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genome upload
by Marion Cerri 25 Jul '17

25 Jul '17

To whom it concerns, I am Marion Cerri, post doc in the Parniske’s lab, in Munich. I am working with ChIP-seq data in the moment. I would like to use the Lotus japonicus (version 3.0) for mapping reads, but the genome is not available on galaxy. Would it be possible to upload it ? Do I have to provide the file to you, and if so in fasta format ? Thanks in advance Best Regards Marion Cerri

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Uncaught Error When Installing Tools From Toolshed
by William, Van Der Pol 24 Jul '17

24 Jul '17

Hello All, I have recently cloned and installed a clean version of Galaxy. I installed a tool from the toolshed and Galaxy says it is properly installed, however when I try to open the tool in the main page all I see is an "Uncaught Error" message. Does anyone have any ideas on what is causing this or at least how I can get a more telling error message? Thanks -Liam

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Creating a tool dependency packages
by Delisle Lucille 24 Jul '17

24 Jul '17

Dear Galaxy list, I do not know if it is the right place to ask my question. I would like to create a tool dependency package for numexpr (a python library). I tried to do it taking examples from different tool dependency packages from iuc for example. I added my repository to the testtoolshed but when I tried to install it. The directory lib/python of my tool is empty. My repository is : package_python_2_7_numexpr_2_6_2<https://testtoolshed.g2.bx.psu.edu/repository/browse_repository?id=23c1f7fe…> The big difference I see between the one from iuc and mine is the url: For example, for pybigwig, the URL is : https://pypi.python.org/packages/source/p/pyBigWig/pyBigWig-0.1.9.tar.gz For my library numexpr I could not find such a url so I put the one I thought would be the good one: https://pypi.python.org/packages/31/43/7777ab9535c416faabd1865453389260fdad… Thank you very much for your help, Lucille Delisle, PhD PostDoc Duboule Lab Laboratory of Developmental Genomics EPFL SV ISREC UPDUB SV 2843 Station 19 CH-1015 Lausanne Tel : +41 21 693 97 08

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Galaxy @ ISMB/ECCB/BOSC 2017: Talks, posters, dinner, BoF, and tutorial
by Dave Clements 20 Jul '17

20 Jul '17

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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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