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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
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Another silent error (failure with no error code) #213

Closed pcm32 closed 3 years ago

pcm32 commented 3 years ago

I found that this error:

INFO:root:Filtering for >5 cells then do sc.tl.rank_genes_groups for meta field 'cell_type'
Traceback (most recent call last):
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@1.0.0/bin/cbImportScanpy", line 10, in <module>
    sys.exit(cbImportScanpyCli())
  File "/Users/pmoreno/miniconda/envs/__ucsc-cell-browser@1.0.0/lib/python3.9/site-packages/cellbrowser/convert.py", line 600, in cbImportScanpyCli
    scanpyToCellbrowser(ad, outDir, datasetName, skipMatrix=options.skipMatrix, useRaw=(not options.useProc),
  File "/Users/pmoreno/miniconda/envs/__ucsc-cell-browser@1.0.0/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 4271, in scanpyToCellbrowser
    adata = runSafeRankGenesGroups(adata, clusterField, minCells=5)
  File "/Users/pmoreno/miniconda/envs/__ucsc-cell-browser@1.0.0/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 4157, in runSafeRankGenesGroups
    import scanpy as sc
ModuleNotFoundError: No module named 'scanpy'

doesn't produce an exit with an error code (>0). This makes Galaxy and any wf environment dizzy.

maximilianh commented 3 years ago

Thanks! fixed now in the develop branch.

On Fri, Apr 16, 2021 at 12:08 PM Pablo Moreno @.***> wrote:

I found that this error:

INFO:root:Filtering for >5 cells then do sc.tl.rank_genes_groups for meta field 'cell_type' Traceback (most recent call last): File @./bin/cbImportScanpy", line 10, in sys.exit(cbImportScanpyCli()) File @./lib/python3.9/site-packages/cellbrowser/convert.py", line 600, in cbImportScanpyCli scanpyToCellbrowser(ad, outDir, datasetName, skipMatrix=options.skipMatrix, useRaw=(not options.useProc), File @./lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 4271, in scanpyToCellbrowser adata = runSafeRankGenesGroups(adata, clusterField, minCells=5) File @./lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 4157, in runSafeRankGenesGroups import scanpy as sc ModuleNotFoundError: No module named 'scanpy'

doesn't produce an exit with an error code (>0). This makes Galaxy and any wf environment dizzy.

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