Moderator: Greg Von Kuster

gravatar for Greg Von Kuster
Reputation:
810
Status:
Trusted
Location:
Penn State University
Website:
http://gregvonkuster.org/
Last seen:
1 year, 8 months ago
Joined:
8 years, 1 month ago
Email:
g***@bx.psu.edu

Posts by Greg Von Kuster

<prev • 75 results • page 1 of 8 • next >
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Answer: A: Unzip files on Galaxy
... It may be the case that your input dataset for the bowtie tool has datatype fastq, while bowtie requires fastqsanger. I'm not sure if Galaxy version 1.1.2 of the tool allows for more datatypes, but Galaxy version 1.1.4 allows for any one of fastqsanger,fastqillumina,fastqsolexa. ...
written 21 months ago by Greg Von Kuster810
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Answer: A: Information about new galaxy releases / changes?
... The Galaxy News Briefs provide information about what's included in each new Galaxy release - the page is here: http://wiki.galaxyproject.org/DevNewsBriefs, and a link to the page ia also available on the Galaxy News page here:http://wiki.galaxyproject.org/News. Galaxy news Briefs are generally pro ...
written 3.5 years ago by Greg Von Kuster810
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Answer: A: galaxy tool dependency
... Hello, based on your comments, you may have installed the repositories before you had set your tool_dependency_dir.  If this is the case, then each repository that defines a tool dependency will show the tool dependency in a Never installed state.  You can either: -uninstall and reinstall all of th ...
written 3.6 years ago by Greg Von Kuster810
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Answer: A: Searching Galaxy Tool Shed Gives Error
... Hello Joachim, Thanks for reporting this. This issue was resolved a couple of weeks ago, but did not make it into the cutoff for the last Galaxy distribution release. It is corrected on the test Galaxy tool shed and will be included in the next Galaxy release. Greg Von Kuster ...
written 5.0 years ago by Greg Von Kuster810
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Answer: A: Bismark Error: Data Table Named 'Bismark_Bs_Indeces' Is Required By Tool But Not
... Hello Sachit, It looks like you installed this from the test tool shed since it is not available on the main tool shed. Assuming I've located the repository you installed, it looks like you'll have to manually add the following entry into your tool_data_table_conf.xml file. This should have been ...
written 5.0 years ago by Greg Von Kuster810
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Answer: A: Downgrading Toolshed Tools
... Hi Paul, From your explanation, it seems that you have 2 versions of the tool installed in your Galaxy instance, the original version and the new version that is broken. If this is the case, just uninstall the newer broken version, and continue to make only the previous working version available t ...
written 5.1 years ago by Greg Von Kuster810
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Comment: C: Errors During Database Migration After Updating Galaxy
... Hello Joel, The main Galaxy tool shed is back up - thanks for reporting this problem. Greg Von Kuster ...
written 5.2 years ago by Greg Von Kuster810
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Comment: C: Tool_Path
... Hello Fabien, This issue is indeed due to the tool design and is not related to the tool shed. I'm not primarily a tool developer, so I'm not the best person to help you with this issue. However, one recommendation would be to place your scripts and binaries that a specific tool wrapper uses in t ...
written 5.4 years ago by Greg Von Kuster810
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Answer: A: Tool_Path
... Hello Fabien, I don't understand the issue - can you provide a sample tool config that includes these hard-coded paths? This initially sounds like an issue with the tool configs, not the tool shed, but I may see the problem with your clarification. Thanks, Greg Von Kuster ...
written 5.4 years ago by Greg Von Kuster810
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Comment: C: Data Upload...
... Is there something helpful in your paster log about the cause? ...
written 5.6 years ago by Greg Von Kuster810

Latest awards to Greg Von Kuster

Scholar 3.5 years ago, created an answer that has been accepted. For A: Information about new galaxy releases / changes?

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