vk setup errors

[mwhj]

Hi - trying to install VCF-kit. Things seem to go OK up until running vk setup I am aware that there might be a problem with Homebrew and the version of Ruby which it is using.

This is what I am seeing:

$ vk setup Traceback (most recent call last): File "/usr/local/bin/vk", line 5, in <module> from pkg_resources import load_entry_point File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 2797, in <module> parse_requirements(__requires__), Environment() File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 580, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (scipy 0.13.0b1 (/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python), Requirement.parse('scipy>=0.13.3'))

[mwhj]

I should add that I'm running OSX El Capitan 10.11.6, and Homebrew 1.3.6 (updated today).

[danielecook]

I don't think it is an issue with homebrew/ruby. It looks like you have scipy 0.13.0b1 installed but vcf-kit requires scipy 0.13.3.

Are you familiar with virtualenv or pyenv? You may want to use that with vcf-kit. I am going to try to update the package in the near future to handle dependencies better.

Or you could overwrite your installation of scipy.

pip install scipy --upgrade

If you are familiar with docker I may make a container for vcf-kit that uses that.

[mwhj]

Hi Daniel, thanks so much for responding so quickly!

I've tried upgrading scipy with pip - this is what I get:

$ pip install scipy --upgrade Collecting scipy Downloading scipy-0.19.1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (16.2MB) 100% |████████████████████████████████| 16.2MB 81kB/s Collecting numpy>=1.8.2 (from scipy) Downloading numpy-1.13.3-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (4.6MB) 100% |████████████████████████████████| 4.6MB 292kB/s Installing collected packages: numpy, scipy Found existing installation: numpy 1.8.0rc1 DEPRECATION: Uninstalling a distutils installed project (numpy) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project. Uninstalling numpy-1.8.0rc1: Exception: Traceback (most recent call last): File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/basecommand.py", line 215, in main status = self.run(options, args) File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/commands/install.py", line 342, in run prefix=options.prefix_path, File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_set.py", line 778, in install requirement.uninstall(auto_confirm=True) File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_install.py", line 754, in uninstall paths_to_remove.remove(auto_confirm) File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_uninstall.py", line 115, in remove renames(path, new_path) File "/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/utils/__init__.py", line 267, in renames shutil.move(old, new) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 302, in move copy2(src, real_dst) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 131, in copy2 copystat(src, dst) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 103, in copystat os.chflags(dst, st.st_flags) OSError: [Errno 1] Operation not permitted: '/var/folders/l_/pbg2g5d10274y5h3qbr_y0drd_sdw9/T/pip-gR8qJR-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy-1.8.0rc1-py2.7.egg-info'

I tried running vk setup after that, but got the same errors as before.

I have heard of virtualenv and pyenv, but I am not familiar with using them. I am familiar with Docker, but do not have it set up on this machine (or any which I have access to). I only need to use vcf-kit for something quick and dirty, so I 'm not sure that it's worth my time configuring extra stuff.

[danielecook]

It looks like you are using the system version of python though. I recommend using:

brew install python

# I think you can then overwrite the system python with
brew link --overwrite python

Then try reinstalling...

[mwhj]

I feel really bad for this, but I'm still getting no luck:

`$ brew install python ==> Installing dependencies for python: sqlite, gdbm ==> Installing python dependency: sqlite ==> Downloading https://homebrew.bintray.com/bottles/sqlite-3.20.1.el_capitan.bottle.tar.gz ==> Downloading from https://akamai.bintray.com/20/2043f5f369b2426559b43ce7d044dbe9dff77f1b5e4658115f5cec14b0d6b183?__gda__=exp=1508852315~hmac=c1323e22eb2e854f42df04bad5c97 ######################################################################## 100.0% ==> Pouring sqlite-3.20.1.el_capitan.bottle.tar.gz ==> Caveats This formula is keg-only, which means it was not symlinked into /usr/local, because macOS provides an older sqlite3.

If you need to have this software first in your PATH run: echo 'export PATH="/usr/local/opt/sqlite/bin:$PATH"' >> ~/.bash_profile

For compilers to find this software you may need to set: LDFLAGS: -L/usr/local/opt/sqlite/lib CPPFLAGS: -I/usr/local/opt/sqlite/include For pkg-config to find this software you may need to set: PKG_CONFIG_PATH: /usr/local/opt/sqlite/lib/pkgconfig

==> Summary 🍺 /usr/local/Cellar/sqlite/3.20.1: 11 files, 3MB ==> Installing python dependency: gdbm ==> Downloading https://homebrew.bintray.com/bottles/gdbm-1.13.el_capitan.bottle.tar.gz ######################################################################## 100.0% ==> Pouring gdbm-1.13.el_capitan.bottle.tar.gz 🍺 /usr/local/Cellar/gdbm/1.13: 19 files, 554.4KB ==> Installing python ==> Downloading https://homebrew.bintray.com/bottles/python-2.7.14.el_capitan.bottle.tar.gz ==> Downloading from https://akamai.bintray.com/ee/ee90369b3812099c0f7eb60b1bfd4e365861a621830968745fb6b4db736c7acf?__gda__=exp=1508852317~hmac=9886059ab71fe2f478acaeaeac235 ######################################################################## 100.0% ==> Pouring python-2.7.14.el_capitan.bottle.tar.gz ==> /usr/local/Cellar/python/2.7.14/bin/python2 -s setup.py --no-user-cfg install --force --verbose --single-version-externally-managed --record=installed.txt --install-scri ==> /usr/local/Cellar/python/2.7.14/bin/python2 -s setup.py --no-user-cfg install --force --verbose --single-version-externally-managed --record=installed.txt --install-scri ==> /usr/local/Cellar/python/2.7.14/bin/python2 -s setup.py --no-user-cfg install --force --verbose --single-version-externally-managed --record=installed.txt --install-scri ==> Caveats This formula installs a python2 executable to /usr/local/bin. If you wish to have this formula's python executable in your PATH then add the following to ~/.bash_profile: export PATH="/usr/local/opt/python/libexec/bin:$PATH"

Pip and setuptools have been installed. To update them pip2 install --upgrade pip setuptools

You can install Python packages with pip2 install

They will install into the site-package directory /usr/local/lib/python2.7/site-packages

See: https://docs.brew.sh/Homebrew-and-Python.html ==> Summary 🍺 /usr/local/Cellar/python/2.7.14: 3,517 files, 48.5MB MACM22295:~ u1693640$ brew link --overwrite python Warning: Already linked: /usr/local/Cellar/python/2.7.14 To relink: brew unlink python && brew link python MACM22295:~ u1693640$ vk setup Traceback (most recent call last): File "/usr/local/bin/vk", line 5, in from pkg_resources import load_entry_point File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 2797, in parse_requirements(requires), Environment() File "/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/pkg_resources.py", line 580, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (scipy 0.13.0b1 (/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python), Requirement.parse('scipy>=0.13.3'))`

[danielecook]

Try:

brew unlink python && brew link python
pip install scipy
pip install vcf-kit

[danielecook]

Also looks like pypi is down...that might be part of it.

https://pypi.python.org/