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Unable to install autodock vina (potentially due to boost)

As part of a script I am writing, I need to install the package autodock vina for the purpose of ligand and protein binding. Every time I attempt to "pip install vina", I recieve an error message " ValueError: Boost library location was not found!". Upon attempting to install boost manually, I have been unable to run the bootstrap file, as it does not make the b2 folder that online tutorials say it will make.
To resolve this issue, I installed conda, and made an active environment with every single prerequisite, including boost, installed. I have checked for the version of all of these prerequisites and confirmed their existence, as well as double and triple-checking that I am in the write active environment. Upon installation, I either get the same issue (using conda install vina) or when using "conda install -c bioconda autodock-vina", I get a message saying that the package does not exist (despite adding cforge and bioconda as active package handlers, and the existence of said package is clearly documented online). Does anyone have any suggestions? I've been attempting to install this piece of software for 3 days and I've completely exhausted the documentation, as well as all other similar question answers, with nothing working.
Full error message:
Collecting vina
Using cached vina-1.2.3.tar.gz (95 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
error: subprocess-exited-with-error
× Getting requirements to build wheel did not run successfully.
│ exit code: 1
╰─> [56 lines of output]
Version found 1.2.3 (from __init__.py)
running egg_info
creating vina.egg-info
writing vina.egg-info\PKG-INFO
writing dependency_links to vina.egg-info\dependency_links.txt
writing requirements to vina.egg-info\requires.txt
writing top-level names to vina.egg-info\top_level.txt
writing manifest file 'vina.egg-info\SOURCES.txt'
Boost library is not installed in this conda environment.
Traceback (most recent call last):
File "C:\Users\chris\AppData\Local\Programs\Python\Python310\lib\site-packages\pip\_vendor\pep517\in_process\_in_process.py", line 363, in <module>
main()
File "C:\Users\chris\AppData\Local\Programs\Python\Python310\lib\site-packages\pip\_vendor\pep517\in_process\_in_process.py", line 345, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "C:\Users\chris\AppData\Local\Programs\Python\Python310\lib\site-packages\pip\_vendor\pep517\in_process\_in_process.py", line 130, in get_requires_for_build_wheel
return hook(config_settings)
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\build_meta.py", line 177, in get_requires_for_build_wheel
return self._get_build_requires(
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\build_meta.py", line 159, in _get_build_requires
self.run_setup()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\build_meta.py", line 174, in run_setup
exec(compile(code, __file__, 'exec'), locals())
File "setup.py", line 346, in <module>
setup(
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\__init__.py", line 87, in setup
return distutils.core.setup(**attrs)
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\core.py", line 148, in setup
return run_commands(dist)
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\core.py", line 163, in run_commands
dist.run_commands()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 967, in run_commands
self.run_command(cmd)
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\dist.py", line 1214, in run_command
super().run_command(command)
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\dist.py", line 986, in run_command
cmd_obj.run()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 308, in run
self.find_sources()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 315, in find_sources
mm.run()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 550, in run
self.add_defaults()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\command\egg_info.py", line 587, in add_defaults
sdist.add_defaults(self)
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\command\sdist.py", line 228, in add_defaults
self._add_defaults_ext()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\command\sdist.py", line 311, in _add_defaults_ext
build_ext = self.get_finalized_command('build_ext')
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\cmd.py", line 299, in get_finalized_command
cmd_obj.ensure_finalized()
File "C:\Users\chris\AppData\Local\Temp\pip-build-env-r7vbpka4\overlay\Lib\site-packages\setuptools\_distutils\cmd.py", line 107, in ensure_finalized
self.finalize_options()
File "setup.py", line 247, in finalize_options
raise ValueError(error_msg)
ValueError: Boost library location was not found!
Directories searched: conda env, /usr/local/include and /usr/include.
[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.

I also get this error. I asked ResearchGate how to solve this problem and Cheng Shen adviced to use WSL/WSL2 to simulate a Linux environment and then run conda install -c bioconda vina (or another command like this)
What I did.
Install WSL and Ubuntu on Windows 2. Run code . in WSL terminal (for installing VS Code [recommended])
Install Anaconda/Miniconda following this guide
Type conda install -c bioconda vina in Ubuntu terminal (bioconda channel will download all required packages - boost, swig, etc.)
Vina should be successfully installed ( vina --version in WSL Terminal to check)
I found it much easier to install packages for docking via WSL and use VS Code to run scripts there. It's VERY easier than trying to solve this problem by configuring boost for Windows. If you have any questions you can ask me in ResearchGate.

installing python module on linux

I am trying to install the python module pyobjus (this is the one that fails to install another module).
But I always get some bug during installation. I tried to switch to other python versions, reinstall pip, use option --no-cache-dir, etc, but couldn't manage to get past this bug:
$ pip3 install pyobjus
Defaulting to user installation because normal site-packages is not writeable
Collecting pyobjus
Using cached pyobjus-1.2.0.tar.gz (165 kB)
Installing build dependencies ... done
Getting requirements to build wheel ... error
ERROR: Command errored out with exit status 1:
command: /usr/bin/python3 /home/denis/.local/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py get_requires_for_build_wheel /tmp/tmpoff64vmf
cwd: /tmp/pip-install-4k26drr5/pyobjus
Complete output (19 lines):
Pyobjus platform is linux
Traceback (most recent call last):
File "/home/denis/.local/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py", line 280, in <module>
main()
File "/home/denis/.local/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py", line 263, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/home/denis/.local/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py", line 114, in get_requires_for_build_wheel
return hook(config_settings)
File "/tmp/pip-build-env-35d2l6hi/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 150, in get_requires_for_build_wheel
config_settings, requirements=['wheel'])
File "/tmp/pip-build-env-35d2l6hi/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 130, in _get_build_requires
self.run_setup()
File "/tmp/pip-build-env-35d2l6hi/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 254, in run_setup
self).run_setup(setup_script=setup_script)
File "/tmp/pip-build-env-35d2l6hi/overlay/lib/python3.6/site-packages/setuptools/build_meta.py", line 145, in run_setup
exec(compile(code, __file__, 'exec'), locals())
File "setup.py", line 35, in <module>
class PyObjusBuildExt(build_ext, object):
NameError: name 'build_ext' is not defined
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/bin/python3 /home/denis/.local/lib/python3.6/site-packages/pip/_vendor/pep517/_in_process.py get_requires_for_build_wheel /tmp/tmpoff64vmf Check the logs for full command output.
Any help would be greatly appreciated.
My OS is Linux Mint 19.3.
I saw this question which is about the same problem, but following the links did not bring any answer. It says PyObjus is designed for MacOS, but then why does the module katrain, supposedly compatible with linux, tries to install it when running "pip3 install katrain" (giving the same error as above) ?
Edit adter Marat's suggestion:
I removed the test for ios, the installation goes a bit further, but fails because Python.h is missing. when trying to install python3-dev, apt-get says that broken packages such as python3.6-dev are flagged "left as is", so it cannot install the required ones. Is there a way to fix the python installation, which seems to be broken ? I am afraid to break all the system if I mess up with it too much, but there is clearly a problem with my installation...
Fixed the above issue by reinstalling stuff, now it is CoreFoundation.h that is missing...

trouble with pip and easy_install to install python packages

I am going to install numpy library as a *.whl file, as numpy-1.9.2rc1+mkl- cp27-none-win32, on my Windows 7 machine...
Here is my approaches to do that, are which pip and easy_install packages...
The odd thing is that both don't work in the case of either Python 3.4 or Python 2.7...
Here are the trace of the attempts in the command prompt:
pip:
"C:\Users\Matinking\Desktop\numpy- 1.9.2rc1+
mkl-cp27-none-win32.whl" f
Exception:
Traceback (most recent call last):
File "c:\python34\lib\site-packages\pip\basecommand.py", line 122, in main
status = self.run(options, args)
File "c:\python34\lib\site-packages\pip\commands\install.py", line 257, in r
InstallRequirement.from_line(name, None))
File "c:\python34\lib\site-packages\pip\req.py", line 172, in from_line
return cls(req, comes_from, url=url, prereleases=prereleases)
File "c:\python34\lib\site-packages\pip\req.py", line 70, in __init__
req = pkg_resources.Requirement.parse(req)
File "c:\python34\lib\site-packages\pip\_vendor\pkg_resources.py", line 2667
in parse
reqs = list(parse_requirements(s))
File "c:\python34\lib\site-packages\pip\_vendor\pkg_resources.py", line 2605
in parse_requirements
line, p, specs = scan_list(VERSION,LINE_END,line,p,(1,2),"version spec")
File "c:\python34\lib\site-packages\pip\_vendor\pkg_resources.py", line 2573
in scan_list
raise ValueError("Expected "+item_name+" in",line,"at",line[p:])
ValueError: ('Expected version spec in', ' C:\\Users\\Matinking\\Desktop\\numer
performance.pdf', 'at', ':\\Users\\Matinking\\Desktop\\numericperformance.pdf'
Storing debug log for failure in C:\Users\Matinking\pip\pip.log
and easy_install:
C:\Python34\Scripts>easy_install.exe "C:\Users\Matinking\Desktop\numpy- 1.9.2rc1+
mkl-cp27-none-win32.whl"
Processing numpy-1.9.2rc1+mkl-cp27-none-win32.whl
Writing C:\Users\MATINK~1\AppData\Local\Temp\easy_install- jr2ijafr\numpy\setup.c
fg
Running numpy\setup.py -q bdist_egg --dist-dir C:\Users\MATINK~1\AppData\Local\T
emp\easy_install-jr2ijafr\numpy\egg-dist-tmp-umy5kseg
This is the wrong setup.py file to run
No eggs found in C:\Users\MATINK~1\AppData\Local\Temp\easy_install-jr2ijafr\nump
y\egg-dist-tmp-umy5kseg (setup script problem?)
Any idea for the problem?!

You should upgrade your pip to version 6.0, the .whl file you're using isn't compatible with earlier versions.
To bump up your pip version on Windows :
python -m pip install -U pip

pip error -> why were you running an install on a pdf? That was never going to work.
easy_install error -> looks like you downloaded a python 2.7 binary and tried to install into a python 3.4 installation.
For scientific stack python, you are hard pressed to beat an Anaconda python distribution.

Install pygtk module for python2.7

My OS is CentOS 6, which contains python 2.6.6 as default. I installed python 2.7 in /usr/local/.....
I tried to use pip to install pygtk in the first place, but it didn't work. So I decided to install it manually. I use:
./configure --prefix=/usr/local/lib/python2.7/site-packages
The error message shows the default version is python 2.6.6, it tried to install in /usr/local/lib/python2.6/... which of course does not exit. I also defined alias of python as python2.7, so when I type python, it will assume it's python2.7. But here it didn't work this way. Any suggestions? Thanks!
BTW: The error message when I installed the pygtk by pip is:
Command python setup.py egg_info failed with error code 1 in /tmp/pip_build_root/pygtk
Storing debug log for failure in /root/.pip/pip.log
Exception information:
Traceback (most recent call last):
File "/usr/local/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/basecommand.py", line 122, in main status = self.run(options, args)
File "/usr/local/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/commands/install.py", line 278, in run requirement_set.prepare_files(finder, force_root_egg_info=self.bundle, bundle=self.bundle)
File "/usr/local/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/req.py", line 1229, in prepare_files req_to_install.run_egg_info()
File "/usr/local/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/req.py", line 325, in run_egg_info command_desc='python setup.py egg_info')
File "/usr/local/lib/python2.7/site-packages/pip-1.5.4-py2.7.egg/pip/util.py", line 697, in call_subprocess % (command_desc, proc.returncode, cwd)) InstallationError: Command python setup.py egg_info failed with error code 1 in /tmp/pip_build_root/pygtk

Python with MySQL on Windows: installation errors

I tried to run the following command, in the folder of my Django project:
$ python manage.py dbshell
It shows me this error:
$python manage.py dbshell
Traceback (most recent call last):
File "manage.py", line 11, in <module>
execute_manager(settings)
File "C:\Python25\lib\site-packages\django\core\management\__init__.py", line
362, in execute_manager
utility.execute()
File "C:\Python25\lib\site-packages\django\core\management\__init__.py", line
303, in execute
self.fetch_command(subcommand).run_from_argv(self.argv)
File "C:\Python25\lib\site-packages\django\core\management\base.py", line 195,
in run_from_argv
self.execute(*args, **options.__dict__)
File "C:\Python25\lib\site-packages\django\core\management\base.py", line 222,
in execute
output = self.handle(*args, **options)
File "C:\Python25\lib\site-packages\django\core\management\base.py", line 351,
in handle
return self.handle_noargs(**options)
File "C:\Python25\lib\site-packages\django\core\management\commands\dbshell.py
", line 9, in handle_noargs
from django.db import connection
File "C:\Python25\lib\site-packages\django\db\__init__.py", line 41, in <modul
e>
backend = load_backend(settings.DATABASE_ENGINE)
File "C:\Python25\lib\site-packages\django\db\__init__.py", line 17, in load_b
ackend
return import_module('.base', 'django.db.backends.%s' % backend_name)
File "C:\Python25\Lib\site-packages\django\utils\importlib.py", line 35, in im
port_module
__import__(name)
File "C:\Python25\lib\site-packages\django\db\backends\mysql\base.py", line 13
, in <module>
raise ImproperlyConfigured("Error loading MySQLdb module: %s" % e)
django.core.exceptions.ImproperlyConfigured: Error loading MySQLdb module: No mo
dule named MySQLdb
First question is, why does Python not simply include this MySQLdb module?
OK, just fine, try to search to solve this message.
I have looked around stackoverflow.com for installing this module but did not have a good result.
Download this module at: http://sourceforge.net/projects/mysql-python/
Comes to the installation of this module on my Windows Vista system.
After the extraction of the package, I run the cmd prompt to continue with the installation:
$ python setup.py install
Again it showed me one other message:
D:\SOFTWARE\PROGRAMMING\MySQL-python-1.2.3c1>python setup.py install
Traceback (most recent call last):
File "setup.py", line 5, in <module>
from setuptools import setup, Extension
ImportError: No module named setuptools
Playing around with this error message, I know that there is the ez_setup.py within the package:
$python ez_setup.py
It seems that everything is OK:
D:\SOFTWARE\PROGRAMMING\MySQL-python-1.2.3c1>python ez_setup.py
Downloading http://pypi.python.org/packages/2.5/s/setuptools/setuptools-0.6c9-py
2.5.egg
Processing setuptools-0.6c9-py2.5.egg
Copying setuptools-0.6c9-py2.5.egg to c:\python25\lib\site-packages
Adding setuptools 0.6c9 to easy-install.pth file
Installing easy_install-script.py script to C:\Python25\Scripts
Installing easy_install.exe script to C:\Python25\Scripts
Installing easy_install-2.5-script.py script to C:\Python25\Scripts
Installing easy_install-2.5.exe script to C:\Python25\Scripts
Installed c:\python25\lib\site-packages\setuptools-0.6c9-py2.5.egg
Processing dependencies for setuptools==0.6c9
Finished processing dependencies for setuptools==0.6c9
Now comes back to the setup.py to install again:
$python setup.py install
It again gave me one other error message:
D:\SOFTWARE\PROGRAMMING\MySQL-python-1.2.3c1>python setup.py install
running install
running bdist_egg
....
copying MySQLdb\constants\CLIENT.py -> build\lib.win32-2.5\MySQLdb\constants
running build_ext
error: Python was built with Visual Studio 2003;
extensions must be built with a compiler than can generate compatible binaries.
Visual Studio 2003 was not found on this system. If you have Cygwin installed,
you can try compiling with MingW32, by passing "-c mingw32" to setup.py.
How can I fix this problem?

Did you try looking here: http://sourceforge.net/projects/mysql-python/files/
That is the download area of MySQLdb project, it has nothing to do with django, so your question is incorrect - django does not make switching database backends hard, you just change one line. And of course, your python installation should support that database first, so by downloading binary package for Windows from the link I gave above (chose correct version to match your version of python) you can avoid all the hassle of compiling the source release.
Most probably you need either MySQL-python-1.2.2.win32-py2.5.exe or MySQL-python-1.2.2.win32-py2.4.exe

Uh, this isn't Django, this is you downloading some unspecified Python environment and expecting it to magically do everything exactly the way you wanted it to. Find a good tutorial on this and follow the instructions.
BTW, this is a very helpful forum, but giving no specifics and then delivering a non-question with an attitude is not a good way to get people to feel helpful.

I once had the same problem running Python and MySQL on the same computer. Like the guys/gals said above, Python does not come with built-in support for MySQL, so you will need to download the connectors.
The link given above by #kibitzer will most likely not work on Windows successfully, so go here to download a copy of the connector that works with windows. It comes with installer and no need to run setup.py script manually.