Admin: Dave B.

gravatar for Dave B.
Dave B.410
Reputation:
410
Status:
Trusted
Location:
United States
Website:
http://usegalaxy.org/
Last seen:
1 month, 2 weeks ago
Joined:
3 years, 7 months ago
Email:
d***@bx.psu.edu

Posts by Dave B.

<prev • 24 results • page 1 of 3 • next >
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Answer: A: Problem with custom tool that uses bioperl modules in local Galaxy instance
... Hello, That method of providing tool dependencies is not really recommended. It would be more robust to specify a dependency on the `perl-bioperl` package, like so: `perl-bioperl` And then configure your galaxy instance to install and resolve conda dependencies as described in this FAQ: https:// ...
written 7 months ago by Dave B.410
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Answer: A: RNA seq beginner
... Patrick, Bérénice Batut, Mallory Freeberg, and Mo Heydarian have written this training material on RNA-Seq which you might find useful: http://galaxyproject.github.io/training-material/RNA-Seq/ ...
written 7 months ago by Dave B.410
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Comment: C: Dealing with a deterministic amount of output files in tool wrapper
... Is there any way you can share your tool xml with me? ...
written 20 months ago by Dave B.410
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Comment: C: Dealing with a deterministic amount of output files in tool wrapper
... That is odd. Have you verified that the files are actually in the job's working directory? If not, to do that, uncomment and set the following option in your `galaxy.ini` file: cleanup_job = never When the tool completes, you can extract the job's working directory from the log and investigate ...
written 20 months ago by Dave B.410
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Answer: A: Dealing with a deterministic amount of output files in tool wrapper
... Good morning, The syntax of the `discover_datasets` tag is very nearly correct, but the `ext` attribute should be set to "fastq", since that is what the gzip contains. I would also recommend decompressing the files before they reach the history, so that galaxy can generate accurate metadata for th ...
written 20 months ago by Dave B.410
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Comment: C: How to test tool_dependencies.xml
... Yes, the PYTHONPATH definition needs to be $INSTALL_DIR/lib/python ...
written 20 months ago by Dave B.410
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Comment: C: How to test tool_dependencies.xml
... Yes, this link will highlight the `set_environment` actions in the xml I referenced above: https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_python_2_7_deeptools_2_0/tool_dependencies.xml#L52-L63 The first two are the important ones for any python package, letting the galaxy f ...
written 20 months ago by Dave B.410
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Answer: A: How to test tool_dependencies.xml
... Hello, The fastest way to make this XML work is by adding the following after the `setup.py install` command in the last `` tag: ` --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin`, then creating a `set_environment` action tag as described at https://wiki.galaxyproject.org/T ...
written 20 months ago by Dave B.410
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Answer: A: Importing a Repository Capsule
... Hello, The documentation may have been unclear, the designed method is to upload the tarball entire to the capsule import interface, then the toolshed will extract that and create the repositories in the order they should be to maintain valid dependency relationships. ...
written 21 months ago by Dave B.410
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Answer: A: Correctly installing to toolshed
... Hello, Is the perl interpreter installed on the cloud instance? I examined your repository on the test toolshed, and everything seems to be configured correctly. I would however recommend changing the first line of the perl script to: #!/usr/bin/env perl This would handle any potential issue ...
written 21 months ago by Dave B.410

Latest awards to Dave B.

Scholar 20 months ago, created an answer that has been accepted. For A: Is data uploaded you my galaxy account privately secured if I upload it via FTP?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Galaxy wrapper for a tool that takes a configfile.txt
Scholar 21 months ago, created an answer that has been accepted. For A: Is data uploaded you my galaxy account privately secured if I upload it via FTP?
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Galaxy wrapper for a tool that takes a configfile.txt
Scholar 23 months ago, created an answer that has been accepted. For A: Is data uploaded you my galaxy account privately secured if I upload it via FTP?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Galaxy wrapper for a tool that takes a configfile.txt
Scholar 23 months ago, created an answer that has been accepted. For A: Is data uploaded you my galaxy account privately secured if I upload it via FTP?
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Galaxy wrapper for a tool that takes a configfile.txt
Scholar 2.7 years ago, created an answer that has been accepted. For A: Is data uploaded you my galaxy account privately secured if I upload it via FTP?
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: cummerbund installation error- R package version
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Galaxy wrapper for a tool that takes a configfile.txt
Appreciated 3.3 years ago, created a post with more than 5 votes. For A: One system Two installation of Galaxy
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: Galaxy wrapper for a tool that takes a configfile.txt
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Galaxy wrapper for a tool that takes a configfile.txt

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