- galaxy-dev - lists.galaxyproject.org

Error resolving Emboss tool dependencies
by Shantanu Pavgi (Campus) 06 Sep '13

06 Sep '13

I have migrated Emboss tool from dist to tool-shed using the migration script and later updated it's revision. The tool was installed along with it's dependencies, but it's failing to find them during job run. It's logging following 'Failed to resolve dependency on 'emboss', ignoring' warning message in the log file. It seems like build_dependency_shell_commands method in '/lib/galaxy/tools/__init__.py' is unable to get installed_tool_dependencies. I am not sure why this would fail and how to resolve it. I have tried resetting tool metadata several times, but that didn't help. Appreciate any help on resolving this error. I am using Galaxy release_2013.06.03 revision. Thanks, Shantanu

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options from_dataset evaluation in workflow
by Wolfgang Maier 06 Sep '13

06 Sep '13

Dear all, in one of my tools I'm populating a list of possible choices from a file in the history using the <options from_dataset> tag. Now using the tool as part of a workflow, the choices are not calculated at the setup stage, but I have to enter free-text and Galaxy seems to evaluate whether that's a legal choice only when the specific tool starts running (way down in my workflow). Is there any workaround for this behavior, so that choices are presented before workflow execution? Thanks for any help, Wolfgang

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workflow_execute.py failing!
by Hakeem Almabrazi 06 Sep '13

06 Sep '13

Hi, I have been trying to use workflow_execute.pl to execute a workflow that has ~50 steps. I keep getting this error after running for few seconds knowing I could run the same workflow from the GUI without any issue. **************** HTTP Error 500: Internal Server Error 500 Internal Server Error The server has either erred or is incapable of performing the requested operation. ********************* And here is some error I capture in the log file> File "/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2126, in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 362, in execute history.add_dataset( data, set_hid = set_output_hid ) File "/usr/local/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py", line 1124, in __getattr__ if key not in self: raise AttributeError, key AttributeError: add_dataset Looking at the created history the first 14 steps get scheduled and executed. But nothing else. Meaning the rest of the steps get omitted. This could be due to the script get crashed before it complete registering the rest of the steps of the workflow. Does anyone has any idea what could be going on here? Best regards.

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[GSoC2013] Week 6 Update
by Saket Choudhary 06 Sep '13

06 Sep '13

Week 6 updates are here : http://galaxy-gsoc2013.blogspot.in/2013/07/week-6-update.html Thanks Saket

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Lost in tool dependencies
by Lionel Guy 06 Sep '13

06 Sep '13

Hi Galaxians, I've been scratching a bit my head about how galaxy builds dependency, fruitlessly so far... Here is my problem: I have a local tool (not installed through a toolshed) that makes use of another tool (aragorn) that I installed from the toolshed. Aragorn requires the aragorn package, as stated in its .xml file: <requirement type="package" version="1.2.36">aragorn</requirement> When I run aragorn, it runs fine, and the dependencies are built fine. galaxy.tools DEBUG 2013-09-05 12:20:14,340 Building dependency shell command for dependency 'aragorn' Now when I run my tool, which has the exact same requirement line: <requirement type="package" version="1.2.36">aragorn</requirement> the dependency is not built correctly, and fail to resolve: galaxy.tools DEBUG 2013-09-05 12:26:22,823 Building dependency shell command for dependency 'aragorn' galaxy.tools WARNING 2013-09-05 12:26:22,823 Failed to resolve dependency on 'aragorn', ignoring The required package is installed in galaxy-dist/tool-dependency-dir/aragorn/1.2.36/bgruening/trna_prediction/d34f31cbc9dd/ and there is an env.sh there that points correctly to the binaries. Now if I copy that env.sh file into galaxy-dist/tool-dependency-dir/aragorn/1.2.36/, it works fine and the dependency command is built all fine, but it is not done automatically when I install aragorn through the toolshed. Am I doing something wrong? Missing something somewhere? Cheers, Lionel

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Tool's toolshed page does not get updated after uploading new version
by Joachim Jacob | VIB | 06 Sep '13

06 Sep '13

Hi all, My issue: I have put a new version of a tool in our local toolshed (via 'hg push'). Now, going to the tool's page, still the old version of the README is displayed. When browsing the repository, the new (last uploaded) version is there. In addition, the tool's page show the latest revision, but displays the former version. Did I go wrong somewhere or is this a bug? [ I don't know whether this is known already - Trello is annoyingly slow, and there is no easy way to swiftly search in the non-existing Trello list Toolshed ( sorry, bear with me please, I needed to point out my issues with Trello at least once ;-) ] Thanks, Joachim -- Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team

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Bug in toolshed: changing public name breaks repo path
by Guest, Simon 05 Sep '13

05 Sep '13

I'm just setting up a local toolshed. After creating a repo, I changed my public name (from the default guestsi to simon-guest) on the web interface, and got this traceback when I tried to look at my repo: Internal Server Error Galaxy was unable to sucessfully complete your request URL: http://galaxy-dev.agresearch.co.nz/toolshed/repository/manage_repository?so… Module galaxy.web.framework.middleware.error:149 in __call__ >> app_iter = self.application(environ, sr_checker) Module paste.debug.prints:106 in __call__ >> environ, self.app) Module paste.wsgilib:543 in intercept_output >> app_iter = application(environ, replacement_start_response) Module paste.recursive:84 in __call__ >> return self.application(environ, start_response) Module galaxy.webapps.tool_shed.framework.middleware.remoteuser:74 in __call__ >> return self.app( environ, start_response ) Module paste.httpexceptions:633 in __call__ >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request >> body = method( trans, **kwargs ) Module galaxy.web.framework:98 in decorator >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.tool_shed.controllers.repository:1883 in manage_repository >> repo_dir = repository.repo_path( trans.app ) Module galaxy.webapps.tool_shed.model:205 in repo_path >> return app.hgweb_config_manager.get_entry( os.path.join( "repos", self.user.username, self.name ) ) Module galaxy.webapps.tool_shed.util.hgweb_config:62 in get_entry >> raise Exception( "Entry for repository %s missing in file %s." % ( lhs, self.hgweb_config ) ) Exception: Entry for repository repos/simon-guest/emboss_5_native missing in file /home/galaxy-dev/hgweb/hgweb.config. It looks like it's trying to use the public name in the repo path, which isn't going to work very well if public names can be changed. Changing my public name back to what it was before made it start working again. cheers, Simon ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

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no module named eggs Error
by Hakeem Almabrazi 05 Sep '13

05 Sep '13

I do not know what happened but I keep getting the following issue when I try to start my Local Galaxy. Can someone tell me how to fix this issue please? Starting galaxy... Traceback (most recent call last): File "./scripts/check_eggs.py", line 32, in <module> from galaxy.eggs import Crate ImportError: No module named eggs Some eggs are out of date, attempting to fetch... Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 28, in <module> from galaxy.eggs import Crate, EggNotFetchable ImportError: No module named eggs Fetch failed. ...done. Regards

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Re: [galaxy-dev] [galaxy-user] version_command tag problem
by Jennifer Jackson 05 Sep '13

05 Sep '13

Hi Wolfgang, I am going to re-post your question over to the galaxy-dev mailing list, which is best for local instance questions. To all: please remove the galaxy-user list from any replies. Thanks! Jen Galaxy team On 9/5/13 1:33 AM, Wolfgang Maier wrote: > Hi everybody, > I'm trying to add the version_command tag to my tools' xml > files, but I run into a problem here. Currently I have: > <version_command interpreter="python3">aln.py > --version</version_command> > in my xml. > When I run the tool Galaxy tells me that it executed this: > python3 /home/me/galaxy-dist/tools/modmapmin/aln.py > --version &> > /home/me/galaxy-dist/database/tmp/GALAXY_VERSION_STRING_1035 > but when I check that temporary file it's empty (and so is > the tool version line at the end of the run). > This is puzzling because when I run that exact command line > from my terminal, it writes > 0.8.2 > to the file just as it should. > Any ideas what goes wrong here? > Thanks and best wishes, > Wolfgang > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

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Re: [galaxy-dev] [galaxy-user] NoClassDefFoundError in Picard Paired Read Mate Fixer
by Jennifer Jackson 05 Sep '13

05 Sep '13

Hello, The easiest way to ensure that dependencies are set up correctly is to install tool dependencies directly from the Tool Shed: http://wiki.galaxyproject.org/DefiningRepositoryDependencies#Complex_reposi… You will want to use: http://toolshed.g2.bx.psu.edu/ "package_picard_1_56_0" For local instance help, please post to the galaxy-dev(a)bx.psu.edu mailing list, as that is the best way to reach the development community. I am going to double post this reply, to resolve the question on the original galaxy-user and to give it visibility on the galaxy-dev list, but going forward on this thread (if needed) please remove galaxy-user from future replies. Best! Jen Galaxy team On 8/31/13 11:19 AM, Nicolas Quizon wrote: > Dear Galaxy Gurus, > > I am a student and still new to Galaxy. I am encountering an error > when trying to run the Picard Paired Read Mate Fixer with default > settings on Galaxy. The code only runs for a few seconds before > failing and displaying the error message. > > ## exit code=1; stdout= > [Mon Aug 19 16:46:15 EDT 2013] net.sf.picard.sam.FixMateInformation > INPUT=[/usr/lib/galaxy-server/database/files/000/dataset_85.dat] > OUTPUT=/usr/lib/galaxy-server/database/tmp/tmpxhbz3T > SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENT VERBOSITY=INFO > QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 > CREATE_INDEX=false CREATE_MD5_FILE=false > [Mon Aug 19 16:46:15 EDT 2013] Executing as root@biolinux-pbcn6 on > Linux 3.2.0-43-generic amd64; OpenJDK 64-Bit Server VM 1.6.0_27-b27; > Picard version: 1.91() > [Mon Aug 19 16:46:15 EDT 2013] net.sf.picard.sam.FixMateInformation > done. Elapsed time: 0.00 minutes. > Runtime.totalMemory()=378470400 > To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp > Exception in thread "main" java.lang.NoClassDefFoundError: > org/itadaki/bzip2/BZip2InputStream > at > net.sf.picard.sam.FixMateInformation.doWork(FixMateInformation.java:84) > at > net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177) > at > net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119) > at > net.sf.picard.sam.FixMateInformation.main(FixMateInformation.java:76) > Caused by: java.lang.ClassNotFoundException: > org.itadaki.bzip2.BZip2InputStream > at java.net.URLClassLoader$1.run(URLClassLoader.java:217) > at java.security.AccessController.doPrivileged(Native Method) > at java.net.URLClassLoader.findClass(URLClassLoader.java:205) > at java.lang.ClassLoader.loadClass(ClassLoader.java:321) > at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) > at java.lang.ClassLoader.loadClass(ClassLoader.java:266) > ... 4 more > > For input I am using data that I have successfully mapped with BWA > for Illumina. I currently have Python version 2.7.3 and Java version > 1.6.0_27, and an working on a machine running Ubuntu 12.04.2 LTS. > > Any help is greatly appreciated! > > Thanks! > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

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