main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
Trying on an AnnData object that we generate we got the following error:
INFO:root:Reading sample names from /private/var/folders/23/wwh84vd95rncnf5mx753cpgh0000gp/T/tmp_1zll3p7/job_working_directory/000/2/working/outdir/meta.tsv
Traceback (most recent call last):
File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.7.15/bin/cbImportScanpy", line 10, in <module>
sys.exit(cbImportScanpyCli())
File "/Users/pmoreno/miniconda/envs/__ucsc-cell-browser@0.7.15/lib/python3.9/site-packages/cellbrowser/convert.py", line 604, in cbImportScanpyCli
build(outDir, options.htmlDir, port=options.port)
File "/Users/pmoreno/miniconda/envs/__ucsc-cell-browser@0.7.15/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 4392, in build
convertDataset(inDir, inConf, outConf, datasetDir, redo)
File "/Users/pmoreno/miniconda/envs/__ucsc-cell-browser@0.7.15/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 3749, in convertDataset
sampleNames, needFilterMatrix = convertMeta(inDir, inConf, outConf, datasetDir, outMetaFname)
File "/Users/pmoreno/miniconda/envs/__ucsc-cell-browser@0.7.15/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 3412, in convertMeta
sampleNames, needFilterMatrix = metaReorder(matrixFname, metaFname, finalMetaFname)
File "/Users/pmoreno/miniconda/envs/__ucsc-cell-browser@0.7.15/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 2195, in metaReorder
metaSampleNames = readSampleNames(metaFname)
File "/Users/pmoreno/miniconda/envs/__ucsc-cell-browser@0.7.15/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 3061, in readSampleNames
for row in lineFileNextRow(fname, noHeaders=False):
File "/Users/pmoreno/miniconda/envs/__ucsc-cell-browser@0.7.15/lib/python3.9/site-packages/cellbrowser/cellbrowser.py", line 668, in lineFileNextRow
Record = namedtuple('tsvCsvRec', headers)
File "/Users/pmoreno/miniconda/envs/__ucsc-cell-browser@0.7.15/lib/python3.9/collections/__init__.py", line 399, in namedtuple
raise ValueError('Field names cannot start with an underscore: '
ValueError: Field names cannot start with an underscore: '_is_in_cluster__'
This is with latest release version 0.7.15
Also, it would be nice if cbImportScanpy would fail with an error code when it fails. In this the tool fails silently (no error code) and Galaxy hence thinks that the import was succesful.
Trying on an AnnData object that we generate we got the following error:
This is with latest release version 0.7.15
Also, it would be nice if cbImportScanpy would fail with an error code when it fails. In this the tool fails silently (no error code) and Galaxy hence thinks that the import was succesful.