Unable to install pysam with Python 3.8 or 3.10

[Chloe Saras Thangavelu]

Hello,

I am trying to install pysam but I get build wheel errors (see below). I have tried multiple versions of python including 3.8 and 3.11, but still get the same error. I have also tried downloading with bioconda instead. 

conda install pysam

Collecting package metadata (current_repodata.json): ...working... done Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve. Note: you may need to restart the kernel to use updated packages.

PackagesNotFoundError: The following packages are not available from current channels: - pysam Current channels: - https://conda.anaconda.org/bioconda/win-64 - https://conda.anaconda.org/bioconda/noarch - https://conda.anaconda.org/conda-forge/win-64 - https://conda.anaconda.org/conda-forge/noarch - https://repo.anaconda.com/pkgs/main/win-64 - https://repo.anaconda.com/pkgs/main/noarch - https://repo.anaconda.com/pkgs/r/win-64 - https://repo.anaconda.com/pkgs/r/noarch - https://repo.anaconda.com/pkgs/msys2/win-64 - https://repo.anaconda.com/pkgs/msys2/noarch 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.

pip install pysam

Collecting pysam Using cached pysam-0.21.0.tar.gz (4.1 MB) Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'error' Note: you may need to restart the kernel to use updated packages.

error: subprocess-exited-with-error Getting requirements to build wheel did not run successfully. exit code: 1 [34 lines of output] # pysam: cython is available - using cythonize if necessary # pysam: htslib mode is shared # pysam: HTSLIB_CONFIGURE_OPTIONS=None '.' is not recognized as an internal or external command, operable program or batch file. '.' is not recognized as an internal or external command, operable program or batch file. # pysam: htslib configure options: None Traceback (most recent call last): File "C:\Users\thangavelucs\AppData\Local\anaconda3\lib\site-packages\pip\_vendor\pep517\in_process\_in_process.py", line 351, in <module> main() File "C:\Users\thangavelucs\AppData\Local\anaconda3\lib\site-packages\pip\_vendor\pep517\in_process\_in_process.py", line 333, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "C:\Users\thangavelucs\AppData\Local\anaconda3\lib\site-packages\pip\_vendor\pep517\in_process\_in_process.py", line 118, in get_requires_for_build_wheel return hook(config_settings) File "C:\Users\thangavelucs\AppData\Local\Temp\1\pip-build-env-xmq85ogs\overlay\Lib\site-packages\setuptools\build_meta.py", line 341, in get_requires_for_build_wheel return self._get_build_requires(config_settings, requirements=['wheel']) File "C:\Users\thangavelucs\AppData\Local\Temp\1\pip-build-env-xmq85ogs\overlay\Lib\site-packages\setuptools\build_meta.py", line 323, in _get_build_requires self.run_setup() File "C:\Users\thangavelucs\AppData\Local\Temp\1\pip-build-env-xmq85ogs\overlay\Lib\site-packages\setuptools\build_meta.py", line 487, in run_setup super(_BuildMetaLegacyBackend, File "C:\Users\thangavelucs\AppData\Local\Temp\1\pip-build-env-xmq85ogs\overlay\Lib\site-packages\setuptools\build_meta.py", line 338, in run_setup exec(code, locals()) File "<string>", line 383, in <module> File "<string>", line 79, in run_make_print_config File "C:\Users\thangavelucs\AppData\Local\anaconda3\lib\subprocess.py", line 421, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "C:\Users\thangavelucs\AppData\Local\anaconda3\lib\subprocess.py", line 503, in run with Popen(*popenargs, **kwargs) as process: File "C:\Users\thangavelucs\AppData\Local\anaconda3\lib\subprocess.py", line 971, in __init__ self._execute_child(args, executable, preexec_fn, close_fds, File "C:\Users\thangavelucs\AppData\Local\anaconda3\lib\subprocess.py", line 1440, in _execute_child hp, ht, pid, tid = _winapi.CreateProcess(executable, args, FileNotFoundError: [WinError 2] The system cannot find the file specified [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error Getting requirements to build wheel did not run successfully. exit code: 1 See above for output. note: This error originates from a subprocess, and is likely not a problem with pip.

[Sebastian Luna Valero]

Hi,

I believe the problem is that pysam is only available for Linux/OSX and you are using Windows:

https://anaconda.org/bioconda/pysam

Do you have a Linux/OSX system to try?

Best regards,

Sebastian

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