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aristoteleo / dynamo-release

Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
https://dynamo-release.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
415 stars 59 forks source link

error when install this program #116

Closed Golden-proteogenomics closed 3 years ago

Golden-proteogenomics commented 3 years ago

when I use the code "python3 -m pip install git+https://github.com:aristoteleo/dynamo-release" to install this software, but the error was rraised as follow. Collecting git+https://github.com:aristoteleo/dynamo-release Cloning https://github.com:aristoteleo/dynamo-release to /tmp/pip-req-build-3yrf835a Running command git clone -q https://github.com:aristoteleo/dynamo-release /tmp/pip-req-build-3yrf835a fatal: unable to access 'https://github.com:aristoteleo/dynamo-release/': URL using bad/illegal format or missing URL ERROR: Command errored out with exit status 128: git clone -q https://github.com:aristoteleo/dynamo-release /tmp/pip-req-build-3yrf835a Check the logs for full command output. So, what your suggestion for this error?

Xiaojieqiu commented 3 years ago

Hi @Golden-proteogenomics , please refer to our installation guidance:

https://dynamo-release.readthedocs.io/en/latest/ten_minutes_to_dynamo.html#how-to-install

If you have further issues, please let me know.

Golden-proteogenomics commented 3 years ago

ok，thanks. but there are a new question when I use the code import matplotlib matplotlib.use('Agg') import dynamo as dyn dyn.get_all_dependencies_version() dyn.configuration.set_figure_params('dynamo', background='white') adata = dyn.sample_data.zebrafish() the error will arise in this formation “ raise err File "/usr/lib/python3.8/socket.py", line 796, in create_connection sock.connect(sa) OSError: [Errno 101] Network is unreachable

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "", line 1, in File "/home/shuai/.local/lib/python3.8/site-packages/dynamo/sample_data.py", line 80, in zebrafish adata = get_adata(url, filename) File "/home/shuai/.local/lib/python3.8/site-packages/dynamo/sample_data.py", line 29, in get_adata urlretrieve(url, filename) # download the data File "/usr/lib/python3.8/urllib/request.py", line 247, in urlretrieve with contextlib.closing(urlopen(url, data)) as fp: File "/usr/lib/python3.8/urllib/request.py", line 222, in urlopen return opener.open(url, data, timeout) File "/usr/lib/python3.8/urllib/request.py", line 525, in open response = self._open(req, data) File "/usr/lib/python3.8/urllib/request.py", line 542, in _open result = self._call_chain(self.handle_open, protocol, protocol + File "/usr/lib/python3.8/urllib/request.py", line 502, in _call_chain result = func(*args) File "/usr/lib/python3.8/urllib/request.py", line 1369, in https_open return self.do_open(http.client.HTTPSConnection, req, File "/usr/lib/python3.8/urllib/request.py", line 1329, in do_open raise URLError(err) urllib.error.URLError: <urlopen error [Errno 101] Network is unreachable>” and Ithis this example_data of zebrafish couldnot download, please could tell me what that reason?

Xiaojieqiu commented 3 years ago

Those datasets are hosted on dropbox. If the dropbox service is blocked, you cannot download it. You may need a VPN to resolve this. Feel free to email me to get those datasets if you still have troubles. I will take some time to host the dataset on our institute's public server sometime soon.

Golden-proteogenomics commented 3 years ago

I am sorry that although we have opened VPN, we still can’t download this data. So, we need your help to give us a way to download the data. On the other hand, the code in the web "https://dynamo-release.readthedocs.io/en/latest/scEU_seq_rpe1_analysis_kinetic.html" is "rpe1 = dyn.read('/Users/xqiu/Dropbox (Personal)/dynamo/dont_remove/rpe1.h5ad')" meaning to use the cell cycle dataset from Battich, et al (2020). So, I want to know what and how to produce those datasets in GEO GSE128365, which mentioned by Battich, et al, because I searched for the data they uploaded, but did not find the file in the format you mentioned.

Xiaojieqiu commented 3 years ago

The source code for the dyn.sample_data.zebrafish() is here: https://github.com/aristoteleo/dynamo-release/blob/master/dynamo/sample_data.py

If you do have vpn, try to download the file linked in the source code: https://www.dropbox.com/s/5wk3q2xhgqai2xq/zebrafish.h5ad?dl=1

The data for rep1 is processed by us. I am extremely busy these days so if you want the data from us, you may need to wait for 1 or two weeks for me to update the package and readthedocs page. If you want the data now, email me to request the data as I mentioned above (xqiu@wi.mit.edu).

(For rep1 data, however, a little thinking and scrambling our github issues (e.g: https://github.com/aristoteleo/dynamo-release/issues/110) from your side should enable you to produce the same data. )

Golden-proteogenomics commented 3 years ago

I'm sorry to bother you so much, and you have been eager to help us. this is my email sun_jinshuai@grmh-gdl.cn for communication issues. Could you give me both data for me in mailbox attachment?