Question: Galaxy deleting bcftools_stats pdf output?
0
gravatar for m28happ95
6 weeks ago by
m28happ9510
University of Nebraska - Lincoln
m28happ9510 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 • 63 views
ADD COMMENTlink modified 6 weeks ago by Jennifer Hillman Jackson23k • written 6 weeks ago by m28happ9510
0
gravatar for Jennifer Hillman Jackson
6 weeks ago by
United States
Jennifer Hillman Jackson23k 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 COMMENTlink written 6 weeks ago by Jennifer Hillman Jackson23k
1

Will do! Thank you!

ADD REPLYlink written 6 weeks ago by m28happ9510

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 REPLYlink modified 6 weeks ago • written 6 weeks ago by Jennifer Hillman Jackson23k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 56 users visited in the last hour