maximilianh
commented
4 years ago Absolutely, I've written a bit of documentation about this here: https://cellbrowser.readthedocs.io/internet.html
And yes, closing the terminal shuts down the webserver and so you can't access it anymore. It's really preferable to have it all copied to some webserver. What is your University? Don't you have a lab website?
Otherwise: we can host your dataset. All you have to do is send us the cellbrowser directory (not the -o html directory, but the directory where you ran cbBuild) and we'll take care of the rest for you.
On Thu, Feb 27, 2020 at 5:48 PM Saeed notifications@github.com wrote:
Dear,
Thanks for the tool. I was wondering, if it would be possible for me to deposit the output of cbBuild on a shared folder (on university server storage which is accessible by everyone at the lab) in the lab and everyone can access it by clicking on index.html file or some other URL? Maybe a silly question, But I don't know how this works. Also, At the moment,now, when I build with -p 8888 option, I am able to open the browser. But after I close the terminal, if I click on index.html, I get the error saying "Could not find a dataset at dataset.json?701c98b551. 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. "
$cbImportSeurat -i SO_Human_Fibrosis_ALL_7_Jan_2020.rds -o fibrosis_2HC_1CD --htmlDir=~/public_html/cb -p 8888 INFO:root:inFname: SO_Human_Fibrosis_ALL_7_Jan_2020.rds, outDir: fibrosis_2HC_1CD, datasetName: fibrosis_2HC_1CD INFO:root:running fibrosis_2HC_1CD/runSeurat.R through Rscript Loading required package: Seurat Reading SO_Human_Fibrosis_ALL_7_Jan_2020.rds Exporting Seurat data to fibrosis_2HC_1CD Seurat Version installed: 3.1.3 Object was created with Seurat version 3.1.1.9020 Writing expression matrix to fibrosis_2HC_1CD/exprMatrix.tsv.gz Embedding tsne does not exist in Seurat object. Skipping. Writing embeddings to fibrosis_2HC_1CD/pca.coords.tsv Writing embeddings to fibrosis_2HC_1CD/umap.coords.tsv Writing meta data to fibrosis_2HC_1CD/meta.tsv Found precomputed markers in obj@misc['markers'] Writing top 100, cluster markers to fibrosis_2HC_1CD/markers.tsv Writing cellbrowser config to fibrosis_2HC_1CD/cellbrowser.conf Prepared cellbrowser directory fibrosis_2HC_1CD Warning messages: 1: In ExportToCellbrowser(sobj, "fibrosis_2HC_1CD", "fibrosis_2HC_1CD", : Embedding pca has more than 2 coordinates, taking only the first 2 2: In x[i] <- value[[j]] : number of items to replace is not a multiple of replacement length 3: In x[i] <- value[[j]] : number of items to replace is not a multiple of replacement length 314.13user 7.43system 5:21.62elapsed 99%CPU (0avgtext+0avgdata 13248796maxresident)k 0inputs+99848outputs (0major+4233026minor)pagefaults 0swaps INFO:root:Wrote logfile of R run to fibrosis_2HC_1CD/analysisLog.txt INFO:root:Copying SO_Human_Fibrosis_ALL_7_Jan_2020.rds to fibrosis_2HC_1CD/seurat.rds INFO:root:Not writing fibrosis_2HC_1CD/desc.conf, already exists INFO:root:dataRoot is not set in ~/.cellbrowser.conf. Dataset hierarchies are not supported. INFO:root:Determining if /home/luna.kuleuven.be/u0119129/public_html/cb/fibrosis_2HC_1CD/exprMatrix.tsv.gz needs to be created INFO:root:Reading headers of file /home/luna.kuleuven.be/u0119129/public_html/cb/fibrosis_2HC_1CD/exprMatrix.tsv.gz INFO:root:current input matrix looks identical to previously processed matrix, same file size, same sample names INFO:root:/home/luna.kuleuven.be/u0119129/public_html/cb/fibrosis_2HC_1CD/meta.tsv has the same md5 as in /home/luna.kuleuven.be/u0119129/public_html/cb/fibrosis_2HC_1CD/dataset.json, no need to rebuild meta data INFO:root:Reading sample names from /home/luna.kuleuven.be/u0119129/public_html/cb/fibrosis_2HC_1CD/meta.tsv INFO:root:Reading sample names from /home/luna.kuleuven.be/u0119129/public_html/cb/fibrosis_2HC_1CD/meta.tsv INFO:root:Loading old config from /home/luna.kuleuven.be/u0119129/public_html/cb/fibrosis_2HC_1CD/dataset.json INFO:root:Matrix and meta sample names have not changed, not indexing matrix again INFO:root:Parsing column Cluster from /home/luna.kuleuven.be/u0119129/public_html/cb/fibrosis_2HC_1CD/meta.tsv INFO:root:Parsing coordinates for Seurat pca INFO:root:Writing coordinates for Seurat pca INFO:root:Parsing coordinates for Seurat umap INFO:root:Writing coordinates for Seurat umap INFO:root:Wrote /home/luna.kuleuven.be/u0119129/public_html/cb/fibrosis_2HC_1CD/desc.json INFO:root:Auto-detecting http://luna.kuleuven.be/u0119129/public_html/cb/fibrosis_2HC_1CD/desc.jsonINFO:root:Auto-detecting number type of /media/u0119129/J-drive/GBW-0446_Targid-Mucosal_Immunology/Matteoli's Lab/Data/scRNA seq Analysis/Human Fibrosis/fibrosis_2HC_1CD/exprMatrix.tsv.gz INFO:root:Auto-detect: Numbers in matrix are of type 'int' INFO:root:Auto-detected gene IDs type: symbols INFO:root:Wrote 28 .tsv.gz files into directory /home/luna.kuleuven.be/u0119129/public_html/cb/fibrosis_2HC_1CD/markers/markers_0 INFO:root:dataRoot not set in ~/.cellbrowser.conf, no need to rebuild hierarchy INFO:root:Wrote /home/luna.kuleuven.be/u0119129/public_html/cb/fibrosis_2HC_1CD/cellbrowser.json.bak INFO:root:Wrote /home/luna.kuleuven.be/u0119129/public_html/cb/fibrosis_2HC_1CD/dataset.json INFO:root:Wrote main config /home/luna.kuleuven.be/u0119129/public_html/cb/fibrosis_2HC_1CD/dataset.json INFO:root:Rebuilding flat list of datasets, without hierarchies INFO:root:Found 1 datasets in subdirectories of directory /home/luna.kuleuven.be/u0119129/public_html/cb INFO:root:Wrote /home/luna.kuleuven.be/u0119129/public_html/cb/dataset.json Interrupt this process, e.g. with Ctrl-C, to stop the webserver Serving /home/luna.kuleuven.be/u0119129/public_html/cb on port 8888 Point your internet browser to http://127.0.0.1:8888 (or the IP address of this server)
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saeedfc
matthewspeir
Gibbsdavidl
Dear,
Thanks for the tool. I was wondering, if it would be possible for me to deposit the output of cbBuild on a shared folder (on university server storage which is accessible by everyone at the lab) in the lab and everyone can access it by clicking on index.html file or some other URL? Maybe a silly question, But I don't know how this works. Also, At the moment,now, when I build with -p 8888 option, I am able to open the browser. But after I close the terminal, if I click on index.html, I get the error saying "Could not find a dataset at dataset.json?701c98b551. 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. "