Closed tiramisutes closed 3 years ago
Hi,
Is there a fix for this issue? I ran into a similar issue when using cellBrowser(v0.7.14) installed from conda. The log is quite similar to the OP's except for this one line:
ERROR:root:/cndd2/junhao/ucsc_cell_browser_test/cellBrowser/sampleData/mini/markers.tsv: the following cluster names are in the meta file but not in the marker file: {''}. Please fix one of the files, clicks onto a label will otherwise not work.
I'm not sure whether this is related but it looks similar to this issue: #152 (which was fixed a while ago...)
Thanks in advance!
@tiramisutes sorry for not following up sooner.
Hmm, there's nothing in either of those output messages that would indicate why you're just seeing a blank screen.
(e.g. the error that @hoholee noted only means that there's a name (blank or '' in this case) in the metadata file that isn't in the markers.tsv. That wouldn't cause the cell browser to just not load.)
In Chrome or Firefox, if you open up the web developers console, are there any errors listed there? Errors are typically indicated by red text or a red x in the console.
@maximilianh any other ideas here?
Hi @matthewspeir,
Yes the console show lots of error:
It seems that the index.html
file generated by cbBuild
imports many javascript files in the ext
and js
folders, which do not exist in the folder built by cbBuild
:
Any ideas?
@hoholee Can you try running cbUpgrade --code -o <same cbBuild output dir>
? The output directory for cbUpgrade
should be the same as the one you specified for cbBuild
.
Oh great, it works after cbUpgrade
! Thank you! I would recommend adding this instruction in the tutorial.
Great! cbBuild
should put those files in place. You should not need to run cbUpgrade
. I'll see if I can replicate this issue so, hopefully, we can track down why cbBuild
doesn't seem to be doing that in some cases.
To that end, @hoholee can you share a bit more about the machine you're running the cell browser on? Is it a laptop or server? Mac, Linux, or Windows?
I'm using a Linux server, Ubuntu 16.04.7 LTS (GNU/Linux 4.4.0-190-generic x86_64).
The cellBrowser version is v0.7.14, installed using conda 4.8.1 via this command:
conda install -c bioconda ucsc-cell-browser
Ohhhh... this is a bug I think! I must have broken something and cbBuild stopped putting the JS files in place automatically... Many thanks !!
On Tue 27 Oct 2020 at 19:32, Junhao Li notifications@github.com wrote:
I'm using a Linux server, Ubuntu 16.04.7 LTS (GNU/Linux 4.4.0-190-generic x86_64). The cellBrowser version is v0.7.14, installed using conda 4.8.1 via this command: conda install -c bioconda ucsc-cell-browser
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Yes, it works after cbUpgrade --code -o <same cbBuild output dir>
. Thanks.
I cannot reproduce this yet, but I'm installing conda now to check what's going wrong here. I know we had this problem two releases ago then I fixed it, but the fix should be in 0.7.14. Thanks for contacting us in any case.
On Wed, Oct 28, 2020 at 3:14 AM hope notifications@github.com wrote:
Yes, it works after cbUpgrade --code -o
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OK, I installed conda and then ran these commands and it's all working fine:
conda install -c bioconda/label/cf201901 ucsc-cell-browser curl -ks https://cells.ucsc.edu/downloads/samples/mini.tgz | tar xvz cd mini cbBuild -o html/ -p 8888
This is as expected as the "blank page" bug was fixed a while ago. So I can't reproduce this bug.
On Thu, Oct 29, 2020 at 9:35 AM Maximilian Haeussler maximilianh@gmail.com wrote:
I cannot reproduce this yet, but I'm installing conda now to check what's going wrong here. I know we had this problem two releases ago then I fixed it, but the fix should be in 0.7.14. Thanks for contacting us in any case.
On Wed, Oct 28, 2020 at 3:14 AM hope notifications@github.com wrote:
Yes, it works after cbUpgrade --code -o
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I also came to the same problem when I used conda to install cellbrowser. ucsc-cell-browser 0.7.14 py_0 bioconda I manually download ucsc-cell-browser-0.7.14-py_0.tar.bz2 and extract site-packages/cellbrowser/cbWeb to pubhtml folder.
Hi luyang93, this is very interesting, can you tell me what you did? Did you download the conda package or the pip package manually?
I don't understand why I can't reproduce a bug that two people report with the same conda command line... hmm...
On Fri, Oct 30, 2020 at 1:46 PM luyang93 notifications@github.com wrote:
I also came to the same problem when I used conda to install cellbrowser. ucsc-cell-browser 0.7.14 py_0 bioconda I manually download ucsc-cell-browser-0.7.14-py_0.tar.bz2 and extract site-packages/cellbrowser/cbWeb to pubhtml folder.
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conda create -n cellbrowser
conda activate cellbrowser
conda install ucsc-cell-browser scanpy
then download sample data https://github.com/maximilianh/cellBrowser/blob/master/sampleData/pbmc_small/anndata.h5ad
cbImportScanpy -i anndata.h5ad -o pbmc3kImportScanpy
cd pbmc3kImportScanpy
cbBuild -o ~/public_html/cb
the public_html folder doesn't have static files
Hi @luyang93, ohh, many thanks for insisting! First, this brought another bug to my attention, I didn't realize that you used an anndata file here. Fixed now in the develop branch. @Matthew Speir mspeir@ucsc.edu I guess this is important enough to push out a release now?
On Sun, Nov 1, 2020 at 6:28 AM luyang93 notifications@github.com wrote:
conda create -n cellbrowser conda activate cellbrowser conda install ucsc-cell-browser scanpy
then download sample data
https://github.com/maximilianh/cellBrowser/blob/master/sampleData/pbmc_small/anndata.h5ad
cbImportScanpy -i anndata.h5ad -o pbmc3kImportScanpy cd pbmc3kImportScanpy cbBuild -o ~/public_html/cb
the public_html folder doesn't have statci files
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@maximilianh Yeah, seems important. Lets try to get the release out there today or tomorrow then.
It's solved.
Thanks for the feedback. I'll close the ticket then.
On Tue, Nov 17, 2020 at 4:20 AM luyang93 notifications@github.com wrote:
It's solved.
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Hi, I install the cellBrowser use conda (
conda install -c bioconda ucsc-cell-browser
) and use sample data to test whether it works.Here is the code that I'm running:
The stdout is normal but returns a blank page when open URL http://127.0.0.1:8888/.