Develop Reference

How to download mwilliamson jq.py on Windows

I have spent more than a week trying to figure out how to install the python binding for JQ https://github.com/mwilliamson/jq.py on my computer but I keep getting this error
Executing: ./configure CFLAGS=-fPIC --prefix=C:\cygwin64\tmp\pip-install-v9ec9n9_\jq_7100d98
9ec2f403c8a7cae32d2f83862\_deps\onig-install-6.9.4
error: [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: Failed building wheel for jq
Failed to build jq
ERROR: Could not build wheels for jq, which is required to install pyproject.toml-based projects
I understand that these bindings/module was not created for windows systems so that is likely why it can't create the bindings but I did see this from the project readme
If a wheel is not available, the source for jq 1.6 is downloaded over
HTTPS and built. This requires:
Autoreconf The normal C compiler toolchain, such as gcc and make.
libtool Python headers.
I have downloaded cygwin to attempt to donwload it through there but since the beforementioned quote is pretty vague in directions, I was wondering how to do this specifically on Windows.

Can't install BGSlibrary(pybgs) library from pypi for python using visual studio 2017

I have been trying for 3 days to install this library. It uses CMake and i can't understand how to add OpenCV path within visual studio. I have tried a lot of things like:
1.use CMake-GUI to generate .sln file then build there is also an error.
2.try to add through cmd with CMake but there I face another error.
I believe there is a simple way of directly doing it through visual studio which I am unfamiliar of and can't seem to find it. If someone is kind enough to tell me in simple way how to install library using visual studio python 3.6.
Here is the error I get in VS 2017 after I try to install pybgs library through pip install pybgs
ERROR: Failed building wheel for pybgs
Failed to build pybgs
Installing collected packages: pybgs
Running setup.py install for pybgs: started
Running setup.py install for pybgs: finished with status 'error'
ERROR: Command errored out with exit status 1:
CMake Error at CMakeLists.txt:113 (find_package):
By not providing "FindOpenCV.cmake" in CMAKE_MODULE_PATH this project has
asked CMake to find a package configuration file provided by "OpenCV", but
CMake did not find one.
Could not find a package configuration file provided by "OpenCV" with any
of the following names:
OpenCVConfig.cmake
opencv-config.cmake

pip install CrossMap failing on OSX: cannot find os/rand.c?

Just trying to run a
pip install CrossMap
on OSX 10.11.6 with a brew installed python (version 2.7.12) and pip (version 9.0.1) and running into this error:
htslib/hts_os.c:30:10: fatal error: 'os/rand.c' file not found
#include "os/rand.c"
^
1 error generated.
error: command 'clang' failed with exit status 1
I have looked everywhere for information on this error and it has come up empty. Where does this dependency come from and how do I install it?
Thanks!

CrossMap depends on pysam which is a wrapper for sam tools. You need to install htslib before compiling pysam.

python installing thread-local storage

I'm trying to install a pysnap library from github. This is part of the output I get. I have no idea how to proceed, any help would be greatly appreciated.
Installed /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pysnap-0.1.1-py2.7.egg
Processing dependencies for pysnap==0.1.1
Searching for cryptography>=1.2.2
Reading https://pypi.python.org/simple/cryptography/
Best match: cryptography 1.2.3
Downloading https://pypi.python.org/packages/source/c/cryptography/cryptography-1.2.3.tar.gz#md5=5474d2b3e8c7555a60852e48d2743f85
Processing cryptography-1.2.3.tar.gz
Writing /tmp/easy_install-7ZnmT5/cryptography-1.2.3/setup.cfg
Running cryptography-1.2.3/setup.py -q bdist_egg --dist-dir /tmp/easy_install-7ZnmT5/cryptography-1.2.3/egg-dist-tmp-rcoXcx
_configtest.c:1:1: error: thread-local storage is unsupported for the current target
__thread int some_threadlocal_variable_42;
1 error generated.
error: unable to create target: 'No available targets are compatible with this triple, see -version for the
available targets.'
1 error generated.

What platform are you trying to install pysnap?
I downloaded and installed pysnap sucessfully from this github location
I do have windows 10 platform and python 2.7 though. I dont' have a linux to replicate this issue.
If you are trying to install on Linux, depending on flavor and its setup , sometimes swap is setup as as /tmp and some applications are not able to write to /tmp. In your case it does looks like its trying to write to /tmp and erroring out.
Can you try pip install cryptography
and see if its able to install cryptography part without issues?
Once that dependency is out of way, you can install pysnap so that pysnap will not try to install cryptography

Error installing Willie irc bot for Python

Trying to install this Python IRC bot called Willie. This is what happens when I run setup.py:
C:\Python34\python.exe "C:\Program Files (x86)\JetBrains\PyCharm Community Edition 4.5.1\helpers\pycharm\pycharm_setup_runner.py" C:\Users\Quibbles\Documents\willie-5.3.0\setup.py
Testing started at 1:35 PM ...
running pycharm_test
Searching for pygeoip
Best match: pygeoip 0.3.2
Processing pygeoip-0.3.2-py3.4.egg
Using c:\users\quibbles\documents\willie-5.3.0\.eggs\pygeoip-0.3.2-py3.4.egg
Searching for pyenchant
Best match: pyenchant 1.6.6
Processing pyenchant-1.6.6-py3.4-win32.egg
Using c:\users\quibbles\documents\willie-5.3.0\.eggs\pyenchant-1.6.6-py3.4-win32.egg
Searching for praw
Best match: praw 2.1.21
Processing praw-2.1.21-py3.4.egg
Using c:\users\quibbles\documents\willie-5.3.0\.eggs\praw-2.1.21-py3.4.egg
Searching for lxml
Reading https://pypi.python.org/simple/lxml/
Best match: lxml 3.4.4
Downloading https://pypi.python.org/packages/source/l/lxml/lxml-3.4.4.tar.gz#md5=a9a65972afc173ec7a39c585f4eea69c
Processing lxml-3.4.4.tar.gz
Writing C:\Users\Quibbles\AppData\Local\Temp\easy_install-p_x9naya\lxml-3.4.4\setup.cfg
Running lxml-3.4.4\setup.py -q bdist_egg --dist-dir C:\Users\Quibbles\AppData\Local\Temp\easy_install-p_x9naya\lxml-3.4.4\egg-dist-tmp-0expfysa
Building lxml version 3.4.4.
Building without Cython.
ERROR: b"'xslt-config' is not recognized as an internal or external command,\r\noperable program or batch file.\r\n"
** make sure the development packages of libxml2 and libxslt are installed **
Using build configuration of libxslt
C:\Python34\lib\distutils\dist.py:260: UserWarning: Unknown distribution option: 'bugtrack_url'
warnings.warn(msg)
cl : Command line warning D9025 : overriding '/W3' with '/w'
lxml.etree.c
C:\Users\Quibbles\AppData\Local\Temp\easy_install-p_x9naya\lxml-3.4.4\src\lxml\includes\etree_defs.h(14) : fatal error C1083: Cannot open include file: 'libxml/xmlversion.h': No such file or directory
error: Setup script exited with error: command 'C:\\Program Files (x86)\\Microsoft Visual Studio 10.0\\VC\\BIN\\cl.exe' failed with exit status 2
Process finished with exit code 1
What am I doing wrong? I downloaded the source code from https://github.com/embolalia/willie/releases/tag/v5.3.0 and tried running setup.py in PyCharm.

It should be fairly obvious by the error messages:
** make sure the development packages of libxml2 and libxslt are installed **
You need to have the dev libxml2 and libxslt installed. It appears either you have the wrong versions perhaps, or don't have them installed properly.

I'L'I's answer gives you a hint of where to start searching next, but isn't a useful answer.
After several attempts on my own, I found that to get the lxml library installed, I needed to do the following:
First, download the lxml library from http://www.lfd.uci.edu/~gohlke/pythonlibs/
This is necessary because the PiPy archives (https://pypi.python.org/pypi/lxml/3.4.4) are way out of date, only giving you the option to install for Python 3.2 for the 3+ series, which of course is useless if you're on 3.4. There's also issues if you're using 64-bit. They may be sufficient if you're using 2.7, though.
Then use the instructions here: How do I install a Python package with a .whl file? to install the .whl file.
However that only fixes half the problem. The willie package appears to be broken in other ways (on Windows) because of trying to reference a unix-like /tmp directory (absolute path) instead of the proper Windows Temp directory.
This issue describes the problem, though no fix has yet been made: https://github.com/embolalia/willie/issues/811
It indicates that it's a Windows-specific bug in the installer. To work around that, download the .tar.gz from https://pypi.python.org/pypi/willie/5.3.0
Unpack it. Go to the willie-5.3.0\willie.egg-info directory, and edit the SOURCES.txt file. The fifth line is /tmp/tmpeAhjCF/willie. Delete that line.
Repackage the directory into a .tar.gz archive. Install via pip install .\willie-5.3.0.tar.gz.
Now it's installed, and you're ready for the next round of problems of actually getting it to run on Windows. Since I haven't actually succeeded in doing that yet, that's as far as I can help for right now.