[BUG] Installed excellgene but web interface won't load.

[dfermin]

Describe the bug Hi

Installed excellgene using the github repo. Tried to load the example-dataset/pbmc3k.h5ad with this command:

excellxgene launch example-dataset/pbmc3k.h5ad --port 5002

I get this error on the terminal:

ERROR:backend.server.app.app:Exception on / [GET]
Traceback (most recent call last):
jinja2.exceptions.TemplateNotFound: index.html

And, when I go to the browser I see: "500 Internal Server Error" "The server encountered an internal error and was unable to complete your request. Either the server is overloaded or there is an error in the application."

Version info Hosted, running in Anaconda environment with Python 3.8.5 Browser: Chrome Version: [excellxgene] Version 2.9.2

Version (please complete the following information):

• Desktop or hosted?:
• Browser (if hosted) [e.g. chrome, safari]:
• Version [e.g. 0.13.0]:

Conda environment packages:

Package                       Version
----------------------------- -------------------
aniso8601                     8.1.1
anndata                       0.7.8
annoy                         1.17.1
async-timeout                 4.0.2
attrs                         20.3.0
Authlib                       1.0.1
backcall                      0.2.0
backports.functools-lru-cache 1.6.1
batchglm                      0.7.4
bbknn                         1.5.1
bleach                        3.2.3
boto3                         1.14.39
botocore                      1.17.44
Brotli                        1.0.9
certifi                       2020.12.5
cffi                          1.14.4
chardet                       4.0.0
charset-normalizer            2.0.12
click                         8.1.3
cryptography                  37.0.4
cycler                        0.10.0
Cython                        0.29.32
dask                          2021.1.1
decorator                     4.4.2
defusedxml                    0.6.0
Deprecated                    1.2.13
diffxpy                       0.7.4
dill                          0.3.5.1
docutils                      0.15.2
entrypoints                   0.3
excellxgene                   2.9.2
fastobo                       0.9.3
fbpca                         1.0
filelock                      3.8.0
Flask                         2.2.2
Flask-Compress                1.8.0
Flask-Cors                    3.0.10
Flask-RESTful                 0.3.9
flask-server-timing           0.1.2
flask-sock                    0.5.2
flask-talisman                0.7.0
flatbuffers                   1.12
flatten-dict                  0.3.0
fsspec                        0.7.4
geosketch                     1.2
get-version                   2.1
grpcio                        1.43.0
gunicorn                      20.0.4
h11                           0.13.0
h5py                          2.10.0
harmonypy                     0.0.6
hnswlib                       0.5.2
idna                          2.10
igraph                        0.9.11
importlib-metadata            4.12.0
iniconfig                     1.1.1
intervaltree                  3.1.0
ipykernel                     5.3.4
ipython                       7.20.0
ipython-genutils              0.2.0
itsdangerous                  2.1.2
jedi                          0.18.0
Jinja2                        3.0.1
jmespath                      0.10.0
joblib                        1.0.0
jsonschema                    3.2.0
jupyter-client                6.1.7
jupyter-core                  4.7.1
jupytext                      1.6.0
kiwisolver                    1.3.1
legacy-api-wrap               1.2
leidenalg                     0.8.10
llvmlite                      0.35.0
markdown-it-py                0.5.8
MarkupSafe                    2.1.1
matplotlib                    3.3.4
mistune                       0.8.4
msgpack                       1.0.4
natsort                       7.1.1
nbconvert                     5.6.1
nbformat                      5.1.2
networkx                      2.5
numba                         0.52.0
numexpr                       2.7.2
numpy                         1.21.5
packaging                     20.9
pandas                        1.2.1
pandocfilters                 1.4.3
parso                         0.8.1
pathlib2                      2.3.5
patsy                         0.5.1
pexpect                       4.8.0
pickleshare                   0.7.5
Pillow                        8.4.0
pip                           20.3.3
plotly                        4.8.1
pluggy                        0.13.1
prompt-toolkit                3.0.14
protobuf                      4.21.5
psutil                        5.9.0
ptyprocess                    0.7.0
py                            1.10.0
pyarrow                       1.0.1
pycairo                       1.20.0
pycparser                     2.20
Pygments                      2.7.4
PyJWT                         2.4.0
pynndescent                   0.5.7
pyparsing                     2.4.7
pyrsistent                    0.17.3
pytest                        6.2.2
python-dateutil               2.8.1
python-dotenv                 0.20.0
python-igraph                 0.9.11
pytz                          2020.5
PyYAML                        5.4.1
pyzmq                         20.0.0
ray                           1.11.0
redis                         4.3.4
requests                      2.26.0
retrying                      1.3.3
rpy2                          3.3.5
s3fs                          0.4.2
s3transfer                    0.3.4
sam-algorithm                 1.0.0
scanorama                     1.7.2
scanpy                        1.8.2
scikit-learn                  1.0.1
scipy                         1.6.0
seaborn                       0.11.1
setuptools                    52.0.0.post20210125
setuptools-scm                5.0.1
simple-websocket              0.8.0
sinfo                         0.3.1
six                           1.15.0
sortedcontainers              2.4.0
sparse                        0.11.2
SQLAlchemy                    1.3.22
statsmodels                   0.12.1
stdlib-list                   0.8.0
tables                        3.6.1
testpath                      0.4.4
texttable                     1.6.3
threadpoolctl                 2.1.0
tiledb                        0.7.7
toml                          0.10.2
toolz                         0.11.1
tornado                       6.1
tqdm                          4.56.0
traitlets                     5.0.5
tzlocal                       2.1
umap-learn                    0.4.6
urllib3                       1.25.11
wcwidth                       0.2.5
webencodings                  0.5.1
Werkzeug                      2.2.2
wheel                         0.36.2
wrapt                         1.14.1
wsproto                       1.2.0
xlrd                          1.2.0
zipp                          3.8.1

[atarashansky]

Unfortunately, installing excellxgene using the github repo will not work. That's meant for development mode only. Please install with pip install excellxgene. Alternatively, you can compile a pypi distribution with make pydist from the root directory of the repository, and then pip install dist/excellxgene-...-.tar.gz