User: Hotz, Hans-Rudolf

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Posts by Hotz, Hans-Rudolf

<prev • 314 results • page 1 of 32 • next >
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Answer: A: What happens to users' jobs when I restart my local Galaxy instance?
... Hi Rokyo The job will get killed resulting in a 'error' state (i.e. red history item). Depending on the actual tool, which was called by the galaxy server, it might 'survive' and finish - but I would not count on this. Regards, Hans-Rudolf ...
written 3 days ago by Hotz, Hans-Rudolf1.8k
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Comment: C: MySQL db connection error or ?
... a few points to check: - it is just '//' in front of "username:password" - try using the full name of the server/host instead of 'localhost' - 'mysqld.sock' should be right, but is the path '/usr/sbin/' correct and just as a comment: why don't you switch from sqlite to PostgreSQL ? Hans-Ru ...
written 4 weeks ago by Hotz, Hans-Rudolf1.8k
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Comment: A: How to update the tool menu
... Hi Lachlan Try removing "integrated_tool_panel.xml" first, before you do a restart. Or re-name it first, then you can easily compare the old and the new tool list. Regards, Hans-Rudolf ...
written 9 weeks ago by Hotz, Hans-Rudolf1.8k
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Comment: C: Can't use cached bed file
... I am glad you solved the problem wrt your next question: It is best to ask a new question (with a different subject). Nevertheless, the quick answer is 'No'. but you need to provide more details. ...
written 3 months ago by Hotz, Hans-Rudolf1.8k
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Comment: C: Can't use cached bed file
... ...that should be visible, if you are logged in as an admin. Anyway, as an alternative, use the reports tool or check directly in the database, e.g.: select command_line from job where id = 1234; ...
written 3 months ago by Hotz, Hans-Rudolf1.8k
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Comment: C: Can't use cached bed file
... The files don't need to be in the tool-data folder (or a sub folder). They can be anywhere. The important think is, that they are listed in the 'loc' file (in your case 'bed_files') with their path. You might also want to check the command galaxy is executing to see whether the path is correct. ...
written 3 months ago by Hotz, Hans-Rudolf1.8k
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Answer: C: Can't use cached bed file
... I assume, you are selecting the bed files via the 'from_data_table' option (see: https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-inputs-param-options) ? and you get the files listed? If so, I guess, the given paths in the data table are not correct? Regards, Hans-Rudolf ...
written 3 months ago by Hotz, Hans-Rudolf1.8k
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Answer: A: Local Galaxy deployment examples
... Hi Sergei It is difficult to give specific advise on how to set up a local installation (for production), as it depends on so many local actors. A good starting point is this doc: https://docs.galaxyproject.org/en/latest/admin/production.html Also, consider joining the Galaxy Developers mailing l ...
written 3 months ago by Hotz, Hans-Rudolf1.8k
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Answer: A: Dot plot between two sequences
... Hi The dots will be the matching sequences: "dottup" (part of EMBOSS) is available on usegalaxy.* Regards, Hans-Rudolf ...
written 3 months ago by Hotz, Hans-Rudolf1.8k
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Comment: C: Problem with new tool definition xml file
... I believe you, that the tool doesn't show up.....my suggestion was 'to restart galaxy and look for the error you get, when it tries to load the tool' If you do that, you will get the following error: "ValueError: An integer is required" well, this is a typical oversight, hence change the line t ...
written 3 months ago by Hotz, Hans-Rudolf1.8k

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