Moderator: Nate Coraor

gravatar for Nate Coraor
Nate Coraor3.1k
Reputation:
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Location:
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Last seen:
1 week, 3 days ago
Joined:
11 years, 5 months ago
Email:
n***@bx.psu.edu

Posts by Nate Coraor

<prev • 324 results • page 1 of 33 • next >
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Answer: A: Job was reported by drmaa as terminal but job state in SLURM is: PENDING, return
... I'm not sure why the drmaa library is considering PENDING jobs as terminal. What version of slurm-drmaa are you using? ...
written 11 days ago by Nate Coraor3.1k
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Comment: C: Requirements for FTP upload
... Ok, let us know if you encounter additional issues. Unfortunately, the only workaround that I'm aware of is for us to disable encryption either fully or partially (which is not well supported) or provide an alternate FTP server that allows such. That said, I'll look in to whether we can set up an s ...
written 20 days ago by Nate Coraor3.1k
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Answer: A: Galaxy moves files prior to job completion
... It looks like you're using the `outputs_to_working_directory` option in `galaxy.ini`? It looks like what's happening here is that Galaxy detects that setting metadata on the job's output datasets has failed and it's trying to do it again on the Galaxy server (`retry_metadata_internally`, which defau ...
written 20 days ago by Nate Coraor3.1k
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Answer: A: Requirements for FTP upload
... Good catch, that port range was indeed a mistake on my part. The actual range is [30000-31000](https://github.com/galaxyproject/usegalaxy-playbook/blob/a71ffea273966efec7805f500beb3edc874d45d0/env/main/group_vars/ftpservers/vars.yml#L53). I've corrected my post. Is that a small enough range to appea ...
written 27 days ago by Nate Coraor3.1k
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Answer: A: cleanup_dataset doesn't free space
... When you run the cleanup scripts, your working directory should be the root of the Galaxy directory, e.g.: cd xxx/galaxy; . ./.venv/bin/activate; python ./scripts/cleanup_datasets/cleanup_datsets.py [args] If your `file_path` in `config/galaxy.ini` is set to a relative path, it will be expecte ...
written 7 weeks ago by Nate Coraor3.1k
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Comment: C: I can't find FreeBayes
... This has been fixed. ...
written 10 weeks ago by Nate Coraor3.1k
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Comment: C: I can't find FreeBayes
... You might want to verify that you are using the same version of FreeBayes as before. ...
written 10 weeks ago by Nate Coraor3.1k
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Comment: C: FileZilla FTP application is not able to retrieve galaxy directory listing
... What's the error message when connecting with implicit FTPS? ...
written 11 weeks ago by Nate Coraor3.1k
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Answer: A: I can't find FreeBayes
... Interesting, it's not showing up for me either, but it's loaded. I'm working on this, but for the moment, you can go directly to the tool with the URL [https://usegalaxy.org/?tool_id=freebayes](https://usegalaxy.org/?tool_id=freebayes), and then using the "Versions" menu at the top to pick 1.0.2.29- ...
written 11 weeks ago by Nate Coraor3.1k
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Answer: A: FileZilla FTP application is not able to retrieve galaxy directory listing
... Is there a firewall at your site that might be interfering? It seems like something - either on the host or on that particular network - is blocking connections. In order to make a passive FTP connection, the FTP client opens a connection to a control channel: port 21 in the case of Explicit FTPS o ...
written 12 weeks ago by Nate Coraor3.1k

Latest awards to Nate Coraor

Teacher 27 days ago, created an answer with at least 3 up-votes. For A: Requirements for FTP upload
Scholar 12 weeks ago, created an answer that has been accepted. For A: FTP Connection Refused
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: FTP Connection Refused
Scholar 10 months ago, created an answer that has been accepted. For A: Tunnel qsub commands
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Errors at http://usegalaxy.org - Follow for details and updates
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Errors at http://usegalaxy.org - Follow for details and updates
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: DynamicDisplayApplicationBuilder error after updating Galaxy to latest_2014.10.0
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Upload To Galaxy Via Ftp
Scholar 3.0 years ago, created an answer that has been accepted. For A: DynamicDisplayApplicationBuilder error after updating Galaxy to latest_2014.10.0
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: When will stampede be accessible through galaxy main?
Scholar 3.3 years ago, created an answer that has been accepted. For A: When will stampede be accessible through galaxy main?
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: When will stampede be accessible through galaxy main?
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Galaxy 101: The first thing you should try do not work...
Centurion 3.7 years ago, created 100 posts.

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