User: Thon deBoer

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Thon deBoer20
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Posts by Thon deBoer

<prev • 11 results • page 1 of 2 • next >
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Answer: A: "Tool error: Unable to finish job" on the DOCKER version of galaxy, but not for
... Seems that that neat_genReads tool has a known issue with BAM files not being properly formatted... Get this when trying to read the BAM file [E::bam_read1] CIGAR and query sequence lengths differ for ecoli-chr-268539/1 [main_samview] truncated file. So, this is NOT a problem with Galaxy and I th ...
written 10 weeks ago by Thon deBoer20
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Comment: C: "Tool error: Unable to finish job" on the DOCKER version of galaxy, but not for
... I updated to the latest Docker version (can't really see what version that is, but guessing 18.something since it had "unsorted.bam as an option). I changed the BAM file format type from "bam" to "unsorted.bam" and this seems to fix the error! Next I just made samtools sort the BAM files to ensure ...
written 11 weeks ago by Thon deBoer20
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Comment: C: "Tool error: Unable to finish job" on the DOCKER version of galaxy, but not for
... Not sure how to check for version numbers on the Galaxy I am using on Docker and Planemo. I looked in the Planemo build and see a file named: release_17.05_receipt So, guessing Planemo version is 17.05 Could not find something similar for the Docker version, but the git entry TOC goes up to 17.09 ...
written 11 weeks ago by Thon deBoer20
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"Tool error: Unable to finish job" on the DOCKER version of galaxy, but not for the usual reasons (missing dependencies) nor is it consistent
... I created a wrapper for the NEAT-genReads NGS simulation tool but I am running into the dreaded "Tool error: Unable to finish job", but only on [ecoli-size genomes][1], only on the DOCKER version of Galaxy and NOT because of missing dependencies (which is the usual reason for this error, as I see in ...
docker software error planemo written 11 weeks ago by Thon deBoer20
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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 3 months ago by Thon deBoer20 • updated 3 months 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 3 months ago by Thon deBoer20
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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 3 months ago by Thon deBoer20
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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 3 months ago by Thon deBoer20
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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 3 months ago by Thon deBoer20
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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 3 months ago by Thon deBoer20 • updated 3 months ago by Jennifer Hillman Jackson25k

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