Moderator: Bjoern Gruening

gravatar for Bjoern Gruening
Bjoern Gruening5.0k
Reputation:
5,030
Status:
Trusted
Location:
Germany
Website:
https://github.com/bgr...
Twitter:
bjoerngruening
Scholar ID:
Google Scholar Page
Last seen:
5 days, 15 hours ago
Joined:
4 years, 10 months ago
Email:
b**************@gmail.com

Posts by Bjoern Gruening

<prev • 722 results • page 1 of 73 • next >
1
vote
2
answers
62
views
2
answers
Answer: A: Local Galaxy error in Create DBKey and Reference Genome
... I would also recommend to not sort with the GATK option. Also try a very tiny genome if you can. It all sounds to me that you are running out of memory. Have you looked at using the CVMFS reference genome, which the community is offering? ...
written 5 days ago by Bjoern Gruening5.0k
1
vote
1
answer
53
views
1
answers
Answer: A: View RNA Structure Prediction Results
... Hi, I do not know the "Iterative Mapping to Get RT Stops to Reactivity Calculation to RNA Structure Prediction" workflow, but if you have a EPS files as output, you can use Galaxy charts module to display the rna_eps filetype with the dot-plot module for example. Which datatype do you have as out ...
written 9 days ago by Bjoern Gruening5.0k
1
vote
2
answers
113
views
2
answers
Answer: A: Please put Xenopus laevis genome on Galaxy
... Xenopus laevis should be available at https://usegalaxy.eu. ...
written 7 weeks ago by Bjoern Gruening5.0k
0
votes
2
answers
83
views
2
answers
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 9 weeks ago by Bjoern Gruening5.0k
2
votes
1
answer
151
views
1
answers
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 9 weeks ago by Bjoern Gruening5.0k
0
votes
1
answer
112
views
1
answers
Comment: C: Using Conda to resolve dependencies
... Everything that is commented out, comes preconfigured with the variable in the commented out section. ...
written 10 weeks ago by Bjoern Gruening5.0k
0
votes
1
answer
112
views
1
answers
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 weeks ago by Bjoern Gruening5.0k
0
votes
1
answer
64
views
1
answers
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 weeks ago by Bjoern Gruening5.0k
1
vote
1
answer
112
views
1
answers
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 weeks ago by Bjoern Gruening5.0k
1
vote
2
answers
185
views
2
answers
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 weeks ago by Bjoern Gruening5.0k

Latest awards to Bjoern Gruening

Scholar 9 weeks ago, created an answer that has been accepted. For A: Featurecounts' added built-in annotations
Scholar 10 weeks ago, created an answer that has been accepted. For A: Featurecounts' added built-in annotations
Scholar 3 months ago, created an answer that has been accepted. For A: Adding admin users
Scholar 3 months ago, created an answer that has been accepted. For A: Adding admin users
Scholar 4 months ago, created an answer that has been accepted. For A: Adding admin users
Popular Question 6 months ago, created a question with more than 1,000 views. For Announcement: Galaxy Docker Images
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Adding admin users
Popular Question 7 months ago, created a question with more than 1,000 views. For Join The Homer Galaxy Wrapper Development!
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Adding admin users
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Adding admin users
Appreciated 11 months ago, created a post with more than 5 votes. For Announcement: Galaxy Docker Images
Popular Question 12 months ago, created a question with more than 1,000 views. For Announcement: Galaxy Docker Images
Popular Question 13 months ago, created a question with more than 1,000 views. For Announcement: Galaxy Docker Images
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Adding admin users
Appreciated 19 months ago, created a post with more than 5 votes. For A: Deploying galaxy instances using docker
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Adding admin users
Scholar 19 months ago, created an answer that has been accepted. For A: Adding admin users
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Galaxy via Docker?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Galaxy via Docker?
Appreciated 21 months ago, created a post with more than 5 votes. For A: Deploying galaxy instances using docker
Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: Deploying galaxy instances using docker
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Creating Appropriate Tool Dependencies for Custom Tool in Galaxy
Scholar 23 months ago, created an answer that has been accepted. For A: ngs.plot on use galaxy.org
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Creating Appropriate Tool Dependencies for Custom Tool in Galaxy
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Announcement: Galaxy Docker Images

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 84 users visited in the last hour