Question: Galaxy deleting bcftools_stats pdf output?
gravatar for misshapp
11 months ago by
University of Nebraska - Lincoln
misshapp10 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
ADD COMMENTlink modified 11 months ago by Jennifer Hillman Jackson25k • written 11 months ago by misshapp10
gravatar for Jennifer Hillman Jackson
11 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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 COMMENTlink written 11 months ago by Jennifer Hillman Jackson25k

Will do! Thank you!

ADD REPLYlink written 11 months ago by misshapp10

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 has many improvements, but the conda bcftools package is still not working
ADD REPLYlink modified 11 months ago • written 11 months ago by Jennifer Hillman Jackson25k
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