Admin: Martin Čech

gravatar for Martin Čech
Martin Čech ♦♦ 4.9k
Reputation:
4,870
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Trusted
Location:
United States
Last seen:
1 day, 5 hours ago
Joined:
4 years, 10 months ago
Email:
m*****@bx.psu.edu

Galaxy Team member

Posts by Martin Čech

<prev • 876 results • page 1 of 88 • next >
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Comment: C: Sharing history by default between users
... The recommended approach is for admin to create data library and then give users permissions to create/access/manage folders with their data to share ...
written 3 days ago by Martin Čech ♦♦ 4.9k
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Answer: A: Jobs at Galaxy Main https://usegalaxy.org remain in executing (yellow) state for
... This should be remedied and all the jobs should run/finish as expected. Thanks for reporting. ...
written 4 days ago by Martin Čech ♦♦ 4.9k
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Answer: A: How to get data into the Galaxy integrated Jupyter R kernel?
... there should be a `put` and a `get` commandline tools that emulate the python `put()` `get()` functions via @bgruening ...
written 4 days ago by Martin Čech ♦♦ 4.9k
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Answer: C: Jobs not running- Is the main galaxy server down?
... Hello ewilli28! We believe that this post does not fit the main topic of this site. temporary issue For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below, we'll b ...
written 4 days ago by Martin Čech ♦♦ 4.9k
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Comment: C: Uploaded files still being imported ito the history after 48h
... Me and my colleague tested bam uploading extensively in an effort to reproduce your problems - including 20GB and 100GB files - and they seem to work correctly at the moment. Are you sure the FTP transfer finished and the files are the same? Are the sizes on the FTP server and on your disk the same/ ...
written 14 days ago by Martin Čech ♦♦ 4.9k
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Answer: A: Get galaxy terminal sh run.sh
... You are facing a problem described here: https://github.com/galaxyproject/galaxy/issues/6470 The following command in Galaxy's root should get you up to speed: ``` ./.venv/bin/pip uninstall -y uwsgi && ./.venv/bin/pip install --index-url https://wheels.galaxyproject.org/simple --no-cache- ...
written 15 days ago by Martin Čech ♦♦ 4.9k
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Comment: C: publicly available traces/logs
... Application logs are usually private by design, since they always contain non-public information like IPs and such. I doubt anybody would share them with you as is. Parsing them and anonymizing them is a lot of work too and prone to errors. If you precisely and atomically specify what data you want ...
written 18 days ago by Martin Čech ♦♦ 4.9k
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Comment: C: Server only works properly when launched as root, not as galaxy user.
... Check out your configuration at `config/galaxy.yml` and look for non-galaxy-folder paths, maybe something like `tool_dependency_dir ` in https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.yml.sample#L217 ...
written 24 days ago by Martin Čech ♦♦ 4.9k
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Comment: C: Jobs don't run, workflows don't initiate
... Ah, I see, sorry for the misunderstanding. Try modifying the JAVA_OPTIONS in your configuration, not in the tool, as described here: https://docs.galaxyproject.org/en/master/admin/jobs.html?highlight=_java_options#environment-modifications I am not sure that will change the behavior, but it is def ...
written 25 days ago by Martin Čech ♦♦ 4.9k
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Answer: A: Jobs don't run, workflows don't initiate
... This was a bug on our side, which has been fixed today. All the queued jobs should be finished or at least running by now. Sorry for the inconvenience. ...
written 28 days ago by Martin Čech ♦♦ 4.9k

Latest awards to Martin Čech

Scholar 4 days ago, created an answer that has been accepted. For A: administrator e-mail designation through galaxy.yml.sample
Scholar 4 days ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 15 days ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 29 days ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 3 months ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to uninstall package which not appear in installed tools menu?
Scholar 4 months ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 4 months ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 5 months ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 5 months ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 5 months ago, created an answer that has been accepted. For A: the storage problem
Scholar 6 months ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 6 months ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 7 months ago, created an answer that has been accepted. For A: Private vs Public Galaxy: different outcomes following Fastq upload
Scholar 7 months ago, created an answer that has been accepted. For A: the storage problem
Scholar 7 months ago, created an answer that has been accepted. For A: the storage problem
Scholar 8 months ago, created an answer that has been accepted. For A: the storage problem
Scholar 10 months ago, created an answer that has been accepted. For A: How to uninstall package which not appear in installed tools menu?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to uninstall package which not appear in installed tools menu?
Scholar 10 months ago, created an answer that has been accepted. For A: How to uninstall package which not appear in installed tools menu?
Scholar 11 months ago, created an answer that has been accepted. For A: How to uninstall package which not appear in installed tools menu?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: How to uninstall package which not appear in installed tools menu?
Scholar 13 months ago, created an answer that has been accepted. For A: Change colour of datasets in the history pane?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Change colour of datasets in the history pane?
Scholar 20 months ago, created an answer that has been accepted. For A: Change colour of datasets in the history pane?

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