User: matt.chambers42

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Posts by matt.chambers42

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Using Ensembl gene annotation with Galaxy
... Yes, now I know where the bogus value came from. It was in my workflow .ga file that I imported. That value no longer existed in the loc file. But even when I overrode the value in the workflow run options, it still said invalid option. So it does seem like a UI bug. You should be able to reproduce ...
written 4 months ago by matt.chambers4250
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Answer: C: Using Ensembl gene annotation with Galaxy
... It seems that I only got this error when overriding the preselected value from the workflow. When I edited the workflow to select a different value, the workflow submitted properly. This is with Galaxy 17.05. ...
written 4 months ago by matt.chambers4250
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Using Ensembl gene annotation with Galaxy
... I'm trying to use ensembl gene annotations for my tool* but I don't understand how to map them to the UCSC dbkeys. There are multiple ensembl releases for each UCSC dbkey. My loc file has the latest ensembl release for each genome assembly/patch and I've tried to map it to the corresponding UCSC dbk ...
dbkey galaxy ucsc ensembl written 4 months ago by matt.chambers4250
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Comment: C: Selecting multiple datasets after filtering
... I'm using the latest release_17.05 from GitHub on a Jetstream instance. Chrome 58.0.3029.110 on Windows 7. I'm trying this on HISAT, but it's hard to imagine that it's a tool problem because the input form allows selecting multiple inputs, it just doesn't let me select them all at once (like it did ...
written 7 months ago by matt.chambers4250
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Selecting multiple datasets after filtering
... Something changed about the multiple dataset selection control. I used to be able to filter for a string like "_1" or "_2" and then easily select all the results. Now I have to manually click each item in the filtered list to select it. Is there a way to get the old behavior? ...
galaxy written 7 months ago by matt.chambers4250 • updated 7 months ago by Jennifer Hillman Jackson23k
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Comment: C: Galaxy: Use header row of tabular data for column names?
... I'd also like to see Galaxy able to read header names when they are present in the tabular file. This is a trivially usable capability in high level languages like R and Python, so Galaxy (which should be even higher level) should not be missing this feature. One good reason to have named columns is ...
written 7 months ago by matt.chambers4250
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Comment: C: Improving python error traces in Galaxy log
... I posted as an answer intentionally. :) My main concern was with being able to more quickly clean information about exceptions from the Galaxy log (now and in the future). Although I should have posted the code change I made! To fix this problem, I tried to manually update the JSON syntax of the ol ...
written 7 months ago by matt.chambers4250
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Comment: A: Improving python error traces in Galaxy log
... After a few false starts, I found that editing some code in lib/galaxy/web/framework/middleware/error.py achieved my desired effect. It is quite verbose because the workflow dictionary is huge, but it actually allowed me to pinpoint the problematic tool: Query to Tabular. Here is the original error ...
written 7 months ago by matt.chambers4250
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Workflow import error - from release 16.07, to release 17.01
... I'm trying to import workflows from a 16.07 instance to a 17.01 one. The tools are slightly different, so I'm getting a lovely Internal Server Error which tells me nothing. So I go to the log and find more detail that is almost, but not entirely, completely unhelpful: 129.114.104.5 - - [24/May/ ...
16.07 galaxy 17.01 import workflow written 7 months ago by matt.chambers4250 • updated 7 months ago by Jennifer Hillman Jackson23k
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Comment: A: Adding tools from the command-line to Galaxy Standalone on Jetstream
... It seems the install-repository script is not intended (?) to work with the Jetstream instance. Instead, it points to using an ansible playbook: https://github.com/afgane/galaxy-tools-playbook ...
written 13 months ago by matt.chambers4250

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