search

interactivereport / cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
https://cellxgenevip-ms.bxgenomics.com
MIT License
129 stars 44 forks source link

error in installation #29

Closed FADHLyemen closed 3 years ago

FADHLyemen commented 3 years ago

Could you help with the below error?

npm@2.15.5 /home/ec2-user/.nvm/versions/node/v4.4.5/lib/node_modules/npm
make[1]: *** [ci] Error 1
make[1]: Leaving directory `/home/ec2-user/downloads/cellxgene_VIP/cellxgene/client'
make: *** [build-client] Error 2
pip uninstall -y cellxgene || :
Found existing installation: cellxgene 0.16.4
Uninstalling cellxgene-0.16.4:
  Successfully uninstalled cellxgene-0.16.4
pip install dist/cellxgene*.tar.gz
WARNING: Requirement 'dist/cellxgene*.tar.gz' looks like a filename, but the file does not exist
Processing ./dist/cellxgene*.tar.gz
ERROR: Could not install packages due to an EnvironmentError: [Errno 2] No such file or directory: '/home/ec2-user/downloads/cellxgene_VIP/cellxgene/dist/cellxgene*.tar.gz'

make: *** [install-dist] Error 1
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'server'
cp: cannot create regular file ‘/server/app/.’: No such file or directory
cp: cannot create regular file ‘/server/common/web/static/.’: No such file or directory
cp: cannot create regular file ‘/server/common/web/static/.’: No such file or directory
cp: cannot create directory ‘/server/common/web/static/.’: No such file or directory
cp: cannot create directory ‘/server/common/web/static/.’: No such file or directory
cp: cannot create regular file ‘/server/common/web/static/.’: No such file or directory
cp: target ‘/server/common/web/static/.’ is not a directory
cp: cannot create directory ‘/server/common/web/static/.’: No such file or directory
cp: cannot create directory ‘/server/common/web/static/.’: No such file or directory
cp: cannot create directory ‘/server/common/web/static/.’: No such file or directory
cp: cannot create regular file ‘/server/app/.’: No such file or directory
cp: cannot create regular file ‘/server/app/.’: No such file or directory
cp: cannot create regular file ‘/server/app/.’: No such file or directory
cp: cannot create regular file ‘/server/app/.’: No such file or directory
cp: cannot create regular file ‘/server/app/.’: No such file or directory

ls -l /server/common/web/static/.

ls: cannot access /server/common/web/static/.: No such file or directory
z5ouyang commented 3 years ago

When you create the conda env in the step 1. Did you used 'VIP.yml' or 'VIP_conda_R.yml'? And could you please share all your command lines of installation before this error?

Will close this one, feel free to reopen if the installation still unsuccessful.

skim245 commented 3 years ago

@z5ouyang I'm having similar issue too; i've previously had cellxgene installed, and when i created the conda env in the step 1, i used VIP.yml. do you have any suggestion on how to resolve this issue?

z5ouyang commented 3 years ago

@skim245 please open a new issue, with details on your command line and error messages that command line caused. Thank you!