Closed pcm32 closed 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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I found that this error:
doesn't produce an exit with an error code (>0). This makes Galaxy and any wf environment dizzy.