Moderator: Bjoern Gruening

gravatar for Bjoern Gruening
Bjoern Gruening5.0k
Reputation:
4,990
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Location:
Germany
Website:
https://github.com/bgr...
Twitter:
bjoerngruening
Scholar ID:
Google Scholar Page
Last seen:
20 hours ago
Joined:
4 years, 8 months ago
Email:
b**************@gmail.com

Posts by Bjoern Gruening

<prev • 719 results • page 1 of 72 • next >
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Answer: A: Tools for annotating unknown sequences?
... This pretty much depends on what you want to annotate. But we have recently updated a bunch of Genome annotation tools on https://usegalaxy.eu. See here: https://usegalaxy-eu.github.io/posts/2018/02/11/genome-annotation-reloaded/plain.html ...
written 23 hours ago by Bjoern Gruening5.0k
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Answer: A: Where is Snippy?
... Hi, which server are you using. Try this one here: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/snippy/snippy/3.2 Cheers, Bjoern ...
written 23 hours ago by Bjoern Gruening5.0k
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Comment: C: Using Conda to resolve dependencies
... Everything that is commented out, comes preconfigured with the variable in the commented out section. ...
written 8 days ago by Bjoern Gruening5.0k
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Comment: C: Using Conda to resolve dependencies
... Ah, now I got it. `tool_dependency_dir` is another variable in your galaxy.yml file, that points you probably to /home/galaxy/galaxy/database/dependencies ...
written 10 days ago by Bjoern Gruening5.0k
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Answer: A: Install common tools into expected locations
... Hi Rob, there are multiple way how you can install hundreds of tools into Galaxy at once. Please read the documentation of [ephemeris][1]. Example yaml file of tools you can find in either Galaxy Docker flavors (e.g. https://github.com/bgruening/docker-galaxy-ngs-preprocessing/blob/master/ngs_prepr ...
written 10 days ago by Bjoern Gruening5.0k
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Answer: A: Using Conda to resolve dependencies
... With a recent Galaxy version you don't need to configure anything to enable Conda. Galaxy will install miniconda3 for you in ` /_conda`. Can you check you see something in this path, after have run `./run.sh` at least once. ...
written 10 days ago by Bjoern Gruening5.0k
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Answer: A: Featurecounts' added built-in annotations
... Thanks to Maria Doyle, Application and Training Specialist at Peter MacCallum Cancer Centre! https://www.petermac.org/research/core-facilities/research-computing-facility ...
written 10 days ago by Bjoern Gruening5.0k
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Answer: A: Arabidopsis genome to HiSat2
... Until we align all our reference genomes, you can use https://usegalaxy.eu where I recently installed the A. thaliana genome. ...
written 16 days ago by Bjoern Gruening5.0k
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Comment: C: Deseq2 error in Galaxy
... How did you installed DESeq2? Can you check which version of Galaxy is installed in this container? http://localhost:8080/api/version for example should tell you, assuming localhost:8080 is were your container is running. ...
written 22 days ago by Bjoern Gruening5.0k
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Comment: C: Unable to install tools from Tool Shed in local Galaxy Docker instance
... Which version of the Docker Galaxy container is this? ...
written 4 weeks ago by Bjoern Gruening5.0k

Latest awards to Bjoern Gruening

Scholar 10 days ago, created an answer that has been accepted. For A: Featurecounts' added built-in annotations
Scholar 5 weeks ago, created an answer that has been accepted. For A: Adding admin users
Scholar 5 weeks ago, created an answer that has been accepted. For A: Adding admin users
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Popular Question 4 months ago, created a question with more than 1,000 views. For Announcement: Galaxy Docker Images
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Adding admin users
Popular Question 5 months ago, created a question with more than 1,000 views. For Join The Homer Galaxy Wrapper Development!
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Adding admin users
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Appreciated 9 months ago, created a post with more than 5 votes. For Announcement: Galaxy Docker Images
Popular Question 10 months ago, created a question with more than 1,000 views. For Announcement: Galaxy Docker Images
Popular Question 11 months ago, created a question with more than 1,000 views. For Announcement: Galaxy Docker Images
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Adding admin users
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Scholar 21 months ago, created an answer that has been accepted. For A: ngs.plot on use galaxy.org
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Popular Question 23 months ago, created a question with more than 1,000 views. For Announcement: Galaxy Docker Images
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: ngs.plot on use galaxy.org

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