User: Thon deBoer

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Thon deBoer10
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Posts by Thon deBoer

<prev • 7 results • page 1 of 1 • next >
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How to write tests for tools that access built-in data from the data tables
... I am writing a tool wrapper for a tool that allows as FASTA file input something from the data-table all_fasta. How do I write tests for these kinds of tools? The tests I wrote that use data provided as test-data in the test-data directory work fine, but I want to test it using the data from a dat ...
planemo data-table development tool tests written 5 days ago by Thon deBoer10 • updated 4 days ago by jmchilton1.1k
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Comment: C: Naming output file according to input file
... Actually..you often don't need the os.path.basename part. That is only needed if you ever pass it a full path (but it doesn't hurt and I just always use it) ...
written 6 days ago by Thon deBoer10
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Answer: A: Naming output file according to input file
... It is possible to use python code in the labels, so this should work: You can't use the { } for the $input1.name, but you DO need it for the python code, but this will do what you want. it will name your output file "myInputFile.something". Adopted from https://stackoverflow.com/questions/6 ...
written 6 days ago by Thon deBoer10
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Comment: C: Force galaxy to use the python 2 version of a dependency of a new tool
... Just checked, and indeed matplotlib is installed using CONDA... genMutModel /home/ubuntu/miniconda3/envs/mulled-v1-808d181c256ea1be661871e558eb70bf5d9047a0855ff85f21331747f4819086 numpy 1.9.1 Conda True /home/ubuntu/miniconda3/envs/mulled-v1-808d181c256ea1be661871e558eb70bf5d9047a0 ...
written 12 days ago by Thon deBoer10
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Comment: C: Force galaxy to use the python 2 version of a dependency of a new tool
... UH?! By using the requirement tag i AM using conda, no? Conda is just one of the dependency resolvers I understand... I am actually using PLANEMO (on the VM) and that is where I see that CONDA is installing the python 3.6 version of all the dependencies ...
written 12 days ago by Thon deBoer10
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Force galaxy to use the python 2 version of a dependency of a new tool
... I am creating a new tool for galaxy based on the NEAT-genReads tool from Zachary Stephens and I am trying to define the dependencies. The tool requires the **matplotlib.pyplot** library since it calls out this import statement: import matplotlib.pyplot as mpl I defined the dependency for the ...
planemo conda development tool dependencies written 13 days ago by Thon deBoer10 • updated 12 days ago by Jennifer Hillman Jackson25k
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Answer: A: Problem In Manage Data Library
... I have a similar problem in the latest galaxy-dist version from Dec 3rd. When I run BWA or BOWTIE2 (but it probably is not limited to those) the resulting SAM/BAM file is shown to be empty and none of the metadata has been updated. When I do a manual "Auto-detect" in the "Edit Attributes" section o ...
written 5.5 years ago by Thon deBoer10

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