July 2017 - galaxy-dev - lists.galaxyproject.org

internal server error when creating or editing a workflow
by Nadia Goué 20 Jul '17

20 Jul '17

Dear Galaxy list, I have installed Galaxy 17.05 locally and I run into an internal servor error while trying to create a workflow and also when I tried to edit an existing workflow created from history. The log file says : xxx/galaxy/.venv/local/lib/python2.7/site-packages/sqlalchemy/orm/relationships.py:1404: SAWarning: Got None for value of column stored_workflow.id; this is unsupported for a relationship comparison and will not currently produce an IS comparison (but may in a future release) "(but may in a future release)" % column) 127.0.0.1 - - [20/juil./2017:11:13:15 +0200] "POST /workflow/create HTTP/1.1" 500 - "http://localhost:8080/workflow/create" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:54.0) Gecko/20100101 Firefox/54.0" Error - <type 'exceptions.AttributeError'>: 'module' object has no attribute '_magic_number' URL: http://localhost:8080/workflow/create File 'xxx/galaxy/.venv/local/lib/python2.7/site-packages/mako/template.py', line 381 in _compile_from_file if module._magic_number != codegen.MAGIC_NUMBER: AttributeError: 'module' object has no attribute '_magic_number' The other options (run, copy, delete ..) in workflow are working correctly. May you help, please. Thanks, Nadia

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How to install Charts in command line ?
by Steven Shen 19 Jul '17

19 Jul '17

Hi all， Cytoscape, Bar diagram(NVD3), Horizontal(NVD3) , and other NVD3 visualization tools are working good on my local galaxy except the jqplots, such as Box plot, Discrete Histogram, with error "This visualization requires the 'charts' tool. Please make sure it is installed." It seems i need to install Charts first. Actually Charts could be installed from the Tool Shed through the Admin Interface, but it failed sometimes as the bad network. so is there any doc about installing Charts/tools through command line? Thank you. Steven

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Adding a visualization plugin to a galaxy local toolshed
by Lisa Perus 18 Jul '17

18 Jul '17

Hi everybody, I am currently working on a galaxy visualization plugin which I would like to share with my colleagues. As it stands, they devised a local toolshed where I can upload my tools and which works very well for uploading tools with their wrappers. However, I have no idea how to upload a visualization plugin so that they can directly install it from the admin menu. I tried looking for answers but have not found a solution yet. Any advice is welcome! Cheers!

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Bugfix - Summary Statistics Script - Python incompatibility
by Previti 14 Jul '17

14 Jul '17

Dear all, I hope this can be of use to somebody... We were having problems with the Summary Statistics Tools /galaxy/tools/stats/gsummary.py As indicated there is a dependency on rpy2 (Version 2.7.8), which requires python 3.5 and comes into conflict with the qsummary.py which uses 2.* Change Line 63: tmp_file = tempfile.NamedTemporaryFile( 'w+b' ) to tmp_file = tempfile.NamedTemporaryFile( 'w+' ) Then it'll work. Cheers, Christopher -- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4434 christopher.previti(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist. Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung. Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.

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inconsistent state set for workflow submissions [using bioblend]
by Aarthi Mohan 13 Jul '17

13 Jul '17

Hi all, I have a local galaxy instance with basic configuration, and automated workflow submission to galaxy using script written with bioblend. Steps within the script: - step1: data upload - step2: dataset_collection creation - step3: workflow submission - step4: every 5 minutes, poll galaxy for the history status; if state == "ok", workflow execution was successful - step5: download the datasets marked available. In my case, when I do a workflow submissions in parallel with different datasets, the status is immediately set to "ok" for few of them after dataset upload and control returns (but galaxy has "queued" the execution when checked from UI). So for these submissions, although it did not fail or raise error, the status is misleading. I didn't find anything strange happening from the galaxy logs as well My question specifically are, 1. Am I correct in using the "*state*" from the following call to say that the execution has done? It has worked for the successfully completed submissions. > historyClient.get_status(history_id)['state'] 2. Should I use a production setup? Strangely, none of these jobs fail and I can see them finishing in the UI, except that their "*state*" is set to "ok" and hence the script ends. Appreciate your thoughts in this. Galaxy version 15.03. Thanks for your help! Best regards, Aarthi

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Cleaning up old exported histories
by Lance Parsons 13 Jul '17

13 Jul '17

I’m running Galaxy on a CentOS6 server, and thus I don’t have the required version of Postgres available to use Nate’s |scripts/pgcleanup.py| script. One major addition in that script is to cleanup old exported history files. Does anyone have any advice, tips, (or scripts) that would help me clean those up? In general, I’m running into disk issues with my Galaxy server and I’d like to try and tighten up disk usage where ever I can. Thanks in advance. -- Lance Parsons - Scientific Programmer Carl C. Icahn Laboratory - Room 136 Lewis-Sigler Institute for Integrative Genomics Princeton University

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problem with column options
by fabien gogé 13 Jul '17

13 Jul '17

Dear All, I try to column options for a param linked to a dataset contained in my history. The first column of my dataset contains sample names. I want it propose me all sample names contained in my dataset. It work when the dataset has few columns but it doesn't work when my dataset has a lot of columns.Someone has a solution? <param name="ysel" type="select" label="enter sample name(s)" multiple="true"> <options from_dataset="Xdata"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> Thank you for help, -- Fabien Gogé UMR ITAP Irstea - SupAgro Information – Technologies – Analyse environnementale – Procédés agricoles Research Group ITAP Irstea - SupAgro Information – Technologies – environmental Analysis – agricultural Processes Irstea BP 5095 ; 34196 MONTPELLIER Cedex 1 ; FRANCE Tel: +33 (0)4 67 16 65 02

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Issue with SLURM-DRMAA
by Dawes, Gwen 12 Jul '17

12 Jul '17

Hi folks, I just had a bit of an interesting problem with Galaxy. We have a configuration whereby work is submitted to our friendly local SLURM cluster via DRMAA. However, the PSNC base version is too old to be able to parse the more modern slurm configs, and was repeatedly failing to submit, stating that it was unable to parse slurm.conf. The updated version of this library by natefoo ( https://github.com/natefoo/slurm-drmaa ) using the multicluster branch works perfectly for submitting to a more modern SLURM, but this isn't referenced at the Admin/Config/Cluster page on galaxyproject.org . Can someone update this information? Thanks!

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tool and planemo problems
by Matthias Bernt 12 Jul '17

12 Jul '17

Dear list, In order to test the job resubmission feature I wrote a little tool for galaxy that just wastes a specified (minimum) time and memory (using different programming languages) for testing the new DRMAA job runner that I wrote. When linting it with planemo seemingly all tests are successful, but in the end I still get a fail -- verbose mode is also of no help here. Applying linter tests... CHECK .. CHECK: 7 test(s) found. Applying linter output... CHECK .. INFO: 1 outputs found. Applying linter inputs... CHECK .. INFO: Found 3 input parameters. Applying linter help... CHECK .. CHECK: Tool contains help section. .. CHECK: Help contains valid reStructuredText. Applying linter general... CHECK .. CHECK: Tool defines a version [0.1.0]. .. CHECK: Tool defines a name [Waste time and memory]. .. CHECK: Tool defines an id [sleepwaste]. .. CHECK: Tool targets 16.01 Galaxy profile. Applying linter command... CHECK .. INFO: Tool contains a command. Applying linter citations... WARNING .. WARNING: No citations found, consider adding citations to your tool. Applying linter tool_xsd... CHECK .. INFO: File validates against XML schema. Failed linting The test of the tool are all successful. Any ideas what is wrong? Once the problems are solved, would such a tool also be useful in the toolshed? Cheers, Matthias -- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt(a)ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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Issues with "bamtools split", running jobs don't show up in history (and fail after several hours)
by Previti 12 Jul '17

12 Jul '17

Dear all, I've been trying to properly install the "BAMTools split" tool in our local DKFZ-Galaxy instance, but it doesn't work properly. The strange thing is that you can launch a bamtools splitter job on our cluster, but it never shows up in the history...until it fails with following "error": "tool error An error occurred with this dataset: Unable to finish job" All versions (Galaxy, bamtools 2.4.0,samtools 1.3.1) are up to date and this is what I installed: Repository bamtools_split Name: bamtools_split Owner: devteam Synopsis: Tool for splitting BAM files Detailed description: Utility for splitting BAM files. It is based on BAMtools suite of tools by Derek Barnett. Content homepage: https://github.com/pezmaster31/bamtools Development repository: https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections… Revision: 2:e2c1b62e1db1 Thanks and best regards, Christopher -- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4434 christopher.previti(a)dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist. Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung. Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.

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