Issues with Viewer

[Coayala]

Good afternoon,

I have finished creating the dataset and adding blast and BUSCO results with no problems. However, when I tried to run blobtools view I had the following problem:

Initializing viewer |████████████████                        | 6/15 secondsWARNING: Directory '/scratch/ch1005/ee_annot/bloobtools/ee_hic' appears to be a BlobDir.
         Hosting the parent directory instead.
Starting BlobToolKit API on port 8000 (pid: 51207)
Starting BlobToolKit viewer on port 8001 (pid: 51225)

> blobtoolkit-viewer@1.1.0 api /home/ch1005/blobtoolkit/viewer
> node src/server/app.js

Something went wrong installing the "sharp" module

Cannot find module '../build/Release/sharp.node'

- Remove the "node_modules/sharp" directory, run "npm install" and look for errors
- Consult the installation documentation at https://sharp.pixelplumbing.com/en/stable/install/
- Search for this error at https://github.com/lovell/sharp/issues

npm ERR! code ELIFECYCLE
npm ERR! errno 1
npm ERR! blobtoolkit-viewer@1.1.0 api: `node src/server/app.js`
npm ERR! Exit status 1
npm ERR!
npm ERR! Failed at the blobtoolkit-viewer@1.1.0 api script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/ch1005/.npm/_logs/2020-10-28T21_36_17_527Z-debug.log

> blobtoolkit-viewer@1.1.0 client /home/ch1005/blobtoolkit/viewer
> webpack-dev-server --mode development --content-base src/client

sh: webpack-dev-server: command not found
npm ERR! code ELIFECYCLE
npm ERR! syscall spawn
npm ERR! file sh
npm ERR! errno ENOENT
npm ERR! blobtoolkit-viewer@1.1.0 client: `webpack-dev-server --mode development --content-base src/client`
npm ERR! spawn ENOENT
npm ERR!
npm ERR! Failed at the blobtoolkit-viewer@1.1.0 client script.
npm ERR! This is probably not a problem with npm. There is likely additional logging output above.

npm ERR! A complete log of this run can be found in:
npm ERR!     /home/ch1005/.npm/_logs/2020-10-28T21_36_18_030Z-debug.log

ERROR: Viewer quit unexpectedly

Please if you can help me with that.

Thanks a lot

-Christian

[rjchallis]

Problems with he sharp module are usually related to the node version it doesn't seem to matter which version you use, so long as it is installed and run under the same version. It may be that you already have node installed and the version in your btk env that is being used to run this command differs from the one used when you ran npm install to install the Viewer.

To fix this, you can delete the node_modules directory that will have been created inside the Viewer directory and run npm install again, making sure to have the same Conda environment activated that you are using to run blobtools view, e.g:

cd viewer
rm -r node_modules
conda activate btk_env
npm install

[Coayala]

Thanks for your help. I have tried to do that multiple times but it is still not working. I tried to install the sharp module by itself but I keep getting the same error.

[rjchallis]

That's curious, can you try pulling the latest code to make see if it works with the most recent release?

[github-actions[bot]]

This issue has being marked as dormant because viewer is being archived. The code is now part of the main BlobToolKit repository.

If you feel the issue has not been resolved, please follow the updated BlobToolKit installation instructions to first confirm that you are using the latest version, and then open a new issue at the main BlobToolKit repository if necessary.

This issue will be automatically closed in 7 days.

[github-actions[bot]]

This issue was closed because it has been inactive for 7 days since being marked as dormant.