any questions. Thanks, The GCC2015 Organising Committee <http://gcc2015.tsl.ac.uk/organisers/> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Manually adding new tools from toolshed
by Ryan G 18 Jan '15

18 Jan '15

Because of the way the infrastructure for my Galaxy instance is set up, I need to download and install tools from the toolshed manually. For most of the tools, this is pretty easy, however I'm now trying to add RSEM to my instance and it has some new datatypes. Along with the new data types is python class file. I'm referring to the exist datatypes_conf.xml.sample but don't see a reference to datatype_files as is coded in the RSEM tool. So my question is, how can I manually install a tool such as RSEM from the toolshed? I've cloned it but not sure where to put the files and what to modify in Galaxy's configuration to see the new files. I can modify the datatypes_conf.xml and include the datatypes, but I get the sense this is not correct. Ryan

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EOF error with tool
by Francis, Warren 18 Jan '15

18 Jan '15

Hello, I'm getting a strange error when trying to debug a tool. Traceback (most recent call last): File "/var/project/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 157, in prepare_job job_wrapper.prepare() File "/var/project/galaxy-dist/lib/galaxy/jobs/__init__.py", line 811, in prepare self.command_line, self.extra_filenames = tool_evaluator.build() File "/var/project/galaxy-dist/lib/galaxy/tools/evaluation.py", line 348, in build self.__build_command_line( ) File "/var/project/galaxy-dist/lib/galaxy/tools/evaluation.py", line 364, in __build_command_line command_line = fill_template( command, context=param_dict ) File "/var/project/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/var/project/galaxy-dist/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_1421072368_91_78155.py", line 139, in respond EOFError: EOF when reading a line The tool is the assembler Trinity. The toolshed version is quite old and the one from the Trinity website does not work, so I tried to fix it (several problems to fix). What is the EOFError? There were a bunch of posts reporting this but no answer as to why this happens. Is there a way to debug a tool without having to restart galaxy each time? Something offline that can check for runtime errors, or at least see if it generates the command correctly. Best, -Warren

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FastQC wrapper not seeing files at gzipped
by Ryan G 18 Jan '15

18 Jan '15

Hi all - I've got a bunch of fatsq files uploaded into a data library in Galaxy. The underlying files is gzipped however Galaxy strips the .gz from the filename and displays it as .fastq. When the python wrapper rgFastQC.py gets called, it correctly sees the fastq.gz file. The wrapper creates a symbolic link to the .gz file in a tmp directory. The link is .fastq. When FastQC tries to read this file, it fails because its compressed. So one of two things is going wrong here: 1) It looks like the wrapper is incorrectly renaming the file, but its using the name given to it in Galaxy. 2) When the file is uploaded into the data library, Galaxy is stripping off the .gz extension. I think #2 is the more correct problem. How can I keep Galaxy from stripping the .gz extension?

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Getting 'No space left on device' at testtoolshed
by Jeltje van Baren 18 Jan '15

18 Jan '15

Hi, I'm trying to upload a tarball to one of my repositories at https://testtoolshed.g2.bx.psu.edu/ but I keep getting the error pasted below my signature. This started at about 1pm PST and is not resolved now, at 3pm. Am I the only one who sees this error and if so, what should I do? Thanks! -Jeltje van Baren Internal Server Error Galaxy was unable to successfully complete your request URL: http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=2e4420df6d37d… Module galaxy.web.framework.middleware.error:*149* in __call__ >> <https://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=2e4420df6d37…> app_iter *=* self*.*application*(*environ*,* sr_checker*)* Module paste.debug.prints:*106* in __call__ >> <https://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=2e4420df6d37…> environ*,* self*.*app*)* Module paste.wsgilib:*543* in intercept_output >> <https://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=2e4420df6d37…> app_iter *=* application*(*environ*,* replacement_start_response*)* Module paste.recursive:*84* in __call__ >> <https://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=2e4420df6d37…> *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ >> <https://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=2e4420df6d37…> *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*132* in __call__ >> <https://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=2e4420df6d37…> *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*185* in handle_request >> <https://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=2e4420df6d37…> kwargs *=* trans*.*request*.*params*.*mixed*(**)* Module webob:*900* in params Module webob:*892* in str_params Module webob:*818* in str_POST Module cgi:*508* in __init__ >> <https://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=2e4420df6d37…> self*.*read_multi*(*environ*,* keep_blank_values*,* strict_parsing*)* Module cgi:*637* in read_multi >> <https://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=2e4420df6d37…> environ*,* keep_blank_values*,* strict_parsing*)* Module cgi:*510* in __init__ >> <https://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=2e4420df6d37…> self*.*read_single*(**)* Module cgi:*648* in read_single >> <https://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=2e4420df6d37…> self*.*file*.*seek*(**0**)* *IOError: [Errno 28] No space left on device*

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Display of file content in a combobox
by christof.pietsch＠kws.com 18 Jan '15

18 Jan '15

Hello, I'd like to display the unique column content of a file in a combobox to give the user the possibility to select factor levels for subsequent analyses, e.g. for combining related factor levels in a meta-analyses. Unfortunately, I failed to connect the tool that reads out the factor levels with the tool that receive the selection via combobox as input argument. I'd be very thankful for any suggestion! Christof

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Re: [galaxy-dev] Create a package with binaries
by KRESS Arnaud (ESP) 18 Jan '15

18 Jan '15

If I create two distincts packages, what should I indicate as package name in the tool_dependencies.xml files ? For example, a binary package: <tool_dependency> <package name="ballast" version="1.0"> <install version="1.0"> <actions> <action type="download_by_url">http://myurl.com/...</action> <action type="move_file"> <source>ballast</source> <destination>$INSTALL_DIR/bin</destination> </action> <action type="chmod"><file mode="750">$INSTALL_DIR/bin/ballast</file></action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> </package> </tool_dependency> and its corresponding tool package: <tool_dependency> <package name="ballast" version="1.0"> <repository name="package_ballast" owner="me" /> </package> </tool_dependency> Should I set the same name ? Thank you, AK Le Lundi 5 Janvier 2015 20:23 CET, John Chilton <jmchilton(a)gmail.com> a écrit: > I could be wrong but I think the <install> tag should have some sort> of download action - I don't think tools are actually stuck in > $INSTALL_DIR like this - $INSTALL_DIR is where you can move or compile > downloaded files to. You might want to try $REPOSITORY_INSTALL_DIR > instead of $INSTALL_DIR - but really if you are going to just stick an > application next to your tool wrapper like this (I would consider this > an anti-pattern) I would just set your PATH in mytool.sh and not worry > about the tool shed install stuff at all. Maybe add something like > > PATH=`dirname $0`/bin:$PATH > export PATH > > To the wrapper mytool.sh. > > As I mentioned - I think bundling applications with tools like this is > something of an anti-pattern even if you can make it work. The best > practice here would be to try to separate packages with binaries from> repositories that contain tools and create a format "package_mytools" > repository that is just responsible for installing the binary mytool.> > Hopefully this helps, > -John > > On Tue, Dec 16, 2014 at 9:43 AM, KRESS Arnaud (ESP) <akress(a)unistra.fr> wrote: > > Hi gentlemen, > > I am currently struggling to create a custom package (to share via a toolshed) that would include a tool definition file and the associated binary. Once installed, I can launch a job but I get the following error message: > > > > mytool.sh: line 14: mytool: unknown command > > > > It seems that the PATH was not correctly set. What am I doing wrong ? > > > > My directory tree in my package: > > . > > ├── mytool.sh > > ├── mytool.xml > > ├── bin > > │ └── mytool > > └── tool_dependencies.xml > > > > Here is my tool_dependencies.xml file content: > > > > <?xml version="1.0"?> > > <tool_dependency> > > <package name="mytool" version="1.0"> > > <install version="1.0"> > > <actions> > > <action type="set_environment"> > > <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> > > </action> > > </actions> > > </install> > > <readme> > > </readme> > > </package> > > </tool_dependency> > > > > Thank you, > > AK > > ___________________________________________________________ > > 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: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/

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