October 2014 - galaxy-dev - lists.galaxyproject.org

Anyone else having issues with cloudman cloudlaunch?
by Chris Dagdigian 10 Oct '14

10 Oct '14

Anyone else having issues using cloudman version of galaxy? No matter what set of AWS keys I use to try to start a new galaxy cluster I always get the vague "Bad Request : Instance failure, but no specific error was detected. Please check your AWS Console." ... error on the launch screen. Nothing obvious in the AWS console. I'm using both my root AWS keys as well as IAM generated keys with full admin rights and no love. I do have one running cluster; does that need to be stopped or paused before I try to launch more? Regards, Chris

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Tool development: Is it possible to pass a user's id in dynamic_options() parameter?
by Dooley, Damion 10 Oct '14

10 Oct '14

This was asked a few years ago but no takers: Galaxy Tool Development: (http://dev.list.galaxyproject.org/Reading-user-id-before-the-execution-of-t…) Seems like this isn't possible, unless there's a way to plant user's name in a text field on the tool's form, so that a dynamic_options() call can refer to it? Thx for insights, Damion

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Is it possible to condition tool wrappers on external inputs?
by Melissa Cline 10 Oct '14

10 Oct '14

Hi Folks, I suspect I know the answer to this question already, but I have to ask just for the sake of completeness... I'm working on a tool for which I'd like to query an external server for the set of expected inputs, and then make that set available as input options. The tool in question will import a Galaxy dataset into an external cancer genomics database. The user will need to specify what cancer cohort the new data belongs under. In the perfect world, I would query this cancer genomics database for the existing cancer cohorts, and use that set of cohorts to populate the set of options for a select-type input parameter. Is anything like this possible? If so, where could I look at some examples? If not, is there anything you can think of to produce similar behavior? Thanks! Melissa

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Data uploaded with new upload tool doesn't get added to history
by Peter van Heusden 10 Oct '14

10 Oct '14

Hey there Using the new upload tool my data uploads but never appears in the history. All I can see in paster.log when I do an upload is: 10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] "POST /tool_runner/index HTTP/1.0" 200 - "https://phillipl.sanbi.ac.za/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0" 10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] "GET /api/histories/f597429621d6eb2b/contents HTTP/1.0" 200 - "https://phillipl.sanbi.ac.za/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0" 10.8.0.2 - - [09/Oct/2014:20:43:58 +0200] "GET /api/histories/f597429621d6eb2b HTTP/1.0" 200 - "https://phillipl.sanbi.ac.za/root" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:32.0) Gecko/20100101 Firefox/32.0" No errors in the javascript console, and this happens with both Chrome and Firefox (on Linux), code is latest galaxy-central. Any ideas where to debug? Thanks, Peter

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SQLalchemy InvalidRequestError
by Ulf Schaefer 09 Oct '14

09 Oct '14

Dear all Maybe one of you can shed some light on this error message that I see in the log file for one of my handler processes. I get about one of them per second. The effect is that most of the jobs remain in the "waiting to run" stage. The postgres database is running on a separate server and appear to be doing just fine. Any help is greatly appreciated. Thanks Ulf --- galaxy.jobs.handler ERROR 2014-10-07 10:32:24,676 Exception in monitor_step Traceback (most recent call last): File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/jobs/handler.py", line 161, in __monitor self.__monitor_step() File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/lib/galaxy/jobs/handler.py", line 184, in __monitor_step hda_not_ready = self.sa_session.query(model.Job.id).enable_eagerloads(False) \ File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/scoping.py", line 114, in do return getattr(self.registry(), name)(*args, **kwargs) File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/session.py", line 1088, in query return self._query_cls(entities, self, **kwargs) File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 108, in __init__ self._set_entities(entities) File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 117, in _set_entities self._setup_aliasizers(self._entities) File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py", line 132, in _setup_aliasizers _entity_info(entity) File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/util.py", line 578, in _entity_info mapperlib.configure_mappers() File "/phengs/hpc_storage/home/galaxy_hpc/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg/sqlalchemy/orm/mapper.py", line 2260, in configure_mappers raise e InvalidRequestError: One or more mappers failed to initialize - can't proceed with initialization of other mappers. Original exception was: When initializing mapper Mapper|Queue|kombu_queue, expression 'Message' failed to locate a name ("name 'Message' is not defined"). If this is a class name, consider adding this relationship() to the <class 'kombu.transport.sqlalchemy.Queue'> class after both dependent classes have been defined. --- ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

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snpEf dataset generation errors
by Iry Witham 09 Oct '14

09 Oct '14

I am trying to resolve an issue with snpEff 3.4 running on a cloudman instance of galaxy. The instance is invoking the following command and failing: java -Xmx6G -jar $SNPEFF_JAR_PATH/snpEff.jar eff -c $SNPEFF_JAR_PATH/snpEff.config -i vcf -o vcf -upDownStreamLen 5000 -spliceSiteSize 1 -stats /mnt/galaxy/files/000/dataset_364.dat -noLog -download GRCh37.68 /mnt/galaxy/files/000/dataset_313.dat > /mnt/galaxy/files/000/dataset_363.dat The error it is reporting is: Fatal error: Exit code 255 (Error) java.lang.RuntimeException: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct. at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.download(SnpEffCmdDownload.java:159) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:234) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:217) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1001) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83) Caused by: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct. at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdDownload.download(SnpEffCmdDownload.java:122) ... 8 more java.lang.RuntimeException: Genome download failed! at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1002) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:963) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:352) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:320) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:83) I have upgraded to java 1.7.0 due to an issue with GATK2. In addition to this when I try to run snpEff I am unable to select a genome source unless I use the "Named on demand" option. How do I get snpEff genome version data configured? The snpEff_genomes.loc file lists all of the genomes I need and many more. I appreciate the help. Regards, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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CloudMan: Autoscaling =Unable to run this job due to a cluster error
by Petit III, Robert A. 09 Oct '14

09 Oct '14

Hello Galaxy Team! I've set up a vanilla CloudMan instance using AWS. I've set the head node to not handle jobs and have set AutoScaling to a minimum of 0 and a maximum of 4 worker nodes. Upon submitting a job, it fails with the following error: Unable to run this job due to a cluster error, please retry it later Now if I set AutoScaling to a minimum of 1 worker node it works fine. But I would rather not always have 1 worker node up. Any recommendations? Thank you very much, Robert ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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Download tool-dependency with using a proxy and functional tests http 403 error
by Marcus.Jaeger＠kws.com 09 Oct '14

09 Oct '14

Hi, I have two problems and I hope you can help me. The first one is, I can't download a package within the tool-dependency description, because our company uses a proxy. How can I define using a proxy in the "tool_dependencies.xml" file? The second one is, I try to run functional tests in our toolshed. But I got a http 403 error. I followed these steps to run the tests: https://wiki.galaxyproject.org/InstallAndTestCertification (in chapter: Using the Install and Test Framework With a Local Tool Shed) When I run the test, it got stuck when installing the testing tool to the temporary galaxy instance. But it is possible to access the temporary galaxy instance in a webbrowser. I found out, that the temporary database is empty and doesn't include any user. So i think that could be the reason for the http 403 error? Can you please give me advice how to resolve these issues? Thank you very much. - marcus

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GATK2 reporting "Invalid argument value '/mnt/galaxy/tools/gatk2/bin/' at position 8."
by Iry Witham 09 Oct '14

09 Oct '14

Hi Team, I have installed GATK2 into a galaxy cloud instance to use the Unified Genotyper for our sequencing course. However, when I run the tool I get the following error message: Dataset 41: Unified Genotyper on data 8 and data 13 (VCF) Tool execution generated the following error message: ERROR ------------------------------------------------------------------------------------------ ERROR A USER ERROR has occurred (version 3.2-2-gec30cee): ERROR ERROR This means that one or more arguments or inputs in your command are incorrect. ERROR The error message below tells you what is the problem. ERROR ERROR If the problem is an invalid argument, please check the online documentation guide ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool. ERROR ERROR Visit our website and forum for extensive documentation and answers to ERROR commonly asked questions http://www.broadinstitute.org/gatk ERROR ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself. ERROR ERROR MESSAGE: Invalid argument value '/mnt/galaxy/tools/gatk2/bin/' at position 8. ERROR ------------------------------------------------------------------------------------------ The following is the command that is being invoked by galaxy: python /mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/gatk2/84584664264c/gatk2/gatk2_wrapper.py --stdout "/mnt/galaxy/files/000/dataset_326.dat" -d "-I" "/mnt/galaxy/files/000/dataset_226.dat" "bam" "gatk_input_0" -d "" "/mnt/galaxy/files/_metadata_files/000/metadata_13.dat" "bam_index" "gatk_input_0" -p ' java -jar "$GATK2_PATH/GenomeAnalysisTK.jar" -T "UnifiedGenotyper" --num_threads ${GALAXY_SLOTS:-4} --out "/mnt/galaxy/files/000/dataset_324.dat" --metrics_file "/mnt/galaxy/files/000/dataset_325.dat" $GATK2_SITE_OPTIONS --num_cpu_threads_per_data_thread 1 --genotype_likelihoods_model "BOTH" --standard_min_confidence_threshold_for_calling "30.0" --standard_min_confidence_threshold_for_emitting "30.0" ' -d "-R" "/mnt/galaxy/files/000/dataset_220.dat" "fasta" "gatk_input" I have reviewed my configuration files and cannot locate where the issue lies. I am also posting this with the GATK Forum to see if they have any ideas. Unfortunately I need to get this resolved ASAP since I need to complete my testing by tomorrow. Thanks, Iry The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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no universe_wsgi.ini & can't install tools from the standard toolshed because: "Initializing repository installation failed"
by Chris Dagdigian 09 Oct '14

09 Oct '14

Hi folks, Got a strange problem - it's hit me on all my self-install options today including using the Chef cookbook as well as the galaxy mecurial install method on Ubuntu 12.04 LTS I'm trying to build a local galaxy that supports a few common extra tools (things like samtools etc.) I can boot a fresh Ubuntu 12.04 LTS and follow the instructions at getgalaxy.org: > hg clone https://bitbucket.org/galaxy/galaxy-dist/ > cd galaxy-dist > hg update stable sh ./run.sh There are two strange things that don't quite match what I'm expecting to see from the docs ... (1) The file "universe_wsgi.ini " no longer gets created in galaxy-dist/ after running "run.sh" for the first time. This is strange because I remember it working days ago but now on fresh server and fresh checkout the file does not get created and I have to manually create one in oder to set "host = 0.0.0.0" (2) I can't even install simple tools like samtools from the standard tool sheds. The status page gets stuck at "installing dependencies" and if I navigate away I get a browser javascript error ("Initializing repository installation failed" Any tips or tricks appreciated, thanks! Regards, Chris

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