- galaxy-dev - lists.galaxyproject.org

bai file missing in history export?!
by Bossers, Alex 17 Dec '12

17 Dec '12

Dear all, Are we the only ones that are missing bam index files (the .bai) when exporting a history that contains for instance bowtie mapped reads. In the original history we can save the bam and bai files but after export to a file (tgz) and later import into another (or the same) galaxy instance, the bai files cannot be accessed/saved anymore.... Alex

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tophat: option --transcriptome-mismatches not recognized
by greg 15 Dec '12

15 Dec '12

I'm running tophat2 like this on my newly installed galaxy: http://snag.gy/OfLND.jpg (parameters not shown are just the defaults) And I'm getting this error: Error in tophat: tophat: option --transcriptome-mismatches not recognized for detailed help see http://tophat.cbcb.umd.edu/manual.html I don't understand why the option is offered in the galaxy UI if it's not available, or is there some kind of bug, or wrong version of tophat2? I'm on TopHat v2.0.6. Thanks, Greg

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"default_cluster_job_runner" setting changed - no longer getting job output from cluster
by greg 14 Dec '12

14 Dec '12

Hi guys, I'm really stuck on this one. In my galaxy config file I changed the setting it uses to launch jobs from: default_cluster_job_runner = drmaa://-V/ (which worked fine) To default_cluster_job_runner = drmaa://-V -pe batch 8/ Now whenever I run a job I see a message like this: "Job output not returned from cluster" (Is there any other information I can use to debug this?) I see the information below in the log file if any of that is useful: galaxy.jobs.manager DEBUG 2012-12-14 13:27:36,961 (104) Job assigned to handler 'main' galaxy.jobs DEBUG 2012-12-14 13:27:37,584 (104) Working directory for job is: /home/galaxy/job_working_directory/000/104 galaxy.jobs.handler DEBUG 2012-12-14 13:27:37,586 dispatching job 104 to drmaa runner galaxy.jobs.handler INFO 2012-12-14 13:27:37,772 (104) Job dispatched galaxy.jobs.runners DEBUG 2012-12-14 13:27:38,078 Copying /home/galaxy/job_working_directory/000/104/global_model.txt to /home/galaxy/000/dataset_155.dat as directed by from_work_dir galaxy.jobs.runners DEBUG 2012-12-14 13:27:38,111 Copying /home/galaxy/job_working_directory/000/104/genes.fpkm_tracking to /home/galaxy/000/dataset_152.dat as directed by from_work_dir galaxy.jobs.runners DEBUG 2012-12-14 13:27:38,135 Copying /home/galaxy/job_working_directory/000/104/isoforms.fpkm_tracking to /home/galaxy/000/dataset_153.dat as directed by from_work_dir galaxy.jobs.runners.drmaa DEBUG 2012-12-14 13:27:38,819 (104) submitting file /home/galaxy/pbs/galaxy_104.sh galaxy.jobs.runners.drmaa DEBUG 2012-12-14 13:27:38,820 (104) command is: python /misc/local/galaxy/galaxy-dist/tools/ngs_rna/cufflinks_wrapper.py --input=/home/galaxy/000/dataset_93.dat --assembled-isoforms-output=/home/galaxy/000/dataset_154.dat --num-threads="4" -I 300000 -F 0.1 -j 0.15; cp /home/galaxy/job_working_directory/000/104/global_model.txt /home/galaxy/000/dataset_155.dat; cp /home/galaxy/job_working_directory/000/104/genes.fpkm_tracking /home/galaxy/000/dataset_152.dat; cp /home/galaxy/job_working_directory/000/104/isoforms.fpkm_tracking /home/galaxy/000/dataset_153.dat; cd /misc/local/galaxy/galaxy-dist; /misc/local/galaxy/galaxy-dist/set_metadata.sh /home/galaxy /home/galaxy/job_working_directory/000/104 . /misc/local/galaxy/galaxy-dist/universe_wsgi.ini /home/galaxy/job_working_directory/tmppjMj2j /home/galaxy/job_working_directory/000/104/galaxy.json /home/galaxy/job_working_directory/000/104/metadata_in_HistoryDatasetAssociation_176_zK8nkf,/home/galaxy/job_working_directory/000/104/metadata_kwds_HistoryDatasetAssociation_176_Dkq7kA,/home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_176_jR0e_Z,/home/galaxy/job_working_directory/000/104/metadata_results_HistoryDatasetAssociation_176_jl8W2w,,/home/galaxy/job_working_directory/000/104/metadata_override_HistoryDatasetAssociation_176_M6ctS5 /home/galaxy/job_working_directory/000/104/metadata_in_HistoryDatasetAssociation_177_Q1vGSc,/home/galaxy/job_working_directory/000/104/metadata_kwds_HistoryDatasetAssociation_177_MG96_w,/home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_177_NWTSVQ,/home/galaxy/job_working_directory/000/104/metadata_results_HistoryDatasetAssociation_177_iTNC5T,,/home/galaxy/job_working_directory/000/104/metadata_override_HistoryDatasetAssociation_177_MO0SIc /home/galaxy/job_working_directory/000/104/metadata_in_HistoryDatasetAssociation_174_HcoiD4,/home/galaxy/job_working_directory/000/104/metadata_kwds_HistoryDatasetAssociation_174_4j5SRC,/home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_174_irlquD,/home/galaxy/job_working_directory/000/104/metadata_results_HistoryDatasetAssociation_174_jfK1zk,,/home/galaxy/job_working_directory/000/104/metadata_override_HistoryDatasetAssociation_174_YQzY4e /home/galaxy/job_working_directory/000/104/metadata_in_HistoryDatasetAssociation_175_rjQ2Gp,/home/galaxy/job_working_directory/000/104/metadata_kwds_HistoryDatasetAssociation_175_HMeDGS,/home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_175_7sjyvl,/home/galaxy/job_working_directory/000/104/metadata_results_HistoryDatasetAssociation_175_cJ_Sw6,,/home/galaxy/job_working_directory/000/104/metadata_override_HistoryDatasetAssociation_175_JY4ngx galaxy.jobs.runners.drmaa INFO 2012-12-14 13:27:38,884 (104) queued as 4076946 galaxy.jobs.runners.drmaa DEBUG 2012-12-14 13:27:39,822 (104/4076946) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2012-12-14 13:27:42,830 (104/4076946) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2012-12-14 13:27:44,065 (104/4076946) state change: job finished normally galaxy.jobs.runners.drmaa DEBUG 2012-12-14 13:27:44,111 Job output not returned from cluster galaxy.jobs DEBUG 2012-12-14 13:27:44,147 Tool did not define exit code or stdio handling; checking stderr for success galaxy.jobs DEBUG 2012-12-14 13:27:44,187 setting dataset state to ERROR galaxy.jobs DEBUG 2012-12-14 13:27:44,206 setting dataset state to ERROR galaxy.jobs DEBUG 2012-12-14 13:27:44,226 setting dataset state to ERROR galaxy.jobs DEBUG 2012-12-14 13:27:44,250 setting dataset state to ERROR galaxy.jobs DEBUG 2012-12-14 13:27:44,432 job 104 ended galaxy.datatypes.metadata DEBUG 2012-12-14 13:27:44,432 Cleaning up external metadata files galaxy.datatypes.metadata DEBUG 2012-12-14 13:27:44,452 Failed to cleanup MetadataTempFile temp files from /home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_176_jR0e_Z: No JSON object could be decoded: line 1 column 0 (char 0) galaxy.datatypes.metadata DEBUG 2012-12-14 13:27:44,475 Failed to cleanup MetadataTempFile temp files from /home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_177_NWTSVQ: No JSON object could be decoded: line 1 column 0 (char 0) galaxy.datatypes.metadata DEBUG 2012-12-14 13:27:44,491 Failed to cleanup MetadataTempFile temp files from /home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_175_7sjyvl: No JSON object could be decoded: line 1 column 0 (char 0) galaxy.datatypes.metadata DEBUG 2012-12-14 13:27:44,510 Failed to cleanup MetadataTempFile temp files from /home/galaxy/job_working_directory/000/104/metadata_out_HistoryDatasetAssociation_174_irlquD: No JSON object could be decoded: line 1 column 0 (char 0) galaxy.objectstore CRITICAL 2012-12-14 13:27:44,544 /home/galaxy/job_working_directory/000/104 delete error [Errno 39] Directory not empty: '/home/galaxy/job_working_directory/000/104' Thanks, -Greg

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cannot "Delete Permanently"
by Fenglou Mao 14 Dec '12

14 Dec '12

I installed a local galaxy server, did some calculation. Now I want to clean datasets for some space. I tried "Delete Permanently" on both datasets and histories, none of them worked. The datasets and histories will be marked as "deleted", but it will not be really deleted even I am using "Delete Permanently". They will not be really removed, and space are not released. Sometimes it will give me a message "this feature is not enabled", sometimes it won't. Any one know how to enable "Delete Permanently" feature? Thanks, Fenglou

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How are jobs counted in multi-threaded tools?
by Carlos Borroto 14 Dec '12

14 Dec '12

Hi all, I'm using 'user_job_limit = 8' and I will like to know if jobs for multi-threaded tools are counted based on some kind of multiple. I see for example a user can only run 2 ncbi_blast_plus jobs with my current configuration. Is this because the default numbers of threads for these jobs is 4? What happen if I modify the xml file and change the numbers of threads? Thanks, Carlos

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Data library and symbolic links
by MONJEAUD 14 Dec '12

14 Dec '12

Hi all, I created data libraries using options "Upload files from filesystem paths" and "_Link to files without copying into Galaxy_". It worked but I use symbolic links because my data are frequently updated The problem is that Galaxy takes the real link (inside "external_filename" column in "dataset" table) and doesn't find the files when it is deleted. For example, I uploaded a dataset for a data library without copying : /databank/uniprot/current/fasta/all.fasta -> /databank/uniprot/01_12_2012/fasta/all.fasta The real path is put in the database and it's a problem when it is deleted. Is there a way for galaxy to take the symbolic link directly in the database instead of the real path. Thanks in advance! Cheers, -- Cyril Monjeaud Equipe Symbiose / Plate-forme GenOuest Bureau D156 IRISA-INRIA, Campus de Beaulieu 35042 Rennes cedex, France Tél: +33 (0) 2 99 84 74 17

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Apologies and some more questions
by Philipe Moncuquet 14 Dec '12

14 Dec '12

Hi, I have been sending twice the same message to the mailing list because it didn't appears on my gmail account and I thought it didn't went true. Clearly it appears on the List archive, I checked my spam and it's not there. Does it have something to do with the fact that I am the author of the message, I guess so. Once again sorry for spamming. I still have one more question, is there anyway to edit the annotation of a workflow once you have created it. You can edit name and contents but I don't see how to edit the annotation. When you publish and realized there is a typo in the annotation, there is no other way than deleting the workflow and start all over. Did I missed something ? Philippe

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Custom Builds Server eroor
by Shaun Webb 14 Dec '12

14 Dec '12

Hello I added a custom build to Galaxy, then deleted it and added a new build with the same name. Now whenever I try to acces my custom builds I am getting a server error. Can you point me towards any faults? Do I need to manually remove the custom builds from the database and if so where can I find them? Thanks Shaun Webb Error - <type 'exceptions.KeyError'>: u'ensembl_Current' URL: http://bifx-core.bio.ed.ac.uk:8080/galaxy/display_application/4100358d24a8f… File '/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/storage/home/galaxy/production/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/storage/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/storage/home/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py', line 740 in display_application display_link = display_app.get_link( link_name, data, dataset_hash, user_hash, trans ) File '/storage/home/galaxy/production/galaxy-dist/lib/galaxy/datatypes/display_applications/application.py', line 189 in get_link return PopulatedDisplayApplicationLink( self.links[ link_name ], data, dataset_hash, user_hash, trans ) File '/storage/home/galaxy/galaxy_env/lib/python2.6/UserDict.py', line 22 in __getitem__ raise KeyError(key) KeyError: u'ensembl_Current' -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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Fw: Questions about Install GATK on local instance
by ygong＠cpdr.org 14 Dec '12

14 Dec '12

Hi, Could anyone give me some suggestions about that? Thanks very much. Anthonel ----- Forwarded by Yixiao Gong/cpdr/hjf on 12/13/2012 10:50 AM ----- From: Yixiao Gong/cpdr/hjf To: galaxy-dev(a)lists.bx.psu.edu Date: 12/12/2012 02:52 PM Subject: Questions about Install GATK on local instance Hi, all, I'm installing GATK on galaxy local instance now and I have some questions may need your help. I downloaded the GATK2 from GATK website htt http://www.broadinstitute.org/gatk/download . the link is http://www.broadinstitute.org/gatk/auth?package=GATK I knew that on galaxy tool dependencies page http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies they gave the link for GATK 1.4 version but I can't figure out how to download and install it, and I noticed that GATK2 have all 1.x version features, so I installed GATK2. In the GATK 1.4 link (https://github.com/broadgsa/gatk ) that shown on http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies, there are multiple folders and files and I got really confused what I need to download. Even I choose "ZIP" to download a zip file, I counld not figure out whether it is the program package and don't know how to install it. Maybe this is the problem. But based on my understanding, GATK is just a set of java package, and all we need to do is put it into /tool-data/shared/jars folder, right? That is how I did it for GATK2. The GATK2 package include a folder called "resources" and a file called "GenomeAnalysisTK.jar" . I put them into /tool-data/shared/jars/gatk folder. I tested the installation following the instruction : http://gatkforums.broadinstitute.org/discussion/1200/how-to-test-your-gatk-… And I request a key from broadinstitute and followed the instruction on http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and… But the galaxy still gave me the error message as followed： ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR A USER ERROR has occurred (version 2.2-16-g9f648cb): ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed ##### ERROR Please do not post this error to the GATK forum ##### ERROR ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments. ##### ERROR Visit our website and forum for extensive documentation and answers to ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk ##### ERROR ##### ERROR MESSAGE: Running with the -et NO_ET or -et STDOUT option requires a GATK Key file. Please see http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and… for more information and instructions on how to obtain a key. ##### ERROR ------------------------------------------------------------------------------------------ I guess I may made mistakes in some point: 1. I should not install GATK2 but only GATK 1.4 so that Galaxy can use it. But I really don't know how to download and install it. I can't find the correct file. 2. GATK2 works on Galaxy but I did something wrong on installing it. Could anyone help me about this? It will be greatly appreciated. Thanks. Anthonel

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tools imported from toolshed stay in "waiting to run status"
by Philipe Moncuquet 14 Dec '12

14 Dec '12

Hi dev, We are running a local instance of Galaxy, last update was the November release (7148:17d57db9a7c0 I think). We are facing problem when trying to run tools that were imported via the toolshed. The never start and the status stays on "waiting to run". Other tools work fine, and this generic to all tools from toolshed. Any suggestions on where should I look to fix this ? Philippe

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