Comments (7)
maximilianh
commented on July 30, 2024
I’ll remove the pdb thing, that’s confusing.
So you haven’t installed igraph. Is there a reason for that? I think it’s
almost required by scanpy. “pip install python-igraph” does that work for
you?
…On Thu, Oct 11, 2018 at 9:25 PM Jeltje ***@***.***> wrote:
../../cellBrowser/src/cbScanpy -e
filtered_gene_bc_matrices/hg19/matrix.mtx -o myscanpyout -n pbmc3k
INFO:root:Creating myscanpyout
cbScanpy $Id: 1e7c40a1801e210aa974d42ddb5ea5f4d3f225e6 $
Input file: filtered_gene_bc_matrices/hg19/matrix.mtx
Start time: 2018-10-11 21:19:08.077474
scanpy==1.3.2 anndata==0.6.11 numpy==1.14.6 scipy==1.1.0 pandas==0.23.4 scikit-learn==0.20.0 statsmodels==0.9.0
INFO:root:Loading expression matrix: mtx format
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
Data has 2700 samples/observations
Data has 32738 genes/variables
Basic filtering: keep only cells with min 200 genes
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
Basic filtering: keep only gene with min 3 cells
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
Remove cells with more than 0.050000 percent of mitochondrial genes
Computing percentage of mitochondrial genes
Remove cells with less than 10 and more than 15000 genes
Filtering cells
After filtering: Data has 2643 samples/observations and 13714 genes/variables
Expression normalization, counts per cell = 10000
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
Finding highly variable genes: min_mean=0.012500, max_mean=3.000000, min_disp=0.500000
Number of variable genes identified: 1844
Did log2'ing of data
Performing initial PCA, number of PCs: 100
Using 20 PCs as configured in config
Performing tSNE
Performing Louvain Clustering, using 20 PCs and 5 neighbors
File "../../cellBrowser/src/cbPyLib/cellbrowser.py", line 3267, in cbScanpyCli
adata = cbScanpy(matrixFname, confFname, figDir, logFname)
File "../../cellBrowser/src/cbPyLib/cellbrowser.py", line 3190, in cbScanpy
sc.tl.louvain(adata, resolution=res)
File "/home/jeltjessh/venvs/cellBrowser/lib/python3.6/site-packages/scanpy/tools/louvain.py", line 103, in louvain
g = utils.get_igraph_from_adjacency(adjacency, directed=directed)
File "/home/jeltjessh/venvs/cellBrowser/lib/python3.6/site-packages/scanpy/utils.py", line 304, in get_igraph_from_adjacency
import igraph as ig
> /home/jeltjessh/venvs/cellBrowser/lib/python3.6/site-packages/scanpy/utils.py(304)get_igraph_from_adjacency()
-> import igraph as ig
(Pdb)
... and then I'm stuck in the (Pdb) interface.
(Pdb) exit
INFO:root:Writing anndata object to myscanpyout/anndata.h5ad
Traceback (most recent call last):
File "../../cellBrowser/src/cbScanpy", line 13, in <module>
cellbrowser.cbScanpyCli()
File "../../cellBrowser/src/cbPyLib/cellbrowser.py", line 3275, in cbScanpyCli
adata.write(adFname)
UnboundLocalError: local variable 'adata' referenced before assignment
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Jeltje
commented on July 30, 2024
igraph isn't a dependency of scanpy:
pip show scanpy
Name: scanpy
Version: 1.3.2
Summary: Single-Cell Analysis in Python.
Home-page: http://github.com/theislab/scanpy
Author: Alex Wolf, Philipp Angerer, Davide Cittaro, Gokcen Eraslan, Fidel Ramirez, Tobias Callies
Author-email: [email protected]
License: BSD
Location: /home/jeltjessh/venvs/cellBrowser/lib/python3.6/site-packages
Requires: numba, natsort, matplotlib, joblib, pandas, h5py, scipy, seaborn, networkx, tables, statsmodels, scikit-learn, anndata
So I pip installed it, but then I got
../../cellBrowser/src/cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o myscanpyout -n pbmc3k 2>&1 | tee cb.log
INFO:root:Creating myscanpyout
File "../../cellBrowser/src/cbPyLib/cellbrowser.py", line 3267, in cbScanpyCli
adata = cbScanpy(matrixFname, confFname, figDir, logFname)
File "../../cellBrowser/src/cbPyLib/cellbrowser.py", line 3064, in cbScanpy
sc.logging.print_versions()
File "/home/jeltjessh/venvs/cellBrowser/lib/python3.6/site-packages/scanpy/logging.py", line 180, in print_versions
_print_versions_dependencies(['scanpy'] + _DEPENDENCIES_NUMERICS)
File "/home/jeltjessh/venvs/cellBrowser/lib/python3.6/site-packages/scanpy/logging.py", line 169, in _print_versions_dependencies
imp = __import__(mod_name)
File "/home/jeltjessh/venvs/cellBrowser/lib/python3.6/site-packages/igraph/__init__.py", line 8, in <module>
raise DeprecationWarning("To avoid name collision with the igraph project, "
cbScanpy $Id: 1e7c40a1801e210aa974d42ddb5ea5f4d3f225e6 $
Input file: filtered_gene_bc_matrices/hg19/matrix.mtx
Start time: 2018-10-12 10:22:04.242416
scanpy==1.3.2 anndata==0.6.11 numpy==1.14.6 scipy==1.1.0 pandas==0.23.4 scikit-learn==0.20.0 statsmodels==0.9.0 > /home/jeltjessh/venvs/cellBrowser/lib/python3.6/site-packages/igraph/__init__.py(8)<module>()
-> raise DeprecationWarning("To avoid name collision with the igraph project, "
It's a cliffhanger! It's listing the installed versions but not telling me what it wants.
Anyway, it then occurred to me you might have changed things since yesterday, so I pulled the latest.
../../cellBrowser/src/cbScanpy -e filtered_gene_bc_matrices/hg19/matrix.mtx -o myscanpyout -n pbmc3k
Traceback (most recent call last):
File "../../cellBrowser/src/cbScanpy", line 13, in <module>
cellbrowser.cbScanpyCli()
File "../../cellBrowser/src/cbPyLib/cellbrowser/cellbrowser.py", line 2950, in cbScanpyCli
if options.init:
AttributeError: 'Values' object has no attribute 'init'
Can you let me know when you have tested the example on a clean system?
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maximilianh
commented on July 30, 2024
I accidentally did a commit yesterday where I should have not committed.
very sorry. I'm trying to fix things now or will revert.
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maximilianh
commented on July 30, 2024
I think I've fixed it all. I'll do test it on someone else's laptop
today, but otherwise the following should work:
pip install cellbrowser
If you're not root and just a normal Unix user, do this:
pip install cellbrowser --user
…On Sat, Oct 13, 2018 at 12:45 PM Maximilian Haeussler ***@***.***> wrote:
I accidentally did a commit yesterday where I should have not committed. very sorry. I'm trying to fix things now or will revert.
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maximilianh
commented on July 30, 2024
OK, now getting back to your igraph question:
did you really install the correct package:
pip install igraph-python
On Sat, Oct 13, 2018 at 2:41 PM Maximilian Haeussler
<[email protected]> wrote:
…
I think I've fixed it all. I'll do test it on someone else's laptop today, but otherwise the following should work:
pip install cellbrowser
If you're not root and just a normal Unix user, do this:
pip install cellbrowser --user
On Sat, Oct 13, 2018 at 12:45 PM Maximilian Haeussler ***@***.***> wrote:
>
> I accidentally did a commit yesterday where I should have not committed. very sorry. I'm trying to fix things now or will revert.
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maximilianh
commented on July 30, 2024
I don't know why igraph is not a requirement for scanpy. De facto, it
is required to do anything useful with scanpy. I think Alex doesn't
want it as a requirement as very often the scanpy installation will
fail, as the igraph package itself has so many dependencies.
His recommended pip command is this one and it does have the requirements:
pip install scanpy python-igraph louvain
Are you using conda? If there is any problem with this pip command,
try using conda...
Let me know how it goes, I've been through this, too. It's the biggest
stumbling block with scanpy.
If everything goes according to plan, you'll soon have a seurat wrapper, too.
On Sat, Oct 13, 2018 at 2:42 PM Maximilian Haeussler
<[email protected]> wrote:
…
OK, now getting back to your igraph question:
did you really install the correct package:
pip install igraph-python
On Sat, Oct 13, 2018 at 2:41 PM Maximilian Haeussler
***@***.***> wrote:
>
> I think I've fixed it all. I'll do test it on someone else's laptop today, but otherwise the following should work:
>
> pip install cellbrowser
>
> If you're not root and just a normal Unix user, do this:
>
> pip install cellbrowser --user
>
>
> On Sat, Oct 13, 2018 at 12:45 PM Maximilian Haeussler ***@***.***> wrote:
> >
> > I accidentally did a commit yesterday where I should have not committed. very sorry. I'm trying to fix things now or will revert.
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maximilianh
commented on July 30, 2024
Closing this one, too, as #11 was closed
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Related Issues (20)
- mtx nomenclature in conf file HOT 2
- Question - Linking cellBrowser through another web-app with dynamic data selection HOT 9
- gene expression and proteins together HOT 4
- stop() instead of error() in the cellbrowser.R script? HOT 1
- Special characters in the column names HOT 1
- os.getLogin() function breaks seurat.py HOT 2
- Question/Issue: Index not showing HOT 28
- Split view by dataset HOT 1
- abstract.html do not working HOT 8
- cache problem of google chrome browser or server httpd setting? HOT 3
- Custom colors for each attribute HOT 8
- Cannot find dataset when refreshing HOT 7
- Cannot read single sample name from the matrix HOT 3
- Spatial data in cell browser HOT 9
- [Feature Request] Find Cells by named selection HOT 6
- --useMtx is ignored if too.big == TRUE in runSeurat.R HOT 6
- On killing cbScanpyImport due to Out of memory, process exits with 0 exit code HOT 1
- `scanpy` docs bug still not resolved HOT 5
- Issue w/ running cbSeurat: argument "counts" is missing, with no default HOT 17
- Error in `[.data.frame`(feature.names, , gene.column) : undefined columns selected HOT 1
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