January 2015 - galaxy-dev - lists.galaxyproject.org

The choice when I integrated slurm and galaxy in job_conf.xml
by xlwang 08 Jan '15

08 Jan '15

hi, Slurm is the DRM in my cluster. When I modified the job_conf.xml, which plugin should I use? slurm or drmaa?

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Dataset deletion / database update after user purge
by Nicolas Lapalu 08 Jan '15

08 Jan '15

Hi Galaxy team, We performed a database and datasets purge of our Galaxy server. We decided to delete and purge few user accounts. We supposed that the purge of a user would trigger cascade deletions in database. So we used the web interface to delete and to purge these accounts. Then we launched cleanup_dataset.py in several ways: python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 1 -1 -r > cleanup_1.log python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 1 -2 -r > cleanup_2.log python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 1 -3 -r > cleanup_3.log python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 1 -5 -r > cleanup_5.log python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 1 -4 -r > cleanup_4.log python scripts/cleanup_datasets/cleanup_datasets.py universe_wsgi.ini -d 1 -6 -r > cleanup_6.log After a simple control, I can see that some datasets belonging to (and only to) purged user accounts are still present with a status : deleted = t and purged = f. Moreover, some datasets (not shared with other users or linked to a library) have the status deleted = f and purged = f. When I look at the history status associated with the dataset, I can obtain deleted = t and purged = f. So, the purge of a user account don't change the status of his histories and datasets. Do you thing that I can change the history status 'deleted = f to deleted = t, and purged = f to purged = t' for all purged users ? I expect that the cleanup script launches the cascade purge ! below the sql command: // all datasets belonging to at least one purged user (shared or not) select D.id as "dataset id",U.email, D.deleted as "dataset deleted", D.purged as "dataset purged" , H.deleted as "history deleted" ,H.purged as "history purged" from galaxy_user U,history H ,history_dataset_association A, dataset D where A.dataset_id=D.id and H.id=A.history_id and U.id=H.user_id and D.id in (select D.id from galaxy_user U,history H ,history_dataset_association A, dataset D where A.dataset_id=D.id and H.id=A.history_id and U.id=H.user_id and U.deleted = 't' and U.purged = 't') order by D.id;

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GCC2015 Training Day Topic Nominations are Open through January 6
by Dave Clements 05 Jan '15

05 Jan '15

Hello all, GCC2015 Training Day <http://gcc2015.tsl.ac.uk/training-day/> topics are nominated by you <http://bit.ly/gcc2015tdnom>, the Galaxy Community. Please take a few minutes to nominate a topic. Any topic of interest to the Galaxy Community can be nominated and you are encouraged to nominate more than one. If you are looking for ideas, see the topics nominated in 2013 <http://bit.ly/1i2j1gN> and 2014 <http://bit.ly/1s6NtMN>, and the Events <https://wiki.galaxyproject.org/Events> and the Events Archives <https://wiki.galaxyproject.org/Events/Archive> pages. Nominated topics will be published on the Training Day <http://gcc2015.tsl.ac.uk/training-day/> page as they come in. *Nominations close 6 January*. Topics will be compiled into a uniform list by the GCC2015 Organising Committee <http://gcc2015.tsl.ac.uk/organisers>, and topics will be voted on by the Galaxy Community 12-23 January. Topics will then be selected and scheduled based on topic interest, and the organisers' ability to confirm instructors for each session. Some very popular sessions may be scheduled more than once. The final schedule will be posted before registration opens. Cheers, GCC2015 Organising Committee <http://gcc2015.tsl.ac.uk/organisers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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Problem with Biopython
by Alfredo Guilherme Silva Souza 05 Jan '15

05 Jan '15

Has anyone used the Biopython in Galaxy ? *Traceback (most recent call last):* * File "/home/steve/galaxy-dist/tools/molecular_dynamics/gromacs.py", line 10, in <module>* * import Bio.PDB.PDBParser* *ImportError: No module named Bio.PDB.PDBParser* Researching I saw that I have to work with eggs in the Galaxy. Has anyone done this with Biopython? Is it really necessary? Thanks -- *Alfredo Guilherme da Silva Souza* Distributed Systems and Computer Networks Federal University of São Carlos - UFSCar Contact +55 16 9115-3035 | alfredo.bioinformatics(a)gmail.com <contato(a)gilsonleite.com.br>

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Problem using FastQC in Galaxy
by Waldron, Michael H 05 Jan '15

05 Jan '15

Having a problem with directing FastQC output in Galaxy. User is running a job whose command line looks like this: # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13836_files /proj/galaxy/job_working_directory/010/10467/dataset_13836_files/SRR016862.fastq Job output looks like this: ## odpath=None: No output found in None. Output for the run was: # FastQC cl = /nas02/apps/galaxy-prod/galaxy-dist/tool-data/shared/jars/FastQC/fastqc --outdir=/proj/galaxy/job_working_directory/010/10467/dataset_13827_files /proj/galaxy/job_working_directory/010/10467/dataset_13827_files/SRR016862.fastq Started analysis of SRR016862.fastq Approx 5% complete for SRR016862.fastq Approx 10% complete for SRR016862.fastq Approx 15% complete for SRR016862.fastq Approx 20% complete for SRR016862.fastq Approx 25% complete for SRR016862.fastq Approx 30% complete for SRR016862.fastq Approx 35% complete for SRR016862.fastq Approx 40% complete for SRR016862.fastq Approx 45% complete for SRR016862.fastq Approx 50% complete for SRR016862.fastq Approx 55% complete for SRR016862.fastq Approx 60% complete for SRR016862.fastq Approx 65% complete for SRR016862.fastq Approx 70% complete for SRR016862.fastq Approx 75% complete for SRR016862.fastq Approx 80% complete for SRR016862.fastq Approx 85% complete for SRR016862.fastq Approx 90% complete for SRR016862.fastq Approx 95% complete for SRR016862.fastq Analysis complete for SRR016862.fastq The job_working_directory/010/10467 directory is created, however it is empty. It appears this "odpath" needs to be set somehow? Does anyone know a solution for this? Mike Waldron Systems Specialist ITS - Research Computing Center University of North Carolina at Chapel Hill

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Create a package with binaries
by KRESS Arnaud (ESP) 05 Jan '15

05 Jan '15

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

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Problem using FastQC in Galaxy
by Alfredo Guilherme Silva Souza 05 Jan '15

05 Jan '15

Has anyone used the Biopython in Galaxy ? *Traceback (most recent call last):* * File "/home/steve/galaxy-dist/tools/molecular_dynamics/gromacs.py", line 10, in <module>* * import Bio.PDB.PDBParser* *ImportError: No module named Bio.PDB.PDBParser* Researching I saw that I have to work with eggs in the Galaxy. Has anyone done this with Biopython? Is it really necessary? Thanks -- *Alfredo Guilherme da Silva Souza* Distributed Systems and Computer Networks Federal University of São Carlos - UFSCar Contact +55 16 9115-3035 | alfredo.bioinformatics(a)gmail.com <contato(a)gilsonleite.com.br>

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Creating a new job handler for Galaxy
by Abdulrahman Azab 05 Jan '15

05 Jan '15

Hi Galaxy developers, In our Elixir project (http://www.elixir-europe.org/) Norway, we have five geographically distributed Galaxy instances. Each is working on a local cluster (mostly SLURM). We are planning to interconnect those five clusters using a meta-scheduler ARC (http://www.nordugrid.org/arc/) to achieve load balancing, so that a galaxy job can be reallocated to an external cluster in case that the local cluster is saturated. ARC manages the interconnection very well. What we need is to create a Galaxy job handler for ARC. Is there a general template or interface for a job handler, i.e. for defining job submission commands ... etc.? and how to compile and integrate this new job handler and integrate it into the Galaxy installation? Thank you, Yours sincerely, Abdulrahman Azab Head engineer, ELIXIR.NO / The Genomic HyperBrowser team Department of Informatics, University of Oslo, Boks 1072 Blindern, NO-0316 OSLO, Norway Email: azab(a)ifi.uio.no, Cell-phone: +47 46797339 ---- Senior Lecturer in Computer Engineering Faculty of Engineering, University of Mansoura, 35516-Mansoura, Egypt Email: abdulrahman.azab(a)mans.edu.eg</owa/abdulrahman.azab(a)mans.edu.eg>

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galaxy.tools.parameters.basic.RuntimeValue not str
by Pandori n 05 Jan '15

05 Jan '15

Hi all! Maybe somebody faced with this problem: 1) in my wf used tool with: "u'model_class': u'Conditional', u'type': u'conditional', u'name': u'reference_genome'}], " 2) when i run wf via web - all ok, and on a second step: "Select a reference genome" is "test" (in view details) But, when i run wf via api: param = {u'mapper_easy' :{u'param': u'reference_genome|index', u'value': u'test'}} nuser.workflows.run_workflow(workflow_id=wf_id, dataset_map=dataset_map, params=param, history_id=hist_id) wf started and on a second step is failed... In details: "Select a reference genome" is "<galaxy.tools.parameters.basic.RuntimeValue object at 0x7f5374266850>" Any help is appreciated. Thanks!

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January 2015 Galaxy News!
by Dave Clements 05 Jan '15

05 Jan '15

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