User: y.hoogstrate

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y.hoogstrate420
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Posts by y.hoogstrate

<prev • 70 results • page 1 of 7 • next >
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Answer: A: Data managers tool: the content of data table disappear after restart Galaxy
... Galaxy makes clones of these loc files for each revision of each installed tool and does not write content always to the loc file directly in ./tool-data. In older versions of Galaxy it was possible to find all corresponding loc files via the web interface but this has disappeared some time ago. Any ...
written 13 days ago by y.hoogstrate420
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Answer: A: Data managers tool: the content of data table disappear after restart Galaxy
... This does not sound like normal Galaxy behaviour. Did you test this in planemo or in a Galaxy instance? Galaxy usually writes to flat LOC files and as far as I know there is no mechanism that automatically reverts or resets. Is the name of the loc file not used by others tools maybe? Does your file ...
written 14 days ago by y.hoogstrate420
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Answer: A: BAM files fail to be recognized
... Those are SAM files, not BAM files. Can you convert (revert?) them with 'SAM-to-BAM convert SAM to BAM' and see if that works out for you? ...
written 20 days ago by y.hoogstrate420
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Answer: A: STAR in multiple threads faces issues in opening genome file
... how much memory do you have in that machine? The Galaxy wrapper has set `--genomeLoad NoSharedMemory` (default STAR option). The consequence is that running two jobs in parallel, makes two copies of the reference genome (~30gb) in the RAM. Could this have anything to do with it? ...
written 9 weeks ago by y.hoogstrate420
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Answer: A: STAR in multiple threads faces issues in opening genome file
... Do you use references genomes from history or from Galaxy's cache and are you running STAR on identical or Different references? ...
written 9 weeks ago by y.hoogstrate420
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Comment: C: User Tool Does Not Initialize
... This is where work starts to become fun ;) ...
written 3 months ago by y.hoogstrate420
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Comment: C: User Tool Does Not Initialize
... Did you configure it in `./config/tool_conf.xml` with the correct PATH (relaltive to ./tools/, and the XML within there? ) or install via a toolshed? ...
written 3 months ago by y.hoogstrate420
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Answer: A: User Tool Does Not Initialize
... ``` Phylip format AXT format ``` This needs options - https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-inputs-param-option Phylip format AXT format ...
written 3 months ago by y.hoogstrate420
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Answer: A: Changing the command syntax of a tool in xml (changed are not applied)
... Planemo makes development very easy: http://galaxyproject.github.io/training-material//Dev-Corner/slides/tool_integration#41 ...
written 3 months ago by y.hoogstrate420
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Comment: C: User Tool Does Not Initialize
... I can interpret your question in 2 ways: (1) `planemo serve` starts, but does not load your tool. This usually means the tool is not correct. What does `planemo lint` tell you? If you're stuck, please drop the latest version of your tool XML and i'll have a quick look at it. (2) `planemo serve` star ...
written 3 months ago by y.hoogstrate420

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