gibbons-lab / isb_course_2021 Goto Github PK

Hi @cdiener,

I hope my issue won't take much time, I have a pop-science talk in 2 weeks about microbiome research and was thinking of "stealing" a very nice interactive gimme_genome feature from your course:) Of course, with appropriate references to your course and ISB, just wanna add some interaction after the talk.

So, I tracked down the bug and it seems to be related to the data.
If you run models.py, !bootstrap command does not work and you will get HTTP Error 500 which leads to the reading of some assembly files.
I'm just wondering if it is a bug or maybe you made those files private intentionally, please, let me know, then I will come up with some other interactive activity.

Full error message:

Traceback (most recent call last):
File "/usr/local/bin/bootstrap", line 5, in
from course.bootstrap import main
File "/usr/local/lib/python3.7/dist-packages/course/init.py", line 1, in
from .utils import gimme_genome, gimme_exchanges, gimme_media, download, add_r_squared
File "/usr/local/lib/python3.7/dist-packages/course/utils.py", line 15, in
"https://github.com/Gibbons-Lab/2021_microbiome_course_data/"
File "/usr/local/lib/python3.7/dist-packages/pandas/util/_decorators.py", line 311, in wrapper
return func(*args, **kwargs)
File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers/readers.py", line 586, in read_csv
return _read(filepath_or_buffer, kwds)
File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers/readers.py", line 482, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers/readers.py", line 811, in init
self._engine = self._make_engine(self.engine)
File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers/readers.py", line 1040, in _make_engine
return mapping[engine](self.f, **self.options) # type: ignore[call-arg]
File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers/c_parser_wrapper.py", line 51, in init
self._open_handles(src, kwds)
File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers/base_parser.py", line 229, in _open_handles
errors=kwds.get("encoding_errors", "strict"),
File "/usr/local/lib/python3.7/dist-packages/pandas/io/common.py", line 614, in get_handle
storage_options=storage_options,
File "/usr/local/lib/python3.7/dist-packages/pandas/io/common.py", line 312, in _get_filepath_or_buffer
with urlopen(req_info) as req:
File "/usr/local/lib/python3.7/dist-packages/pandas/io/common.py", line 212, in urlopen
return urllib.request.urlopen(*args, **kwargs)
File "/usr/lib/python3.7/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/usr/lib/python3.7/urllib/request.py", line 531, in open
response = meth(req, response)
File "/usr/lib/python3.7/urllib/request.py", line 641, in http_response
'http', request, response, code, msg, hdrs)
File "/usr/lib/python3.7/urllib/request.py", line 569, in error
return self._call_chain(*args)
File "/usr/lib/python3.7/urllib/request.py", line 503, in _call_chain
result = func(*args)
File "/usr/lib/python3.7/urllib/request.py", line 649, in http_error_default
raise HTTPError(req.full_url, code, msg, hdrs, fp)

Dear Creator,

I found your very useful qiime course on the YouTube and finally find the materials for the course here. However, when I tried to follow exactly the video and install it on the google Colab, it never accomplished.

!git clone https://github.com/gibbons-lab/isb_course_2021 materials
%cd materials
%run setup_qiime2

Even I tried your suggested commend (bellow) in forum, it did not work.

!wget https://github.com/Gibbons-Lab/isb_course_2021/raw/main/setup_qiime2
%run setup_qiime2

As I want to run my code on the google Colab, do you have any suggestions for me?

Best Regards,
Ghs