User: david.roquis

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david.roquis30
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2 months, 3 weeks ago
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1 year, 2 months ago
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Posts by david.roquis

<prev • 18 results • page 1 of 2 • next >
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Answer: A: No module named Galaxy when running an old tool (PeakRanger)
... Dear Hans-Rudolf Thank you for your message. I was able to solve the issue in a very unorthodox way. I will describe it here in case some people want to use this tool and face the same problem as I have. 1. First of all, the link to download the tool in "tool_dependencies.xml" is obsolete. As an ...
written 3 months ago by david.roquis30
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No module named Galaxy when running an old tool (PeakRanger)
... Dear Galaxy Community I have recently installed PeakRanger from the Toolshed. I struggled a bit because the wrapper is old, the link to download the dependency was not working (in tool_dependencies.xml), and there were a lot of identation problems with the python wrapper called to execute the tool ...
python galaxy peakranger written 3 months ago by david.roquis30
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Answer: A: Galaxy stalled at startup when "Loading tool panel finished"
... Hi, Sorry for my late answer. I finally figured out what the problem was and it was absolutely not related to Galaxy. It was a faulty disk controller that was messing up. Once fixed, galaxy was working normally agai. Thanks for your help. ...
written 3 months ago by david.roquis30
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Galaxy stalled at startup when "Loading tool panel finished"
... Dear Galaxy Community I have a small production instance of galaxy, installed following the tutorials from the galaxy team (using PostGres, NGINX, supervisord, virtualenv, etc.). Lately, I noticed that my galaxy was slow and laggy. Sometimes, it would not even refresh properly. I decided to restart ...
galaxy startup tool panel written 4 months ago by david.roquis30
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Comment: C: HTML display problem on Galaxy v17.09 with Bismark Pretty Report
... Hi Dannon, Thanks for your very fast answer. I am the Galaxy Admin for my group, but a very basic one ;) I have followed your suggestion, and whitelisted Bismark Pretty Report tool. However, when I now click on any link from any report datatset for visualisation, I get a 404 not found error. The d ...
written 5 months ago by david.roquis30
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HTML display problem on Galaxy v17.09 with Bismark Pretty Report
... Dear Galaxy Community Since my recent upgrade to Galaxy v17.09 (from version 17.05), I am having some issues with the tool "Bismark Pretty Report", from the package Bismark v7 2017-05-06, on the toolshed. This tool generates an HTML report which can normally be viewed in the browser. Clicking on t ...
galaxy html bismark written 5 months ago by david.roquis30 • updated 5 months ago by Dannon Baker3.7k
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Comment: C: Attribute error when running some tools after updating to galaxy 17.05
... Hi Dan, Thanks for this very quick answer. I have applied the fix, and it now works flawlessly! Sincerely David ...
written 11 months ago by david.roquis30
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Attribute error when running some tools after updating to galaxy 17.05
... Dear Galaxy Community, I recently update my cluster-oriented local instance of Galaxy from version 17.01 to 17.05. Since then, I have faced an issue with some of my tools (such as bismark methylation extractor, which I got from the toolshed). Galaxy is unable to finish any of the jobs with this too ...
galaxy software error attributeerror written 11 months ago by david.roquis30 • updated 11 months ago by Daniel Blankenberg ♦♦ 1.7k
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Comment: C: Issue with ${GALAXY_SLOTS} and SGE cluster
... It works! Thanks a lot for your very precise,quick and efficient answer! I need to be more careful when working with XML code in the future. ...
written 12 months ago by david.roquis30
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Issue with ${GALAXY_SLOTS} and SGE cluster
... Dear Galaxy Community, I have been trying to configure my job_conf.xml for a cluster usage. We are working with Son of the GRID ENGINE (SGE) v8.1.9, which has a default installation/configuration. I have no problem submitting jobs from galaxy to SGE. However, the ${GALAXY_SLOTS} variable from var ...
galaxy cluster job_conf.xml galaxy_slots sge written 12 months ago by david.roquis30 • updated 12 months ago by Devon Ryan1.9k

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