- galaxy-dev - lists.galaxyproject.org

Manually adding new tools from toolshed
by Ryan G 19 Jan '15

19 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 19 Jan '15

19 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 19 Jan '15

19 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 19 Jan '15

19 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 19 Jan '15

19 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) 19 Jan '15

19 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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new user : galaxy install error
by Abhishek Pratap 17 Jan '15

17 Jan '15

**Did the following** hg clone https://bitbucket.org/galaxy/galaxy-dist/ test cd test/ hg update stable Machine: Mac Yosemite(10.10.1) **Got the following error** Some eggs are out of date, attempting to fetch... Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.4.2-py2.7.egg Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 46, in <module> c.resolve() # Only fetch eggs required by the config File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py", line 347, in resolve egg.resolve() File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py", line 192, in resolve if e.args[1].key != e.args[0].key: IndexError: tuple index out of range Fetch failed. Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py", line 1049, in run invoke(command, command_name, options, args[1:]) File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke exit_code = runner.run(args) File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py", line 220, in run result = self.command() File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/serve.py", line 643, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py", line 375, in loadobj return context.create() File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py", line 813, in create return self.object_type.invoke(self) File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py", line 249, in invoke return fix_call(context.object, context.global_conf, **context.local_conf) File "/Users/apratap/softwares/test/lib/galaxy/util/pastescript/loadwsgi.py", line 97, in fix_call val = callable(*args, **kw) File "/Users/apratap/softwares/test/lib/galaxy/webapps/galaxy/buildapp.py", line 54, in app_factory webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) File "/Users/apratap/softwares/test/lib/galaxy/web/framework/webapp.py", line 119, in add_ui_controllers module = import_module( module_name ) File "/Users/apratap/softwares/test/lib/galaxy/util/backports/importlib/__init__.py", line 37, in import_module __import__(name) File "/Users/apratap/softwares/test/lib/galaxy/webapps/galaxy/controllers/cloudlaunch.py", line 21, in <module> eggs.require('bioblend') File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py", line 411, in require return c[req.project_name].require() File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py", line 239, in require dists = self.resolve() File "/Users/apratap/softwares/test/lib/galaxy/eggs/__init__.py", line 170, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/Users/apratap/softwares/test/lib/pkg_resources.py", line 569, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (bioblend 0.4.2 (/Users/apratap/softwares/test/eggs/bioblend-0.4.2-py2.7.egg), Requirement.parse('poster')) galaxy.jobs.handler INFO 2015-01-16 16:40:58,095 sending stop signal to worker thread galaxy.jobs.handler INFO 2015-01-16 16:40:58,096 job handler queue stopped galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LWRRunner: Sending stop signal to monitor thread galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LWRRunner: Sending stop signal to 3 worker threads galaxy.jobs.runners INFO 2015-01-16 16:40:58,096 LocalRunner: Sending stop signal to 5 worker threads galaxy.jobs.handler INFO 2015-01-16 16:40:58,097 sending stop signal to worker thread galaxy.jobs.handler INFO 2015-01-16 16:40:58,098 job handler stop queue stopped

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Baltimore Area Galaxy Meetup @ Johns Hopkins, January 22
by Dave Clements 16 Jan '15

16 Jan '15

Hey Everyone! The Galaxy Project is holding a "meetup" style event <https://wiki.galaxyproject.org/Events/Meetups/Baltimore/2015-01-22> on Thursday, January 22, starting at 6pm in the Department of Biology on the Homewood Campus. The meetup is open to anyone interested in analyzing the large datasets that are typical of contemporary research. Johns Hopkins is one of the two hubs for the project. We will be kicking things off with a discussion of Galaxy and how researchers around the world are leveraging it. See the meetup page <https://wiki.galaxyproject.org/Events/Meetups/Baltimore/2015-01-22> for more information. Please RSVP <http://bit.ly/1Bz3Nrk> as space is limited. We are hoping this will be the first of many meetups, both in the Baltimore area, and elsewhere. If you are interested in hosting a meetup in your area, please contact Galaxy Outreach and we will help you get the word out. Thanks, Enis Afgan and Nitesh Turaga, of the Galaxy Team -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Re: [galaxy-dev] Configuring external user authentication
by Waldron, Michael H 15 Jan '15

15 Jan '15

Eric, Thanks for the response. That made me take a closer look at the apache/shibboleth configuration, and it turns out that adjusting some settings in the shibboleth config fixed the problem. Mike Waldron ________________________________________ From: Eric Rasche [rasche.eric(a)yandex.ru] Sent: Thursday, January 15, 2015 11:28 AM To: Waldron, Michael H Subject: Re: [galaxy-dev] Configuring external user authentication Hi Mike, On January 15, 2015 1:37:24 PM GMT+00:00, "Waldron, Michael H" <mwaldron(a)email.unc.edu> wrote: >We have an older galaxy installation (uses universe_wsgi.ini config >file), that's configured for external user authentication, provided by >our Apache proxy setup which uses Shibboleth to our campus >authentication system. This works just fine. > >I'm setting up a new galaxy installation, the configuration files are >now different, i.e. galaxy.ini, etc., and am having trouble getting the >same authentication mechanism to work. I have the same Apache proxy >configuration that I do on the old galaxy, and I've set >"use_remote_user = True" in galaxy.ini. When I go to the new galaxy >URL, it correctly goes to our Shibbleth authentication screen, but upon >returning to galaxy after successful authentication, I get an error >"The proxy server received an invalid response from an upstream >server." That response sounds like there's something amiss in your apache/nginx conf, not Galaxy. That's not a Galaxy error message if memory serves. >I have verified that Shibboleth is returning the same information to >both the old galaxy server and the new galaxy server. I believe galaxy >is looking for the REMOTE_USER value, which is indeed being provided. >In my case it provides: >(REMOTE_USER) mwaldron >(HTTP_REMOTE_USER) If you need to set Galaxy to check a different header, you can set remote_user_header = HTTP_REMOTE_USER >Am I missing something in the galaxy configuration? > >Mike Waldron >Systems Specialist >ITS - Research Computing Center >University of North Carolina at Chapel Hill > > > >------------------------------------------------------------------------ > >___________________________________________________________ >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/ Hope that helps, Cheers, Eric -- Sent from my Android device with K-9 Mail. Please excuse my brevity.

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Multiple select input error after update
by Alexandre Defelicibus 15 Jan '15

15 Jan '15

Hi all, I've updated a Galaxy server with the latest stable distribution "latest_2015.01.13" and now a I got an error: cannot open galaxy.tools.wrappers.DatasetFilenameWrapper: No such file The tool has a multiple select field: <param name="input_pdbs" type="data" multiple="true" format="pdb" label="PDB Files" /> On the job details, the select files on the multiple select (there are on my history already), are showed at the Job command line as follow: python /home/alexandre/mestrado/protpred-galaxy/galaxy-dist/tools/analysis/dominance_ranking.py -i [<galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a653290>, <galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a653bd0>, <galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a653d90>, <galaxy.tools.wrappers.DatasetFilenameWrapper object at 0x7f4e1a61de10>] The command on XML is: <command interpreter="python"> dominance_ranking.py -i $input_pdbs </command> This tool was working fine before the update. Any ideas what Is going wrong? Thanks a lot, Alexandre -- Alexandre Defelicibus Mestrando em Bioengenharia Programa de Pós-Graduação em Bioengenharia Universidade de São Paulo - USP

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