User: Devon Ryan

gravatar for Devon Ryan
Devon Ryan1.3k
Reputation:
1,300
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Location:
Germany
Twitter:
dpryan79
Last seen:
8 hours ago
Joined:
1 year, 11 months ago
Email:
d*******@gmail.com

Bioinformatician / data manager at the Max Planck Institute for Immunobiology and Epigenetics in Freiburg, Germany. I'm one of the developers for deepTools (among other packages).

Posts by Devon Ryan

<prev • 211 results • page 1 of 22 • next >
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Comment: C: Persisting cron.hourly jobs with my Galaxy-docker-stable instance
... Once again, look at the actual file. You can always edit your crontab (`crontab -e` as root, since that's what it's running as). ...
written 1 day ago by Devon Ryan1.3k
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Comment: C: Persisting cron.hourly jobs with my Galaxy-docker-stable instance
... Regardless, have a look at that file and see what it's doing. ...
written 1 day ago by Devon Ryan1.3k
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Comment: C: How to fix an error on tool loading?
... It needs at least one of the aforementioned .loc files. ...
written 2 days ago by Devon Ryan1.3k
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Comment: C: Persisting cron.hourly jobs with my Galaxy-docker-stable instance
... What's in your hourly cron jobs? Last I checked the container itself doesn't run any cron jobs. ...
written 2 days ago by Devon Ryan1.3k
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Comment: C: Limitations of DAVID pathways
... KEGG itself has been subscription only for the past few years and it's unlikely that DAVID has a license that allows external people to use it. You could email them and ask though. ...
written 5 days ago by Devon Ryan1.3k
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Comment: C: 'print reads' throwing 'eof marker is absent' on my BAM file
... The GATK tools available in Galaxy are not the best practice and I would suggest that you not use them without a good reason. You'd be better served with freeBayes or samtools/bcftools. ...
written 6 days ago by Devon Ryan1.3k
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Answer: A: Limitations of DAVID pathways
... The "hasn't been updated since 2010" thing is no longer the case, it has a new team taking care of it. The common critique applied to DAVID and similar tools is that they're only as good as their underlying databases. DAVID and most other tools use public databases, which can never compete with priv ...
written 6 days ago by Devon Ryan1.3k
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Answer: C: 'print reads' throwing 'eof marker is absent' on my BAM file
... I suggest clicking on the "bug report" button on one of the history items. The most likely cause of this is that the underlying tool is returning a broken file. The error message you're seeing is probably from Galaxy attempting to index it. What are you trying to have `print reads` do? There are li ...
written 7 days ago by Devon Ryan1.3k
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Answer: A: deepTools computeMatrix sorted values WITH gene identifiers
... You want the list of sorted regions, which should include the gene name. ...
written 9 days ago by Devon Ryan1.3k
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Answer: C: htseq-count failed with error no exon found
... I've replied to this on [the main biostars](https://www.biostars.org/p/236997/#237590) site. ...
written 10 days ago by Devon Ryan1.3k

Latest awards to Devon Ryan

Scholar 4 weeks ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
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