User: david.roquis

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david.roquis10
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9 months, 3 weeks ago
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d***********@tum.de

Posts by david.roquis

<prev • 14 results • page 1 of 2 • next >
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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 13 days ago by david.roquis10
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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 13 days ago by david.roquis10 • updated 13 days ago by Dannon Baker3.6k
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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 6 months ago by david.roquis10
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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 6 months ago by david.roquis10 • updated 6 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 7 months ago by david.roquis10
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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 7 months ago by david.roquis10 • updated 7 months ago by Devon Ryan1.7k
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Comment: C: Batch workflow with two different inputs each time?
... Thanks! For some reason, Collection Operations tools where not present in my tool menu, but the problem is now fixed! Sincerely David ...
written 8 months ago by david.roquis10
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Comment: C: Batch workflow with two different inputs each time?
... Hello again! I have been trying to follow your suggestion to build my workflow, but I am blocking at some point. As you explained, I have created a list of of paired datasets, with one "mate" being the vcf file and the other one being the corresponding fastq file. However, while building my workflo ...
written 8 months ago by david.roquis10
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Comment: C: Batch workflow with two different inputs each time?
... Hi, Thanks for this very detailed answer and this workaround! I will give it a try and keep it updated here! Sincerely David ...
written 8 months ago by david.roquis10
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Comment: C: Batch workflow with two different inputs each time?
... Hi Jen and Galaxy Team, Thank you for your very quick answer. I am a biologist with some IT skills, but not really at scripting. It is a reason why I went for Galaxy, as the pipeline scripts left by our previous bioinformatician were not really flexible. I'll ask a friend to see if he can help me w ...
written 8 months ago by david.roquis10

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