User: Devon Ryan

gravatar for Devon Ryan
Devon Ryan1.9k
Reputation:
1,920
Status:
Trusted
Location:
Germany
Twitter:
dpryan79
Last seen:
1 month, 2 weeks ago
Joined:
3 years, 6 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 • 345 results • page 2 of 35 • next >
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Comment: C: Incorrect dependencies used during job run
... `cd` into one of the job working directories and look at the tool script. It will have a section where it activates the various environments. Run that as the galaxy user, run `hash -r` and then `which samtools`. My guess is that for some reason one or more of the conda packages didn't get installed ...
written 6 months ago by Devon Ryan1.9k
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Comment: C: inquiry about the analysis of a dominant mutant with GALAXY
... You'll need to specify which particular tools in Galaxy you're using, specifically which one you're using to produce the plot you mention. ...
written 6 months ago by Devon Ryan1.9k
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Comment: C: safari can't connect to the server "localhost".
... Did you restart Galaxy after changing the settings? If yes, check the error logs. ...
written 6 months ago by Devon Ryan1.9k
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Comment: C: interval file to fastq conversiosn
... Post a line or two of the interval file. ...
written 8 months ago by Devon Ryan1.9k
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Comment: C: Visualizing BigWig is UCSC genome browser: link not available
... Which Galaxy instance are you using? If you're using the DeepTools2 Galaxy server then this tended not to work, so I think I disabled it (it didn't work due to institute firewall policies). ...
written 8 months ago by Devon Ryan1.9k
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Comment: C: Help with using the multiBam Summary tool - error message
... It looks like the bigWig file is corrupt or empty. ...
written 8 months ago by Devon Ryan1.9k
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Answer: C: Problem with dependencies: Conda/freebayes
... Can you manually create the `__parallel@20170422` conda environment (it should have parallel-20170422 and perl-5.22.0.1)? I'm also running 17.09 and this all installed OK on my instance via conda. What may be happening is that conda is having trouble resolving a dependency for some odd reason (this ...
written 9 months ago by Devon Ryan1.9k
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Answer: C: Why does my GFF3 file not have any exons in the annotation lines read by HTseq-c
... Yes, it's missing exons. You should ask the authors why this is, since that's quite annoying. ...
written 9 months ago by Devon Ryan1.9k
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Comment: C: what i can do with this error
... Please post the actual error message. ...
written 9 months ago by Devon Ryan1.9k
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Answer: A: Can we map fastq files with paired ends using bwa mem on galaxy?
... Yes, bwa-mem can take a paired-end collection. ...
written 9 months ago by Devon Ryan1.9k

Latest awards to Devon Ryan

Scholar 5 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Scholar 9 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Teacher 9 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 10 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Scholar 15 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Scholar 17 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 17 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 20 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 20 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Teacher 21 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 21 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Guru 22 months ago, received more than 100 upvotes.
Supporter 23 months ago, voted at least 25 times.
Scholar 24 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Scholar 2.0 years ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 2.0 years ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 2.0 years ago, created an answer that has been accepted. For A: Specificy runner to use per tool
Scholar 2.0 years ago, created an answer that has been accepted. For C: gtf file error
Scholar 2.0 years ago, created an answer that has been accepted. For C: gtf file error
Scholar 2.1 years ago, created an answer that has been accepted. For C: gtf file error
Centurion 2.1 years ago, created 100 posts.
Scholar 2.2 years ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10
Scholar 2.2 years ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10

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