search

maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
105 stars 42 forks source link

0.4.35 fails to run for Seurat on conda install #67

Closed pcm32 closed 5 years ago

pcm32 commented 5 years ago

cbImportSeurat2 fails when run on a conda install due to the R script not being installed:

Fatal error: Exit code 1 ()
INFO:root:inFname: seurat.rds, outDir: output, datasetName: output
Traceback (most recent call last):
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.4.35/bin/cbImportSeurat2", line 11, in <module>
    load_entry_point('cellbrowser==0.4.35', 'console_scripts', 'cbImportSeurat2')()
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.4.35/lib/python3.6/site-packages/cellbrowser/seurat.py", line 407, in cbImportSeurat2Cli
    cbImportSeurat2(inFname, outDir, datasetName, options)
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.4.35/lib/python3.6/site-packages/cellbrowser/seurat.py", line 365, in cbImportSeurat2
    cmds = readExportScript(cmds)
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.4.35/lib/python3.6/site-packages/cellbrowser/seurat.py", line 322, in readExportScript
    for line in open(fname):
FileNotFoundError: [Errno 2] No such file or directory: '/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.4.35/lib/python3.6/site-packages/cellbrowser/R/ExportToCellbrowser-seurat2.R'
pcm32 commented 5 years ago

I have a PR in the make for this... just a few minutes...

maximilianh commented 5 years ago

Ooops... I must have forgotten to add the script to setup.py...

On Wed, Jan 30, 2019 at 3:40 PM Pablo Moreno notifications@github.com wrote:

I have a PR in the make for this... just a few minutes...

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/maximilianh/cellBrowser/issues/67#issuecomment-458967548, or mute the thread https://github.com/notifications/unsubscribe-auth/AAS-TTggxyKalOl1tsM8Zjfx1hjXCz-Sks5vIa7ZgaJpZM4aaVv0 .