pip install velocyto: ERROR: Command errored out with exit status 1:

[sruthi-hub]

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There is a problem installing velocyto - both on macOS and in Windows. Any help is appreciated!

All the dependencies were installed successfully using: conda install numpy scipy cython numba matplotlib scikit-learn h5py click

My system info: Python 3.7.0 (default, Jun 28 2018, 08:04:48) [MSC v.1912 64 bit (AMD64)] :: Anaconda, Inc. on win32

Complete error: (base) C:\Users\sruth>pip install velocyto Collecting velocyto Using cached velocyto-0.17.17.tar.gz (198 kB) Requirement already satisfied: numpy in c:\users\sruth\appdata\local\continuum\anaconda3\lib\site-packages (from velocyto) (1.18.1) Requirement already satisfied: scipy in c:\users\sruth\appdata\local\continuum\anaconda3\lib\site-packages (from velocyto) (1.4.1) Requirement already satisfied: cython in c:\users\sruth\appdata\local\continuum\anaconda3\lib\site-packages (from velocyto) (0.29.17) Requirement already satisfied: numba in c:\users\sruth\appdata\local\continuum\anaconda3\lib\site-packages (from velocyto) (0.49.0) Requirement already satisfied: matplotlib in c:\users\sruth\appdata\local\continuum\anaconda3\lib\site-packages (from velocyto) (3.1.3) Requirement already satisfied: scikit-learn in c:\users\sruth\appdata\local\continuum\anaconda3\lib\site-packages (from velocyto) (0.22.1) Requirement already satisfied: h5py in c:\users\sruth\appdata\local\continuum\anaconda3\lib\site-packages (from velocyto) (2.10.0) Collecting loompy Using cached loompy-3.0.6.tar.gz (41 kB) Collecting pysam Using cached pysam-0.15.4.tar.gz (1.6 MB) ERROR: Command errored out with exit status 1: command: 'c:\users\sruth\appdata\local\continuum\anaconda3\python.exe' -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'C:\Users\sruth\AppData\Local\Temp\pip-install-jregty3v\pysam\setup.py'"'"'; file='"'"'C:\Users\sruth\AppData\Local\Temp\pip-install-jregty3v\pysam\setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base 'C:\Users\sruth\AppData\Local\Temp\pip-install-jregty3v\pysam\pip-egg-info' cwd: C:\Users\sruth\AppData\Local\Temp\pip-install-jregty3v\pysam
Complete output (23 lines): # 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 "", line 1, in File "C:\Users\sruth\AppData\Local\Temp\pip-install-jregty3v\pysam\setup.py", line 241, in htslib_make_options = run_make_print_config() File "C:\Users\sruth\AppData\Local\Temp\pip-install-jregty3v\pysam\setup.py", line 68, in run_make_print_config stdout = subprocess.check_output(["make", "-s", "print-config"]) File "c:\users\sruth\appdata\local\continuum\anaconda3\lib\subprocess.py", line 376, in check_output **kwargs).stdout File "c:\users\sruth\appdata\local\continuum\anaconda3\lib\subprocess.py", line 453, in run with Popen(*popenargs, **kwargs) as process: File "c:\users\sruth\appdata\local\continuum\anaconda3\lib\subprocess.py", line 756, in init restore_signals, start_new_session) File "c:\users\sruth\appdata\local\continuum\anaconda3\lib\subprocess.py", line 1155, in _execute_child startupinfo) FileNotFoundError: [WinError 2] The system cannot find the file specified ---------------------------------------- ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

[alexanderlewis99]

I have this same issue :(

[hemadelon]

Me too. Any solution?

[sruthi-hub]

After a year and a half, I still have the same error. How to install pysam dependency successfully? If anyone figured it out, help is appreciated! Thanks!