User: Hotz, Hans-Rudolf

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Switzerland
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Joined:
8 years, 3 months ago
Email:
h**@fmi.ch

Posts by Hotz, Hans-Rudolf

<prev • 298 results • page 1 of 30 • next >
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Answer: C: Creating simple tool to downsample sam files, doesn't complete
... Hi "$output1" is missing in the command tag if your tool writes to stdout, then you should have something like: downsample_sam.py '$pvalue' '$input' > $output1 if your tool expects a particular option (like: -outfile), then you should have something like: downsample_sam.py '$pvalue' '$in ...
written 26 days ago by Hotz, Hans-Rudolf1.7k
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Answer: C: No module named Galaxy when running an old tool (PeakRanger)
... Hi David Have you tried setting "preserve_python_environment = legacy_only" in galaxy.ini ? and list your tool in ~/lib/galaxy/tools/__init__.py : "GALAXY_LIB_TOOLS_UNVERSIONED = [..." (# Tools that require Galaxy's Python environment to be preserved.) Regards, Hans-Rudolf ...
written 3 months ago by Hotz, Hans-Rudolf1.7k
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Answer: A: problem for run.sh in galaxy
... Hi "socket.error: [Errno 98] Address already in use" is the key in this error message. - are you sure, Galaxy is not already running? make sure, you kill it before you execute run.sh again - or is there another 'service' running on this port? you might need to change the port number in the gala ...
written 4 months ago by Hotz, Hans-Rudolf1.7k
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Answer: A: tools, uploading, clusters and destinations
... Hi Just by comparing with our job_config.xml file, I suggest: Regards, Hans-Rudolf ...
written 4 months ago by Hotz, Hans-Rudolf1.7k
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Comment: C: old version galaxy update
... Hi Jane two comments first: - make a backup of your datasets! and set up an automatic backup system for the future. - although MySQL is (still) supported ( https://docs.galaxyproject.org/en/latest/admin/production.html ), I recommend to switch to PostgreSQL eventually (it is a pain, but it is d ...
written 4 months ago by Hotz, Hans-Rudolf1.7k
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Answer: A: old version galaxy update
... Hi Jane In theory, an update should be possible despite the fact that Galaxy has changed from mercurial to git in 2015. Have a look at: https://galaxyproject.org/develop/source-code/#How_to_migrate_a_Galaxy_instance_from_Mercurial_Bitbucket_to_Git_GitHub Once you have changed, you can then do the ...
written 4 months ago by Hotz, Hans-Rudolf1.7k
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Answer: A: How to prevent parsing ">" into "__lt__" in Galaxy wrapper
... Hi Marija Special characters are sanitized for security purposes. See: ~/lib/galaxy/util/__init__.py for all the mapped characters. Have a look at: https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-inputs-param-sanitizer for ways to handle this on a per tool basis. However, keep in mi ...
written 5 months ago by Hotz, Hans-Rudolf1.7k
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Comment: C: Workflow in Galaxy
... just double checking: are you logged in ? Regards, Hans-Rudolf ...
written 5 months ago by Hotz, Hans-Rudolf1.7k
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Comment: C: New data type
... "class ibd(_Binary ): " is the "_" a typo in your mail? what happens if you remove the " subclass="true" " ...
written 5 months ago by Hotz, Hans-Rudolf1.7k
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Comment: C: New data type
... ...but can you manually set the format to ibd for a existing history item or using the upload tool? ...
written 5 months ago by Hotz, Hans-Rudolf1.7k

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