Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Tool (Krona) produce HTML viewable output, but is marked red in history
0
gravatar for vebaev
22 months ago by
vebaev • 130
vebaev • 130 wrote:

I have tried both sanitize_all_html = False and True (with checking the tool on the whitelist) but, the result is the same.

I am using the tool Visualize with Krona (krona_text) The tool I think works and produce chart (see image attached), however after completion the result became red and produse this when bug icon is clicked:

Tool execution generated the following error message:

tput: No value for $TERM and no -T specified

The tool produced the following additional output:
starting
2 Fats Saturated fat
3 Fats Unsaturated fat Monounsaturated fat
3 Fats Unsaturated fat Polyunsaturated fat
13 Carbohydrates Sugars
4 Carbohydrates Dietary fiber
21 Carbohydrates
5 Protein
2 Fats Saturated fat
3 Fats Unsaturated fat Monounsaturated fat
3 Fats Unsaturated fat Polyunsaturated fat
13 Carbohydrates Sugars
4 Carbohydrates Dietary fiber
21 Carbohydrates
5 Protein
/export/tool_deps/krona-tools/2.6/saskia-hiltemann/krona_text/b14f1444e464/scripts:/export/tool_deps/krona-tools/2.6/saskia-hiltemann/krona_text/b14f1444e464:/galaxy_venv/bin:/galaxy_venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
Writing text.krona.html...

enter image description here

PS: I have no problem with FastQC which also produce HTMLs
krona html sanitize_all_html • 522 views
ADD COMMENT • link •
modified 22 months ago by Hotz, Hans-Rudolf • 1.8k • written 22 months ago by vebaev • 130
0
gravatar for Hotz, Hans-Rudolf
22 months ago by
Hotz, Hans-Rudolf • 1.8k
Switzerland
Hotz, Hans-Rudolf • 1.8k wrote:

Hi

as far as I can see, your tool does produce an error mesage: "No value for $TERM and no -T specified", doesn't-it?

Try to get rid of it by changing the command Galaxy is executing, or try to catch it with the help of the Tool Config Syntax - stdio, regex, and exit_code tag sets (see: https://docs.galaxyproject.org/en/latest/dev/schema.html#tool-stdio-regex )

Hope this helps Regards, Hans-Rudolf
ADD COMMENT • link written 22 months ago by Hotz, Hans-Rudolf • 1.8k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 179 users visited in the last hour