Question: NG-CHM visulaization tab is not updating
0
gravatar for aswathym
4 weeks ago by
aswathym0
aswathym0 wrote:

Request for help

As mentioned in documentation

The Galaxy visualization component does not install automatically. You will need to run the following commands in terminal mode: NOTE: The following assumes /galaxy-central is the home directory for your Galaxy instance, otherwise replace /galaxy-central with your Galaxy instance's root directory

  1. mv /galaxy-central/../shed_tools/toolshed.g2.bx.psu.edu/repos/md-anderson-bioinformatics/ngchm/*/ngchm/mda_heatmap_viz /galaxy-central/config/plugins/visualizations/
  2. cd /galaxy-central/config/plugins/visualizations/
  3. unzip mda_heatmap_viz.zip

Then you must restart Galaxy for the visualization portion to take effect.

  1. cd /galaxy-central
  2. sh run.sh

I have have done everything

ngs@ngs-OptiPlex-9020:~/galaxy/config/plugins/visualizations$ pwd
/home/ngs/galaxy/config/plugins/visualizations
ngs@ngs-OptiPlex-9020:~/galaxy/config/plugins/visualizations$ ls
additional_template_paths.xml  circster  csg       mda_heatmap_viz      phyloviz    scatterplot  trackster  visualization.dtd
charts                         common    graphviz  mda_heatmap_viz.zip  README.txt  sweepster    unipept

I did restart galaxy but. I am not getting the visualization option. The path is not updating in localhost either.

/home/ngs/shed_tools/toolshed.g2.bx.psu.edu/repos/md-anderson-bioinformatics/heat_map_creation/58437af2d675/heat_map_creation/heatm

what must have gone wrong ?

ADD COMMENTlink modified 4 weeks ago by Jennifer Hillman Jackson25k • written 4 weeks ago by aswathym0
0
gravatar for Jennifer Hillman Jackson
4 weeks ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

For troubleshooting help with the install, try contacting the tool authors. They will know best about how to configure the tool to work in a local Galaxy. Or you could first try following the instructions for the related heat_map_creation_advanced tool instead -- it includes more help plus a video. If that does not clear things up, then contacting the authors is the next step.

How-to: Log into the ToolShed https://usegalaxy.org/toolshed (create an account if needed), navigate to the tool, and in the upper right corner will be a menu named "Repository Actions". One of the options is to contact the repository owner.

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Jennifer Hillman Jackson25k
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