User: Wolfgang Maier

gravatar for Wolfgang Maier
Reputation:
440
Status:
Trusted
Location:
Germany
Last seen:
2 days, 12 hours ago
Joined:
4 years, 5 months ago
Email:
w*************@biologie.uni-freiburg.de

Posts by Wolfgang Maier

<prev • 50 results • page 2 of 5 • next >
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Answer: A: Tools not running on local Galaxy
... Hi Monika, which tools are you trying to use? Are they declaring their requirement like this (in the tool wrapper .xml files): python3 ? In addition, I just checked the toolshed recipe for the package_python_3_4 installation and I think it does not automatically make the installed zlib available ...
written 14 months ago by Wolfgang Maier440
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Comment: C: SNAP Aligner errors via MIMoDd
... MiModD has its own [forum][1] for asking questions like this. You can also post there via email to mimodd@googlegroups.com. In general, this should be the place to turn to if you suspect something is wrong with MiModD itself, while this forum here is for asking questions about Galaxy. As another not ...
written 15 months ago by Wolfgang Maier440
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Comment: C: VCF-VCFintersect error - invalid literal for int() with base 10: 'false'
... Hi Jen, I filed the report. Thanks, Wolfgang ...
written 17 months ago by Wolfgang Maier440
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Comment: C: VCF-VCFintersect error - invalid literal for int() with base 10: 'false'
... Hi Jen, I don't think this is a problem with the input file. I just tried the tool on main and can confirm that it gives the above error, but to me it looks like a bug in parsing the tool parameters. When I enable advanced options for the tool I'm getting a slightly different error: ValueError: inva ...
written 17 months ago by Wolfgang Maier440
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Comment: C: Problem with cloudmap workflow
... Hi Felix, here's your data replotted on our MiModD NacreousMap server => http://mapping-by-sequencing.vm.uni-freiburg.de:8080/u/wolma/h/felix. See my answer to Wenming in [this related post][1] for more information. Best, Wolfgang [1]: https://biostar.usegalaxy.org/p/17389/ ...
written 21 months ago by Wolfgang Maier440
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Answer: A: Eerror with cloudmap workflow
... I guess, the long, technical answer to your question is that the Hawaiian SNP mapping tool from the Tool Shed is not completely functional. It misses a requirement for R in its .xml. If this diagnosis is correct, it needs a fix in the Tool Shed. The good news is that your run still generated correc ...
written 21 months ago by Wolfgang Maier440
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Answer: A: "No such file or directory" when using mpileup
... Apart from Jen's comments, is bcftools available in your $PATH? The error you are seeing seems to be caused by Galaxy trying to index the file after its been created. In the case of a BCF file, I think it relies on the bcftools index command to do so. ...
written 2.3 years ago by Wolfgang Maier440
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Answer: A: Problems converting a file to FASTA
... Do not believe what notepad shows you. Notepad is a really, really basic editor that cannot handle UNIX-style newlines ('\n'),  but only Windows ones ('\r\n'). What does the content look like in Galaxy? Try to open your file with any other editor and most likely the file's content will look just f ...
written 2.3 years ago by Wolfgang Maier440
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Comment: C: Local galaxy is not run on new Mac OSX (El capitan)
... Ah, this is *different*. The original error is gone, but that revealed a new one in /Users/jaeilhan/Downloads/galaxy-dev/eggs/kombu-3.0.24-py2.7.egg/kombu/five.py . That file suffers from the exact same problem as the previous one so modify it like you did before. Hope that is it. ...
written 2.4 years ago by Wolfgang Maier440
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Comment: C: Local galaxy is not run on new Mac OSX (El capitan)
... Unfortunately, I do not have access to our El Capitan test machine right now to verify this. Can you try to change the line again and post the error message if it appears again? I would be surprised if it's the same as above. ...
written 2.4 years ago by Wolfgang Maier440

Latest awards to Wolfgang Maier

Scholar 8 days ago, created an answer that has been accepted. For A: Fetch Sequences for multiple datasets
Popular Question 7 months ago, created a question with more than 1,000 views. For importing gzipped files without having them decompressed
Scholar 2.3 years ago, created an answer that has been accepted. For A: Fetch Sequences for multiple datasets
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: GALAXY_SLOTS not working
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: GALAXY_SLOTS not working
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Can't get admin right in Galaxy local
Scholar 3.3 years ago, created an answer that has been accepted. For A: Fetch Sequences for multiple datasets
Scholar 3.5 years ago, created an answer that has been accepted. For A: Fetch Sequences for multiple datasets
Scholar 3.6 years ago, created an answer that has been accepted. For A: Fetch Sequences for multiple datasets
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Can't get admin right in Galaxy local
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Fetch Sequences for multiple datasets
Scholar 3.7 years ago, created an answer that has been accepted. For A: Fetch Sequences for multiple datasets

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