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

Example build fails on mac #35

Closed mxposed closed 6 years ago

mxposed commented 6 years ago

Hi

I'm on MacOS with python 3.6, and the example command ../../src/cbBuild -o ~/tmp/blah -p8888 in the sampleData/sample1 folder fails with

INFO:root:Copying+reordering+trimming /Users/markov/Documents/Misharin Cell Browser/cellBrowser/sampleData/sample1/exprMatrix.tsv.gz to /Users/markov/tmp/blah/sample/exprMatrix.tsv.gz, keeping only the 4261 columns with a sample name in the meta data
Traceback (most recent call last):
  File "../../src/cbBuild", line 10, in <module>
    cellbrowser.convertAndCopyCli()
  File "../../src/cbPyLib/cellbrowser.py", line 2348, in convertAndCopyCli
    convertAndCopy(confFnames, outDir, port)
  File "../../src/cbPyLib/cellbrowser.py", line 2322, in convertAndCopy
    convertDataset(inConf, outConf, datasetDir)
  File "../../src/cbPyLib/cellbrowser.py", line 2091, in convertDataset
    convertExprMatrix(inConf, outMatrixFname, outConf, sampleNames, geneToSym, datasetDir, needFilterMatrix)
  File "../../src/cbPyLib/cellbrowser.py", line 1792, in convertExprMatrix
    copyMatrixTrim(matrixFname, outMatrixFname, metaSampleNames, needFilterMatrix)
  File "../../src/cbPyLib/cellbrowser.py", line 1396, in copyMatrixTrim
    matIter.open(inFname)
  File "../../src/cbPyLib/cellbrowser.py", line 657, in open
    assert(len(self.sampleNames)!=0)
AssertionError