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Question: Galaxy deleting bcftools_stats pdf output?
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gravatar for misshapp
11 months ago by
misshapp • 10
University of Nebraska - Lincoln
misshapp • 10 wrote:

Hi guys -

I'm running a local instance of galaxy (17.09) and using bcftools_stats to create some summary statistics on multiple vcf files. This results in a text file with the info that is automatically plotted using "plot-vcfstats" to create a pdf with summary charts/graphs. The job runs successfully however, when I click to view the pdf it says "failed to load pdf document". There is also no download button for the pdf and I can't find it in my galaxy files from the command prompt using "sudo find . -name". Is galaxy treating it like a temp file? I can, however, get to the text file. Using bcftools_stats with the option to create a pdf leads to the creation of 2 jobs, and it seems the one responsible for generating the pdf is having some sort of issue even though it claims to have ran just fine.

In addition, when I run the tools from the command line, the pdf is created normally.

pdf bcftools • 359 views
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modified 11 months ago by Jennifer Hillman Jackson ♦ 25k • written 11 months ago by misshapp • 10
0
gravatar for Jennifer Hillman Jackson
11 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hi,

This might be a tool bug related to dependencies. I checked and it hasn't been reported yet. You can report it to the IUC tool authors two ways:

Thanks! Jen, Galaxy team
ADD COMMENT • link written 11 months ago by Jennifer Hillman Jackson ♦ 25k
1

Will do! Thank you!

ADD REPLY • link written 11 months ago by misshapp • 10

For others that may encounter this problem, the IUC team confirmed that the tool has a known issue, still open, details captured in a PR:

Nicola Soranzo @nsoranzo 15:04
@_misshapp_twitter pdf creation in bcftools_stats is broken
https://github.com/galaxyproject/tools-iuc/pull/1416 has many improvements, but the conda bcftools package is still not working
ADD REPLY • link modified 11 months ago • written 11 months ago by Jennifer Hillman Jackson ♦ 25k
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