September 2013 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Need your helps about Galaxy
by Lei Yan 24 Sep '13

24 Sep '13

Dear James, Thanks so much for your info. Dumping database is a good idea. But the problem is that the two Galaxy are running on different servers, and the Galaxy versions are very different. Thanks again. Lei Yan Center for Integrative and Translational Genomics UTHSC On Mon, Sep 23, 2013 at 2:37 PM, James Taylor <james(a)taylorlab.org> wrote: > There is not a simple way to do this. You will need to dump the > accounts from your old database and load into the new database. Are > they running the same database server? > > Please send questions like this to the galaxy-dev mailing list. > > -- > James Taylor, Associate Professor, Biology/CS, Emory University > > > On Mon, Sep 23, 2013 at 3:31 PM, Lei Yan <leiyan2000(a)gmail.com> wrote: > > Dear James, > > > > I built a new cloud Galaxy instance today. > > Would you please tell me how to transfer some given accounts from an old > > Galaxy to this new one? > > This is old Galaxy: http://galaxylocal.genenetwork.org:8080/ > > This is new Galaxy: http://galaxyclass.genenetwork.org/ > > Thanks a lot. > > > > > > Lei Yan > > Center for Integrative and Translational Genomics > > UTHSC >

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ImportError: No module named paramiko
by Peter Cock 24 Sep '13

24 Sep '13

Hi all, Has something changed recently on galaxy-central with the fabric egg, and a possible missing dependency? $ ./run.sh ... galaxy.jobs.handler INFO 2013-09-24 16:40:21,849 job handler stop queue started galaxy.jobs.handler INFO 2013-09-24 16:40:21,867 job handler queue started galaxy.sample_tracking.external_service_types DEBUG 2013-09-24 16:40:21,870 Loaded external_service_type: Simple unknown sequencer 1.0.0 galaxy.sample_tracking.external_service_types DEBUG 2013-09-24 16:40:21,873 Loaded external_service_type: Applied Biosystems SOLiD 1.0.0 galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,899 Enabling 'data_admin' controller, class: DataAdmin galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,903 Enabling 'requests_common' controller, class: RequestsCommon galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,905 Enabling 'forms' controller, class: Forms galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,974 Enabling 'workflow' controller, class: WorkflowController galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,975 Enabling 'async' controller, class: ASync galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,975 Enabling 'library' controller, class: Library galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,982 Enabling 'data_manager' controller, class: DataManager galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,983 Enabling 'error' controller, class: Error galaxy.web.framework.base DEBUG 2013-09-24 16:40:22,213 Enabling 'cloudlaunch' controller, class: CloudController galaxy.eggs WARNING 2013-09-24 16:40:22,480 Warning: paramiko (a dependent egg of Fabric) cannot be fetched Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/eggs/Fabric-1.7.0-py2.6.egg/fabric/network.py", line 24, in <module> import paramiko as ssh ImportError: No module named paramiko There was a problem importing our SSH library (see traceback above). Please make sure all dependencies are installed and importable ... Also what is this CloudController and can I turn it off instead? Thanks, Peter

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Repository tool dependencies and virtualenv install
by Carlos Borroto 24 Sep '13

24 Sep '13

Hi, I have created a tool that depends on biopython. I don't like the idea of having several copies of biopython around and also for best practice making workflows using my tool reproducible, I chose to make my package repository[1] dependent of package_biopython_1_62. [1]http://testtoolshed.g2.bx.psu.edu/view/cjav/package_ngs_tools_0_1_6 I'm installing my package using the virtualenv option. As you can see below I marked biopython as prior_installation_required="True". However, I can see that virtualenv is installing a copy of biopython in 'venv' under my tool install(see below). This doesn't sound right. I was expecting that by making my repository dependent of biopython's one that source would be used in my tool. My plan is to create any non-existing "Tool dependency definition" repository for every package my tool requires. This way you can always count the same version of any of these packages is being used. I thought that was the point, right? Full ool_dependencies.xml: <?xml version="1.0"?> <tool_dependency> <package name="biopython" version="1.62"> <repository changeset_revision="ac9cc2992b69" name="package_biopython_1_62" owner="biopython" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> </package> <package name="ngs-tools" version="0.1.6"> <install version="1.0"> <actions> <action type="setup_virtualenv">ngs-tools==0.1.6</action> </actions> </install> </package> </tool_dependency> Contents of site-packages in my tool install dir: $ ls -1 shed_tools_dependencies.central/ngs-tools/0.1.6/cjav/package_ngs_tools_0_1_6/3c646b8328bb/venv/lib/python2.7/site-packages/ Bio biopython-1.62-py2.7.egg-info BioSQL docopt-0.6.1-py2.7.egg-info docopt.py docopt.pyc easy-install.pth Levenshtein.so ngs ngs_tools-0.1.6-py2.7.egg-info pip-1.3.1-py2.7.egg python_Levenshtein-0.10.2-py2.7.egg-info setuptools-0.6c11-py2.7.egg setuptools.pth Thanks, Carlos

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cluster error
by Philippe Moncuquet 23 Sep '13

23 Sep '13

Hi guys, Since the last upgrade we have observed this error. When submitting a job it sometimes come back failed with the following error tool error An error occurred with this dataset: *Unable to run this job due to a cluster error, please retry it later* * * It is not reproducible as when you relaunch the job it works but still very annoying when demonstrating Galaxy. It looks to me that there is something wrong with torque/pbs and that when one submit a number of jobs, it reaches an internal limit of some kind, and then stops communicating with torque (the batch system). galaxy.jobs DEBUG 2013-09-24 14:05:08,692 (4264) Working directory for job is: /data/galaxyTools/galaxydev/database/job_working_directory/004/4264 galaxy.jobs.handler DEBUG 2013-09-24 14:05:08,700 (4264) Dispatching to pbs runner galaxy.jobs.runners.pbs DEBUG 2013-09-24 14:05:08,885 (4263/9034.galaxy-compute) PBS job state changed from N to R galaxy.jobs DEBUG 2013-09-24 14:05:08,925 (4264) Persisting job destination (destination id: pbs:///) galaxy.jobs.handler INFO 2013-09-24 14:05:09,014 (4264) Job dispatched galaxy.jobs.runners.pbs ERROR 2013-09-24 14:05:09,524 (4262) All attempts to submit job failed galaxy.jobs.runners.pbs DEBUG 2013-09-24 14:05:15,795 (4264) submitting file /data/galaxyTools/galaxydev/database/pbs/4264.sh galaxy.jobs.runners.pbs DEBUG 2013-09-24 14:05:15,795 (4264) command is: python /data/galaxyTools/galaxydev/tools/fastq/fastq_groomer.py '/data/galaxyTools/galaxydev/database/files/007/dataset_7546.dat' 'sanger' '/data/galaxyTools/galaxydev/database/files/007/dataset_7610.dat' 'sanger' 'ascii' 'summarize_input'; cd /data/galaxyTools/galaxydev; /data/galaxyTools/galaxydev/set_metadata.sh ./database/files /data/galaxyTools/galaxydev/database/job_working_directory/004/4264 . /data/galaxyTools/galaxydev/universe_wsgi.ini /data/galaxyTools/galaxydev/database/tmp/tmpcdfNIZ /data/galaxyTools/galaxydev/database/job_working_directory/004/4264/galaxy.json /data/galaxyTools/galaxydev/database/job_working_directory/004/4264/metadata_in_HistoryDatasetAssociation_9064_Zk1kgC,/data/galaxyTools/galaxydev/database/job_working_directory/004/4264/metadata_kwds_HistoryDatasetAssociation_9064_yBjKtV,/data/galaxyTools/galaxydev/database/job_working_directory/004/4264/metadata_out_HistoryDatasetAssociation_9064_RBQTv6,/data/galaxyTools/galaxydev/database/job_working_directory/004/4264/metadata_results_HistoryDatasetAssociation_9064_zBFTMS,,/data/galaxyTools/galaxydev/database/job_working_directory/004/4264/metadata_override_HistoryDatasetAssociation_9064_0W_zYn galaxy.jobs.runners.pbs WARNING 2013-09-24 14:05:15,796 (4264) pbs_submit failed (try 1/5), PBS error 15033: No free connections galaxy.jobs.runners.pbs WARNING 2013-09-24 14:05:17,798 (4264) pbs_submit failed (try 2/5), PBS error 15033: No free connections galaxy.jobs.runners.pbs WARNING 2013-09-24 14:05:19,800 (4264) pbs_submit failed (try 3/5), PBS error 15033: No free connections Did you guys have ever experienced the same problem and if so how did you solve it ? Regards, Philippe

1 0

How to make a Tool Shed private?
by Serrano Pereira 23 Sep '13

23 Sep '13

Hello, Is it possible to make a Galaxy Tool Shed private? The only method I can think of at this moment is to use Apache's configuration to restrict access to certain IP addresses. I was wondering if there are alternative methods. Regards, Serrano

2 2

my history not visible
by Robert Jackman 23 Sep '13

23 Sep '13

Hi, For some reason my history has stopped being visible on Galaxy today. I was using Galaxy a lot last week and this morning I find only this message: An error occurred getting the history data from the server. Please contact a Galaxy administrator if the problem persists. Robert Jackman ---------------------------------------- Robert Jackman Research Associate Professor 635 Commonwealth Avenue/ Sar443 Boston, MA 02215 rjackman(a)bu.edu 617-353-2719

2 1

Grant authority missing when create new repository on Tool Shed
by Peter Cock 23 Sep '13

23 Sep '13

Hi all, I think I've found a bug, or at least an area for improvement, 1. Goto http://testtoolshed.g2.bx.psu.edu/ 2. Login, e.g. as IUC 3. Create new repository, e.g. package_blast_plus_2_2_27 4. Fill in description and 5. Look for "Grant authority to make changes" Actual result: No "Grant authority to make changes" box present. Expected result: "Grant authority to make changes" box present. Workaround: 6. Click on "My writable repositories" 7. Click on new repository 8. Now there is a "Grant authority to make changes" box. Regards, Peter

2 1

Regarding Jellyfish or other k-mer analysis software
by Johan Schedin 23 Sep '13

23 Sep '13

Hello! I hope that everybody has a great day! In a pre-assemble analysis step I want to perform a k-mer analysis of the fastq-file to visualize the k-mer coverage distribution (too estimate genome size, heterozygosity, repeats etc). This would preferably be done with Jellyfish. Is there an existing wrapper for jellyfish or any similar k-mer analysis software? I have been searching the toolshed and with Google without any success. I am farly new to Galaxy so any help/input would really be appreciated! Thanks, Johan Schedin

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[GSoC2013] Final Update!
by Saket Choudhary 22 Sep '13

22 Sep '13

Posted my final update[well only for the GSoC period, the blog is going to be alive otherwise] here: http://galaxy-gsoc2013.blogspot.com/2013/09/and-it-comes-to-end.html Thanks for all your suggestions and feedback :-) Its been quite a wonderful learning experience working with & on Galaxy Project! Saket Choudhary Senior Undergraduate Department of Chemical Engineering IIT Bombay India

1 0

History will not load
by Maria Hoffman 22 Sep '13

22 Sep '13

Hello, I have been having trouble with Galaxy since yesterday. I have been trying to run cuffdiff which has been waiting to run since Friday afternoon and now my history will not even load (red error message shows up). Any incite would be much appreciated. Maria

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