issues installing vcf-kit on Mac

[seraphim711]

Hello, I'm having issue installing VCF-kit on my macOS High Sierra machine. It seems to be a permission issue

~ ❯❯❯ pip install vcf-kit ⏎ Collecting vcf-kit Requirement already satisfied: cython>=0.24.1 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from vcf-kit) Collecting yahmm==1.1.2 (from vcf-kit) Requirement already satisfied: setuptools in ./Library/Python/2.7/lib/python/site-packages (from vcf-kit) Requirement already satisfied: docopt in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from vcf-kit) Requirement already satisfied: awesome-slugify in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from vcf-kit) Requirement already satisfied: cyvcf2>=0.6.5 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from vcf-kit) Collecting requests (from vcf-kit) Using cached requests-2.18.4-py2.py3-none-any.whl Collecting tabulate (from vcf-kit) Requirement already satisfied: numpy in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from vcf-kit) Collecting clint (from vcf-kit) Collecting intervaltree==2.1.0 (from vcf-kit) Requirement already satisfied: biopython in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from vcf-kit) Requirement already satisfied: matplotlib in ./Library/Python/2.7/lib/python/site-packages (from vcf-kit) Requirement already satisfied: scipy in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from vcf-kit) Requirement already satisfied: jinja2 in ./Library/Python/2.7/lib/python/site-packages (from vcf-kit) Collecting networkx==1.11 (from vcf-kit) Using cached networkx-1.11-py2.py3-none-any.whl Requirement already satisfied: Unidecode<0.05,>=0.04.14 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from awesome-slugify->vcf-kit) Requirement already satisfied: regex in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from awesome-slugify->vcf-kit) Requirement already satisfied: certifi>=2017.4.17 in ./Library/Python/2.7/lib/python/site-packages (from requests->vcf-kit) Collecting chardet<3.1.0,>=3.0.2 (from requests->vcf-kit) Using cached chardet-3.0.4-py2.py3-none-any.whl Collecting idna<2.7,>=2.5 (from requests->vcf-kit) Using cached idna-2.6-py2.py3-none-any.whl Collecting urllib3<1.23,>=1.21.1 (from requests->vcf-kit) Using cached urllib3-1.22-py2.py3-none-any.whl Collecting args (from clint->vcf-kit) Collecting sortedcontainers (from intervaltree==2.1.0->vcf-kit) Using cached sortedcontainers-1.5.9-py2.py3-none-any.whl Requirement already satisfied: functools32 in ./Library/Python/2.7/lib/python/site-packages (from matplotlib->vcf-kit) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in ./Library/Python/2.7/lib/python/site-packages (from matplotlib->vcf-kit) Requirement already satisfied: python-dateutil in ./Library/Python/2.7/lib/python/site-packages (from matplotlib->vcf-kit) Requirement already satisfied: cycler>=0.10 in ./Library/Python/2.7/lib/python/site-packages (from matplotlib->vcf-kit) Requirement already satisfied: subprocess32 in ./Library/Python/2.7/lib/python/site-packages (from matplotlib->vcf-kit) Requirement already satisfied: pytz in ./Library/Python/2.7/lib/python/site-packages (from matplotlib->vcf-kit) Requirement already satisfied: six>=1.10 in ./Library/Python/2.7/lib/python/site-packages (from matplotlib->vcf-kit) Requirement already satisfied: MarkupSafe>=0.23 in ./Library/Python/2.7/lib/python/site-packages (from jinja2->vcf-kit) Requirement already satisfied: decorator>=3.4.0 in ./Library/Python/2.7/lib/python/site-packages (from networkx==1.11->vcf-kit) Installing collected packages: networkx, yahmm, chardet, idna, urllib3, requests, tabulate, args, clint, sortedcontainers, intervaltree, vcf-kit Found existing installation: networkx 2.0 Uninstalling networkx-2.0: Successfully uninstalled networkx-2.0 Rolling back uninstall of networkx Exception: Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip/basecommand.py", line 215, in main status = self.run(options, args) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip/commands/install.py", line 342, in run prefix=options.prefix_path, File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip/req/req_set.py", line 784, in install **kwargs File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip/req/req_install.py", line 851, in install self.move_wheel_files(self.source_dir, root=root, prefix=prefix) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip/req/req_install.py", line 1064, in move_wheel_files isolated=self.isolated, File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip/wheel.py", line 377, in move_wheel_files clobber(source, dest, False, fixer=fixer, filter=filter) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip/wheel.py", line 316, in clobber ensure_dir(destdir) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pip/utils/__init__.py", line 83, in ensure_dir os.makedirs(path) File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 13] Permission denied: '/Library/Frameworks/Python.framework/Versions/2.7/share/doc/networkx-1.11'

I have admin rights on this machine but I don't know if it's ok to change the permission here ~ ❯❯❯ ls -lthr /Library/Frameworks/Python.framework/Versions/2.7/share/ total 0 drwxrwxr-x 3 root admin 96B Sep 16 12:02 man drwxr-xr-x 3 root admin 96B Jan 9 10:23 doc

[danielecook]

Hi Seraphim711 - I do not envision this being an issue.

However - I highly recommend using something like pyenv to manage your python installation.