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group related datasets into a hierarchy ending with errors of copying exprMatrix.tsv.gz to itself #237
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Hi, Robin. Can your provide the full error message you are receiving when trying to run cbBuild for these datasets? |
Thanks matthew. Here is it. root@bioinformatics:/home/CellBrowser/OPC/otx169to176integrated# cbBuild -i cellbrowser.conf -o /home/CellBrowser last time I run cbBuild in "/home/anaconda/opc211101/otx169to176integrated/" successfully. I found the inMatrix md5 is different from outMatrix in the dataset.json { |
Robin, can you share more details about how you installed the cellBrowser package (i.e. pip, conda)? And maybe what operating system you're running on (i.e. Windows, Mac OSX, or Linux)? @maximilianh Do you have ideas? I've never seen this error before:
|
Hi Matthew, I installed it by pip two years ago and upgrade it recently. would you mind to suggest what is the best way to re-set the cellbrowser with hierarchy? Thanks Robin |
Hmm, that's odd that the hierarchy stuff didn't work for you. Just to be sure, you've removed the 'dataRoot' line from the .cellbrowser.conf file in your home directory? |
I did not have a .cellbrowser.conf before. |
Hi Matthew, How do you add a dataset to a collection with hierarchy? Thanks Robin |
Could you try setting up a .cellbrowser.conf (note the '.' at the beginning of the file name) in your home directory with the dataRoot line to see if that helps? |
Yes without the config file it will not work. I believe that we must know
the root directory otherwise we don’t know how deep we are in the tree…
…On Wed 23 Mar 2022 at 19:23, Matt Speir ***@***.***> wrote:
Could you try setting up a .cellbrowser.conf (note the '.' at the
beginning of the file name) in your home directory with the dataRoot line
to see if that helps?
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I had ".cellbrowser.conf" with dataRoot line. For redundancy, I also set CBDATAROOT=/home/CellBrowser/. my error came from here 2515 shutil.copyfile(inFname, outFname) when I move the default outputs of cbSeurat to a subdirector of dataRoot and run cbBuild there: So I renamed file 'exprMatrix.tsv.gz' to 'oldMatrix.tsv.gz' in the output of cbSeurat and run cbBuild again, it works. |
I don't fully understand what your setup is, but for us, it never happens
that outDir == inDir. We have a htdocs directory for the webserver and a
data root directory, totally different directory trees:
My conf has these lines in it:
htmlDir = "/usr/local/apache/htdocs-cells"
dataRoot = "/hive/data/inside/cells/datasets/"
outDirs = {"alpha" : "/usr/local/apache/htdocs-cells", "beta" :
"/usr/local/apache/htdocs-cells-beta/" }
…On Wed, Mar 23, 2022 at 10:10 PM yesonse ***@***.***> wrote:
I had ".cellbrowser.conf" with dataRoot line. For redundancy, I also set
CBDATAROOT=/home/CellBrowser/.
my error came from here
2515 shutil.copyfile(inFname, outFname)
when I move the default outputs of cbSeurat to a subdirector of dataRoot
and run cbBuild there:
outDir == inDir, inFname == outFname and errors happened.
So I renamed file 'exprMatrix.tsv.gz' to 'oldMatrix.tsv.gz' in the output
of cbSeurat and run cbBuild again, it works.
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I managed an internal bioinformatic server and used it to host the cell browser for my colleagues of 30-40 people. Several colleagues might add some datasets sometime independently. I did not make a specific htmlDir or dataRoot. So my case could be special and I thought I could set outDir as the dataRoot. I have not realized that hierarchy need a specific "dataRoot" other than outDir for 'cbBuild -o'. I figured out that I just need to put the input files needed for cbBuild in other places, put their paths in the cellbrowser.conf under a tree of directories, run cbBuild under each subdirectory. I also modified the codes and make it works when outDir == inDir :), not re-write the exprMatrix, which make it easy to rebuild the tree of outputs anytime. Thank you very much for your great of work of build the cellbrowser! |
Hi, @yesonse. Can we close this ticket? Or are you still running into issues? |
I am fine now. |
Hi Robin,
thanks for your question. I'm sure we can quickly help you fix this.
I tried to run cbBuild in the subdirectory end with errors of copying
exprMatrix.tsv.gz to itself.
It sounds as if this is the source of the problem. Can you show us the
exact error?
And show us your directory structure: I imagine there is one root
directory, under it a directory for the collection, and in this directory,
one directory for each dataset? And all of these directories have a
cellbrowser.conf ?
It's possible that we'll have to improve the documentation. Few groups are
using the collections yet but they have always been working well for us
for three years now.
…On Sun, Mar 20, 2022 at 5:58 AM yesonse ***@***.***> wrote:
Dear there,
I have a host with about 20 datasets. Now I like to group them into
collections as here
https://cellbrowser.readthedocs.io/en/master/collections.html.
After I run "cbBuild -r", the cell browser showed the collections well,
but could not find each dataset in each collection.
I found there was no cellbrowser.conf in the subdirectory of collection,
and made one for each. I tried to run cbBuild in the subdirectory end with
errors of copying exprMatrix.tsv.gz to itself.
I tried to read some codes from the source, and believe it is right to put
the dataset under the collection first, then run cbBuild in the
sub-directory of the dataset.
I also tried to run cbBuild in directory not under dataRoot but end with
deactivating the hierarchy.
Please advise the best way to recovery the dataset in each collection and
add new dataset into a collections.
I appreciated the great of work building the cell browser.
Thanks a lot.
Robin
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Oh.... now I understand! You never made an htdocs directory.
yes, this won't work. I never thought that someone would not have two
separate directories. It sounds like we should mention that somewhere in
the documentation, that they really must be separate, as otherwise cbBuild
will overwrite its own output files...
…On Thu, Mar 24, 2022 at 8:44 PM yesonse ***@***.***> wrote:
I managed an internal bioinformatic server and used it to host the cell
browser for my colleagues of 30-40 people. Several colleagues might add
some datasets sometime independently. I did not make a specific htmlDir or
dataRoot.
I just simply made one directory and have httpd visit that directory.
So my case could be special and I thought I could set outDir as the
dataRoot. I have not realized that hierarchy need a specific "dataRoot"
other than outDir for 'cbBuild -o'.
I have thought hierarchy only need a tree of outputs of cbBuild, not
related to where and how you run cbBuild.
I figured out that I just need to put the input files needed for cbBuild
in other places, put their paths in the cellbrowser.conf under a tree of
directories, run cbBuild under each subdirectory.
Thank you very much for your great of work of build the cellbrowser!
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Dear there,
I run a local host with about 20 datasets.
Now I like to group them into collections as suggested https://cellbrowser.readthedocs.io/en/master/collections.html.
After I run "cbBuild -r", the cell browser showed the collections well, but could not find each dataset in each collection.
I found there was no cellbrowser.conf in the subdirectory of collection, and made one for each. I tried to run cbBuild in the subdirectory end with errors of copying exprMatrix.tsv.gz to itself.
I tried to read some codes from the source, and believe it is right to put the dataset under the collection first, then run cbBuild in the sub-directory of the dataset.
I also tried to run cbBuild in directory not under dataRoot but end with deactivating the hierarchy.
Please advise the best way to recovery the dataset in each collection and add new dataset into a collections.
I appreciated the great of work building the cell browser.
Thanks a lot.
Robin
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