User: Hotz, Hans-Rudolf

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Posts by Hotz, Hans-Rudolf

<prev • 312 results • page 2 of 32 • next >
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Answer: A: Problem with new tool definition xml file
... Hi The whitespace character in the name attribute are most like the culprit. The name is used as variable in the command line. Also, the type="data_meta" only works as an attribute for 'filter', as far as I know (for full details see: https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-i ...
written 11 weeks ago by Hotz, Hans-Rudolf1.8k
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Answer: A: "Upload" of files > 2GB into Galaxy
... Hi Have a look at Galaxy Data Libraries (see: https://galaxyproject.org/data-libraries/ ). You can upload data with the option: "Link files instead of copying" Hope this helps Regards, Hans-Rudolf ...
written 3 months ago by Hotz, Hans-Rudolf1.8k
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Answer: A: Problem updating Galaxy 18.01 to 18.05 when switching from .ini to .yaml admin c
... Hi I don't think converting your 'galaxy.ini' file to a yaml file is related to this error. It rather looks to me, as if you have modified the 'galaxy.ini.sample' ? I suggest to re-name 'galaxy.ini.sample' (eg: 'galaxy.ini.sample.copy') and try the update again Hans-Rudolf ...
written 4 months ago by Hotz, Hans-Rudolf1.8k
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Answer: A: Rscripts warning, the results error
... Hi Have a look at this similar question: "R job in galaxy" ( https://biostar.usegalaxy.org/p/17251/#17309 ) Regards, Hans-Rudolf ...
written 4 months ago by Hotz, Hans-Rudolf1.8k
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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 5 months ago by Hotz, Hans-Rudolf1.8k
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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 8 months ago by Hotz, Hans-Rudolf1.8k
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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 8 months ago by Hotz, Hans-Rudolf1.8k
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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 8 months ago by Hotz, Hans-Rudolf1.8k
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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 9 months ago by Hotz, Hans-Rudolf1.8k
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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 9 months ago by Hotz, Hans-Rudolf1.8k

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