User: hortowe

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hortowe10
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10
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Last seen:
14 hours ago
Joined:
2 years, 5 months ago
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h******@ohsu.edu

Posts by hortowe

<prev • 10 results • page 1 of 1 • next >
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Answer: A: Error: package "GenomeInfoDb" could not be loaded
... Not exactly a solution, but I was able to fix this by turning off `conda_copy_dependencies`. I initially had switched that to `true` so that I could install [MiXCR](https://anaconda.org/bioconda/mixcr) while running a particular tool. I had the following behavior: * `conda_copy_dependencies: fal ...
written 14 hours ago by hortowe10
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Error: package "GenomeInfoDb" could not be loaded
... I have a local instance of galaxy (release 18.05) and am trying to use a custom R script that uses the bioconductor package ShortRead. I am developing tools in a context where I have been instructed to use conda to handle all dependencies, so am trying to find a solution in this manner. When I run ...
galaxy conda software error written 4 days ago by hortowe10
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Comment: C: Tool Installation from Tool Shed
... I ended up just switching to a new computer...not much of a solution but at least I don't have to worry about it anymore! Thanks for your help. ...
written 2.3 years ago by hortowe10
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Answer: A: Use multiple inputs in same script
... Figured out a solution that at least works for my specific case. xml file: R --vanilla --file=/path/to/file.R --args $output $inputs The inputs come in as a character string composed of all of the paths to each of the datasets selected in ...
written 2.4 years ago by hortowe10
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Comment: C: Use multiple inputs in same script
... As far as the R code goes: 1. set a directory path as the argument 2. Create a list of all of the files in that directory (csv's with 260 rows and 5 columns) 3. Read in the first file 4. Get the number of rows for the new matrix (260) from first file 5. Get the number of columns for the new mat ...
written 2.4 years ago by hortowe10
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Use multiple inputs in same script
... Hi all, I have a batch of 170 samples (represented by 170 comma-separated files) and am attempting to have them all as inputs into a single R script that will produce 1 output using data from each sample. When I run this script outside of galaxy, the input is a directory of the files. I feel that t ...
galaxy written 2.4 years ago by hortowe10
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Comment: C: Empty table output
... Hanz, That worked like a charm, thank you! I am looking to have more than one argument eventually, but I believe I saw a few questions and maybe a wiki entry about it that I will check out. Thanks again. ...
written 2.4 years ago by hortowe10
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Empty table output
... Hi all, I'm attempting to run an Rscript that outputs a few tables, but can't get that to work. I then created a super simple test script that just prints a table, but the output is empty. When I go to the tool on the galaxy interface, I run it and everything works fine, but when I click on the out ...
galaxy written 2.4 years ago by hortowe10 • updated 2.4 years ago by Hotz, Hans-Rudolf1.8k
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Comment: C: Tool Installation from Tool Shed
... Thanks for the reply Martin. I don't think that python bug applies to me, my python version is Python 2.7.10 and I'm running OS X Yosemite 10.10.5. I followed the instructions in the final answer on that stack overflow link and have this: ~$ which python /usr/local/bin/python ~$ ls -la /usr/local/ ...
written 2.4 years ago by hortowe10
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Tool Installation from Tool Shed
... Hi all, I recently downloaded and installed a local version of Galaxy and am following some basic tutorials. I'm currently attempting to install a tool from the toolshed (https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial). I checked the tool_sheds_conf.xml file and the main to ...
galaxy written 2.4 years ago by hortowe10 • updated 2.4 years ago by Martin Čech ♦♦ 4.8k

Latest awards to hortowe

Scholar 2.3 years ago, created an answer that has been accepted. For A: Use multiple inputs in same script

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