I am new to Python, Anaconda, and coding in general. I'm trying to install pysam. I need it to install HTSeq so that I can convert bam files to count files for a class project. Once they are count files, I plan to use edgeR for the rest of the data analysis. I was able to install NumPy without a problem. I've tried multiple codes for installing pysam, so I'm wondering if I'm missing some sort of dependency? Do I need to install samtools or something before I can install pysam?
In addition to tips for installing pysam, I am also open to advice for other methods for converting bam files to count files. Is it possible to download and use HTSeq for this purpose without pysam? Converting the file is the only thing I need to use HTSeq for to complete my class project. Is there another program other than HTSeq that I could use?
I appreciate any advice, and sorry if I'm leaving out any critical information. This is my first big coding project and the first time I've had to ask a stack question.
Thanks!
Here is what I have tried to install pysam:
conda config --add channels r
Warning: 'r' already in 'channels' list, moving to the top
conda config --add channels bioconda
Warning: 'bioconda' already in 'channels' list, moving to the top
conda install pysam
conda install -c bioconda pysam
conda install -c "bioconda/label/cf201901" pysam
For every conda install I get the same output:
Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve.
PackagesNotFoundError: The following packages are not available from current channels:
pysam
Current channels: a bunch of links here that stack won't let me post 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.
```
```
I also tried:
conda config --append channels conda-forge
Warning: 'conda-forge' already in 'channels' list, moving to the bottom
And when I tried the conda install I got the same output as before.
Even though it's not recommended, I also tried to install with pip using:
pip install pysam
Collecting pysam Using cached pysam-0.20.0.tar.gz (4.0 MB) Preparing metadata (setup.py) ... error error: subprocess-exited-with-error
python setup.py egg_info did not run successfully. exit code: 1 [24 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. Traceback (most recent call last): File "<string>", line 2, in <module> File "<pip-setuptools-caller>", line 34, in <module> File "C:\Users\Emily\AppData\Local\Temp\pip-install-q06_8qe9\pysam_31e61bb6d116452f888986de7135a214\setup.py", line 381, in <module> htslib_make_options = run_make_print_config() File "C:\Users\Emily\AppData\Local\Temp\pip-install-q06_8qe9\pysam_31e61bb6d116452f888986de7135a214\setup.py", line 79, in run_make_print_config stdout = subprocess.check_output(["make", "-s", "print-config"]) File "C:\ProgramData\Anaconda3\lib\subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "C:\ProgramData\Anaconda3\lib\subprocess.py", line 505, in run with Popen(*popenargs, **kwargs) as process: File "C:\ProgramData\Anaconda3\lib\subprocess.py", line 951, in __init__ self._execute_child(args, executable, preexec_fn, close_fds, File "C:\ProgramData\Anaconda3\lib\subprocess.py", line 1420, in _execute_child hp, ht, pid, tid = _winapi.CreateProcess(executable, args, FileNotFoundError: [WinError 2] The system cannot find the file specified pysam: htslib configure options: None [end of output]
note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed
Encountered error while generating package metadata. See above for output.
note: This is an issue with the package mentioned above, not pip. hint: See above for details.
I also restarted my laptop, uninstalled and reinstalled Python and Anaconda. I am using Windows, and working in VS through Anaconda as an administrator.
