maximilianh
commented
5 years ago First, thanks for opening this ticket!
The first issue looks like some confusion about the output directory. Which webserver are you using ?
The second one is a stupid bug that I’ll fix as soon as I can.
On Fri 2 Aug 2019 at 10:38, baracus37 notifications@github.com wrote:
Hi,
I am looking to convert a Seurat object (v3.0.2) into a CellBrowser. I followed the instructions here https://cellbrowser.readthedocs.io/seurat.html using the ExportToCellBroswer function and tested it with the pbmc_small datatset (my own dataset show the same error) provided together with Seurat:
ExportToCellbrowser(object = pbmc_small, dataset.name = "PBMC", dir = "out",cb.dir = "./out/test")
Writing expression matrix to out/exprMatrix.tsv.gz Writing embeddings to out/tsne.coords.tsv Writing meta data to out/meta.tsv cellbrowser.conf already exists in target directory, refusing to overwrite it Prepared cellbrowser directory out Converting cellbrowser directory to html/json files INFO:root:Creating ./out/test/PBMC INFO:root:Creating ./out/test/PBMC/metaFields INFO:root:Checking and reordering meta data to ./out/test/PBMC/meta.tsv INFO:root:Reading sample names from /media/pgm/Data/tobias/52-NGS-260219-0/Seurat/EPDC_CF_aCF_combined/out/meta.tsv INFO:root:Reading headers of file /media/pgm/Data/tobias/52-NGS-260219-0/Seurat/EPDC_CF_aCF_combined/out/exprMatrix.tsv.gz INFO:root:Data contains 80 samples/cells INFO:root:Converting to numbers and compressing meta data fields INFO:root:Field Cell: type uniqueString, 80 different values INFO:root:Field nCountRNA: type int, 71 different values INFO:root:Field nFeatureRNA: type int, 48 different values INFO:root:Field Cluster: type enum, 3 different values INFO:root:Indexing meta file ./out/test/PBMC/meta.tsv to ./out/test/PBMC/meta.index INFO:root:Kept 80 cells present in both meta data file and expression matrix INFO:root:Determining if ./out/test/PBMC/exprMatrix.tsv.gz needs to be created INFO:root:./out/test/PBMC/exprMatrix.tsv.gz does not exist. INFO:root:Auto-detecting number type of /media/pgm/Data/tobias/52-NGS-260219-0/Seurat/EPDC_CF_aCF_combined/out/exprMatrix.tsv.gz INFO:root:Auto-detect: Numbers in matrix are of type 'float' INFO:root:Auto-detected gene IDs type: symbols INFO:root:Copying/compressing /media/pgm/Data/tobias/52-NGS-260219-0/Seurat/EPDC_CF_aCF_combined/out/exprMatrix.tsv.gz to ./out/test/PBMC/exprMatrix.tsv.gz INFO:root:converting ./out/test/PBMC/exprMatrix.tsv.gz to ./out/test/PBMC/exprMatrix.bin and writing index to ./out/test/PBMC/exprMatrix.json, type None INFO:root:Compressing gene expression vectors... INFO:root:Auto-detecting number type of ./out/test/PBMC/exprMatrix.tsv.gz INFO:root:Auto-detect: Numbers in matrix are of type 'float' INFO:root:Wrote ./out/test/PBMC/cellbrowser.json.bak INFO:root:Wrote ./out/test/PBMC/cellbrowser.json.bak INFO:root:Wrote ./out/test/PBMC/dataset.json INFO:root:Wrote ./out/test/PBMC/dataset.json INFO:root:Parsing column Cluster from ./out/test/PBMC/meta.tsv INFO:root:Parsing coordinates for Seurat tsne INFO:root:Creating ./out/test/PBMC/coords/coords_0 INFO:root:Writing coordinates for Seurat tsne INFO:root:Calculating cluster midpoints for Seurat tsne INFO:root:/media/pgm/Data/tobias/52-NGS-260219-0/Seurat/EPDC_CF_aCF_combined/out/summary.html does not exist INFO:root:/media/pgm/Data/tobias/52-NGS-260219-0/Seurat/EPDC_CF_aCF_combined/out/methods.html does not exist INFO:root:/media/pgm/Data/tobias/52-NGS-260219-0/Seurat/EPDC_CF_aCF_combined/out/downloads.html does not exist INFO:root:/media/pgm/Data/tobias/52-NGS-260219-0/Seurat/EPDC_CF_aCF_combined/out/thumb.png does not exist INFO:root:/media/pgm/Data/tobias/52-NGS-260219-0/Seurat/EPDC_CF_aCF_combined/out/protocol.pdf does not exist INFO:root:/media/pgm/Data/tobias/52-NGS-260219-0/Seurat/EPDC_CF_aCF_combined/out/desc.conf does not exist INFO:root:Wrote ./out/test/PBMC/cellbrowser.json.bak INFO:root:Wrote ./out/test/PBMC/cellbrowser.json.bak INFO:root:Wrote ./out/test/PBMC/dataset.json INFO:root:Wrote ./out/test/PBMC/dataset.json INFO:root:Copying js, css and img files to ./out/test INFO:root:Creating ./out/test/ext/images INFO:root:Creating ./out/test/img INFO:root:Creating ./out/test/js INFO:root:Creating ./out/test/css INFO:root:Found 1 datasets INFO:root:Wrote ./out/test/index.html, added datasets: PBMC
This creates all files but when i open the index.html file and try to load the dataset, I get the following error:
Could not find a dataset at PBMC/dataset.json?d99f645d8a. If you are sure that the link is correct, please contact the administrator of this server, or cells@ucsc.edu if this is running at UCSC.
I also tried to create a rds file, but this fails as well:
cbImportSeurat -i pbmc_small.rds -o pbmc3kImport
Traceback (most recent call last): File "/home/tobias/.local/lib/python3.6/site-packages/pkg_resources/init.py", line 2354, in resolve return functools.reduce(getattr, self.attrs, module) AttributeError: module 'cellbrowser.seurat' has no attribute 'cbImportSeurat2Cli'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/usr/local/bin/cbImportSeurat", line 11, in load_entry_point('cellbrowser==0.5.45', 'console_scripts', 'cbImportSeurat')() File "/home/tobias/.local/lib/python3.6/site-packages/pkg_resources/init.py", line 487, in load_entry_point return get_distribution(dist).load_entry_point(group, name) File "/home/tobias/.local/lib/python3.6/site-packages/pkg_resources/init.py", line 2728, in load_entry_point return ep.load() File "/home/tobias/.local/lib/python3.6/site-packages/pkg_resources/init.py", line 2346, in load return self.resolve() File "/home/tobias/.local/lib/python3.6/site-packages/pkg_resources/init.py", line 2356, in resolve raise ImportError(str(exc)) ImportError: module 'cellbrowser.seurat' has no attribute 'cbImportSeurat2Cli'
Any help would be appreciated!
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baracus37
Hi,
I am looking to convert a Seurat object (v3.0.2) into a CellBrowser. I followed the instructions here using the ExportToCellBroswer function and tested it with the pbmc_small datatset (my own dataset show the same error) provided together with Seurat:
ExportToCellbrowser(object = pbmc_small, dataset.name = "PBMC", dir = "out",cb.dir = "./out/test")This creates all files but when i open the index.html file and try to load the dataset, I get the following error:
I also tried to create a rds file, but this fails as well:
cbImportSeurat -i pbmc_small.rds -o pbmc3kImportAny help would be appreciated!