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Merck / deepbgc

BGC Detection and Classification Using Deep Learning
https://doi.org/10.1093/nar/gkz654
MIT License
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Installing deepBGC #56

Open planctoqueen opened 3 years ago

planctoqueen commented 3 years ago

I am trying to install deepBGC on my pc but I'm havig some issues that I cannot solve.

I am using Python3.7.0 and conda and already added all the necessary channels. However, everytime I try to install deepBGC I get this issue:

image

I already try with and without forcing the deepBGC version and get the same error everytime.

Can you please help?

Thanks!~

prihoda commented 3 years ago

Hi @planctoqueen can you share the full error output and also the output of conda info ?

planctoqueen commented 3 years ago

Hi @prihoda ,

thanks for the wquick answer.

This is the full error output image

And here the conda info: image Thank you!

prihoda commented 3 years ago

Hmm, not sure what could be wrong honestly. I hope this is not a broader issue. Anyway, you should be able to install the dependencies from conda manually and then install deepbgc using pip:

conda install prodigal hmmer
pip install deepbgc
alohith commented 3 years ago

Is there an update on this? I'm having a similar issue and looks like the same error when trying 'conda install deepbgc' with and without the '-c conda-forge' flag

the solution proposed by @prihoda on May 18th 'looks' like it worked, but when i try to do the first cmd on the tutorial 'deepbgc download' i get the following:

(deepbgc) PS A:\Akshar> conda install prodigal hmmer Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with initial frozen solve. Retrying with flexible solve.

PackagesNotFoundError: The following packages are not available from current channels:

Current channels:

To search for alternate channels that may provide the conda package you're looking for, navigate to

https://anaconda.org

and use the search bar at the top of the page.

(deepbgc) PS A:\Akshar> deepbgc download

| _ \ __ | ) / ) / ) | | \ \/ \/ \ | \ | | | | | |/ / / / |) | |) || |_| || | |____/ \|___| _/|__/ __| __) =================|_|===== version 0.1.29 ===== INFO 05/10 14:11:46 Creating download directory: C:\Users\TRaveler\AppData\Local\deepbgc\deepbgc\data\0.1.0 INFO 05/10 14:11:46 ================================================================================ INFO 05/10 14:11:46 Checking: C:\Users\TRaveler\AppData\Local\deepbgc\deepbgc\data\0.1.0\detector\deepbgc.pkl INFO 05/10 14:11:46 Downloading: https://github.com/Merck/deepbgc/releases/download/v0.1.0/deepbgc.pkl ERROR 05/10 14:11:46 0 Traceback (most recent call last): File "C:\Users\TRaveler.conda\envs\deepbgc\lib\site-packages\deepbgc\main.py", line 113, in main run(argv) File "C:\Users\TRaveler.conda\envs\deepbgc\lib\site-packages\deepbgc\main.py", line 102, in run args.func.run(*args_dict) File "C:\Users\TRaveler.conda\envs\deepbgc\lib\site-packages\deepbgc\command\download.py", line 25, in run util.download_files(DOWNLOADS) File "C:\Users\TRaveler.conda\envs\deepbgc\lib\site-packages\deepbgc\util.py", line 403, in download_files download_file(url=url, target_path=target_path, checksum=checksum, gzipped=gzipped) File "C:\Users\TRaveler.conda\envs\deepbgc\lib\site-packages\deepbgc\util.py", line 425, in download_file File "C:\Users\TRaveler.conda\envs\deepbgc\lib\urllib\request.py", line 247, in urlretrieve with contextlib.closing(urlopen(url, data)) as fp: File "C:\Users\TRaveler.conda\envs\deepbgc\lib\urllib\request.py", line 222, in urlopen return opener.open(url, data, timeout) File "C:\Users\TRaveler.conda\envs\deepbgc\lib\urllib\request.py", line 525, in open response = self._open(req, data) File "C:\Users\TRaveler.conda\envs\deepbgc\lib\urllib\request.py", line 543, in _open '_open', req) File "C:\Users\TRaveler.conda\envs\deepbgc\lib\urllib\request.py", line 503, in _call_chain result = func(args) File "C:\Users\TRaveler.conda\envs\deepbgc\lib\urllib\request.py", line 1393, in https_open context=self._context, check_hostname=self._check_hostname) File "C:\Users\TRaveler.conda\envs\deepbgc\lib\urllib\request.py", line 1318, in do_open h = http_class(host, timeout=req.timeout, **http_conn_args) File "C:\Users\TRaveler.conda\envs\deepbgc\lib\http\client.py", line 1416, in init context = ssl._create_default_https_context() File "C:\Users\TRaveler.conda\envs\deepbgc\lib\ssl.py", line 589, in create_default_context File "C:\Users\TRaveler.conda\envs\deepbgc\lib\ssl.py", line 490, in load_default_certs self._load_windows_store_certs(storename, purpose) File "C:\Users\TRaveler.conda\envs\deepbgc\lib\ssl.py", line 482, in _load_windows_store_certs self.load_verify_locations(cadata=certs) ssl.SSLError: unknown error (_ssl.c:4034) ERROR 05/10 14:11:46 ================================================================================ ERROR 05/10 14:11:46 DeepBGC failed with SSLError ERROR 05/10 14:11:46 ================================================================================ ERROR 05/10 14:11:46 unknown error (_ssl.c:4034)

Also, I don't think hmmer or prodigal have actually been installed..

prihoda commented 3 years ago

Hey @alohith this looks like a network issue, can you try creating a separate environment and paste the log here?

conda create -n deepbgc python=3.7
conda activate deepbgc
conda install deepbgc
alohith commented 3 years ago

Hi @prihoda here's what it looks like. Very similar to what I was seeing before, also the same if I instead say 'python=3.6'

 (base) PS A:\Akshar> conda create -n deepbgc python=3.7
 Collecting package metadata (current_repodata.json): done
 Solving environment: done

 ## Package Plan ##

   environment location: C:\Users\TRaveler\.conda\envs\deepbgc

   added / updated specs:
     - python=3.7

 The following packages will be downloaded:

     package                    |            build
     ---------------------------|-----------------
     ca-certificates-2021.5.30  |       h5b45459_0         171 KB  conda-forge
     openssl-3.0.0              |       h8ffe710_1        10.0 MB  conda-forge
     pip-21.2.4                 |     pyhd8ed1ab_0         1.1 MB  conda-forge
     python-3.7.10              |h900ac77_102_cpython        17.9 MB  conda-forge
     python_abi-3.7             |          2_cp37m           4 KB  conda-forge
     setuptools-58.2.0          |   py37h03978a9_0         1.0 MB  conda-forge
     sqlite-3.36.0              |       h8ffe710_2         1.2 MB  conda-forge
     ucrt-10.0.20348.0          |       h57928b3_0         1.2 MB  conda-forge
     vc-14.2                    |       hb210afc_5          13 KB  conda-forge
     vs2015_runtime-14.29.30037 |       h902a5da_5         1.3 MB  conda-forge
     wheel-0.37.0               |     pyhd8ed1ab_1          31 KB  conda-forge
     ------------------------------------------------------------
                                            Total:        33.9 MB

 The following NEW packages will be INSTALLED:

   ca-certificates    conda-forge/win-64::ca-certificates-2021.5.30-h5b45459_0
   openssl            conda-forge/win-64::openssl-3.0.0-h8ffe710_1
   pip                conda-forge/noarch::pip-21.2.4-pyhd8ed1ab_0
   python             conda-forge/win-64::python-3.7.10-h900ac77_102_cpython
   python_abi         conda-forge/win-64::python_abi-3.7-2_cp37m
   setuptools         conda-forge/win-64::setuptools-58.2.0-py37h03978a9_0
   sqlite             conda-forge/win-64::sqlite-3.36.0-h8ffe710_2
   ucrt               conda-forge/win-64::ucrt-10.0.20348.0-h57928b3_0
   vc                 conda-forge/win-64::vc-14.2-hb210afc_5
   vs2015_runtime     conda-forge/win-64::vs2015_runtime-14.29.30037-h902a5da_5
   wheel              conda-forge/noarch::wheel-0.37.0-pyhd8ed1ab_1
 Proceed ([y]/n)? y

 Downloading and Extracting Packages
 python_abi-3.7       | 4 KB      | ############################################################################ | 100%
 ucrt-10.0.20348.0    | 1.2 MB    | ############################################################################ | 100%
 openssl-3.0.0        | 10.0 MB   | ############################################################################ | 100%
 python-3.7.10        | 17.9 MB   | ############################################################################ | 100%
 sqlite-3.36.0        | 1.2 MB    | ############################################################################ | 100%
 ca-certificates-2021 | 171 KB    | ############################################################################ | 100%
 pip-21.2.4           | 1.1 MB    | ############################################################################ | 100%
 wheel-0.37.0         | 31 KB     | ############################################################################ | 100%
 vc-14.2              | 13 KB     | ############################################################################ | 100%
 setuptools-58.2.0    | 1.0 MB    | ############################################################################ | 100%
 vs2015_runtime-14.29 | 1.3 MB    | ############################################################################ | 100%
 Preparing transaction: done
 Verifying transaction: done
 Executing transaction: done
 #
 # To activate this environment, use
 #
 #     $ conda activate deepbgc
 #
 # To deactivate an active environment, use
 #
 #     $ conda deactivate

 (base) PS A:\Akshar> conda activate deepbgc
 (deepbgc) PS A:\Akshar> conda install deepbgc
 Collecting package metadata (current_repodata.json): done
 Solving environment: failed with initial frozen solve. Retrying with flexible solve.
 Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
 Collecting package metadata (repodata.json): done
 Solving environment: failed with initial frozen solve. Retrying with flexible solve.
 Solving environment: -
 Found conflicts! Looking for incompatible packages.
 This can take several minutes.  Press CTRL-C to abort.
 failed

 UnsatisfiableError: The following specifications were found to be incompatible with each other:

 Output in format: Requested package -> Available versions

 (deepbgc) PS A:\Akshar>
planctoqueen commented 2 years ago

Hi!

I don't know if this is the correct solution but what solve the problem for me was to remove the conda-forge channel. conda config --remove channels conda-forge

hope it helps!~

Christabelteh commented 1 year ago

I have tried to run commands in anaconda powershell with conda create -n deepbgc python=3.7 hmmer prodigal, conda activate deepbgc and pip install deepbgc and seems hmmer and prodigal have been successfully downloaded . I have attached the output of following commands. conda create -n deepbgc python=3.7 hmmer prodigal output: Screenshot (2776) pip install deepbgc output: Screenshot (2779) end...: Screenshot (2780) However, every time I run the command conda install deepbgc, it keep showing me this issue:
Screenshot (2774) Btw, this is the info of my conda: Screenshot (2782)

Could somebody help me to solve the issue, your help would greatly appreciated for me. Thank you.