User: Devon Ryan

gravatar for Devon Ryan
Devon Ryan1.9k
Reputation:
1,850
Status:
Trusted
Location:
Germany
Twitter:
dpryan79
Last seen:
8 hours ago
Joined:
2 years, 9 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 • 329 results • page 2 of 33 • next >
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Comment: C: Docker Galaxy Job conf file and SLURM
... Add something like `-n 4` to the . That'll make everything default to 4 cores. ...
written 6 weeks ago by Devon Ryan1.9k
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Comment: C: RNA-Seq Alignment too Big for Galaxy?
... Those aren't too big. Are you running this on usegalaxy.org or a different Galaxy server? ...
written 6 weeks ago by Devon Ryan1.9k
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Comment: C: Docker Galaxy Job conf file and SLURM
... Are you using the default `slurm` job runner or have you already changed something in `job_conf.xml`? ...
written 6 weeks ago by Devon Ryan1.9k
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Answer: A: problem of active my history
... If you've permanently deleted it (it has size of 0 and the history items show up as having been permanently deleted) then you can't make it your active history and you can't recover the files. ...
written 6 weeks ago by Devon Ryan1.9k
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Answer: C: Error installing Galaxy locally with Conda environment
... Maybe make your life easier and use the [docker version of Galaxy](https://github.com/bgruening/docker-galaxy-stable). It uses conda for tool dependency resolution and you don't have to bother with all of the setup. ...
written 9 weeks ago by Devon Ryan1.9k
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Answer: C: galaxy with ubuntu on windows
... I suspect you'll have an easier time by just using Docker with the [dockerized version of Galaxy](https://github.com/bgruening/docker-galaxy-stable). Then instead of needing to get all of Galaxy set up, you really only need to get Docker installed. ...
written 10 weeks ago by Devon Ryan1.9k
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Comment: C: multibamsummary vs multibigwigsummary
... Yes, it's more of whatever you're IPing in that area. ...
written 10 weeks ago by Devon Ryan1.9k
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Answer: A: Fastq format to final format
... You don't need to do any conversion, `fastqsanger` is `fastq` with a specific quality encoding. All fastq files produced in the past 5 or so years are "fastqsanger" in Galaxy terminology. ...
written 10 weeks ago by Devon Ryan1.9k
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Comment: C: multibamsummary vs multibigwigsummary
... You can make the bigWig files from whatever you like. It's impossible to tell whether higher signal in a given bin corresponds to greater signal width vs. greater height. It's simply showing a greater average signal. ...
written 11 weeks ago by Devon Ryan1.9k
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Comment: C: SAM-to-BAM (NGS: SAMtools)
... S288C is the reference strain. The genome version of that you're using is `sacCer2`. One can determine this by looking at the chromosome sizes, which match those of `sacCer2`. Note that the only thing the genome is actually used for here is adding the chromosome names and sizes, so even if it weren' ...
written 11 weeks ago by Devon Ryan1.9k

Latest awards to Devon Ryan

Scholar 9 days ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Teacher 9 days ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 4 weeks ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Scholar 6 months ago, created an answer that has been accepted. For A: Docker Galaxy Job conf file and SLURM
Scholar 8 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 8 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 11 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 11 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 12 months ago, created an answer with at least 3 up-votes. For C: Galaxy Tool Unit Test
Scholar 12 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Guru 13 months ago, received more than 100 upvotes.
Supporter 14 months ago, voted at least 25 times.
Scholar 15 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10
Scholar 15 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 15 months ago, created an answer that has been accepted. For A: Specificy runner to use per tool
Scholar 15 months ago, created an answer that has been accepted. For A: Sub groups within galaxy shed tool conf file
Scholar 15 months ago, created an answer that has been accepted. For C: gtf file error
Scholar 15 months ago, created an answer that has been accepted. For C: gtf file error
Scholar 15 months ago, created an answer that has been accepted. For C: gtf file error
Centurion 16 months ago, created 100 posts.
Scholar 17 months ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10
Scholar 18 months ago, created an answer that has been accepted. For A: Unicode error after installing package_python_2_7_10
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Unicode error after installing package_python_2_7_10

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