acoffman

import requests

entrez_symbol = 'BRAF'

gene_url = 'https://civicdb.org/api/genes/{}?identifier_type=entrez_symbol'.format(entrez_symbol)
gene_response = requests.get(gene_url)
gene_body = gene_response.json()

variant_details = []

acoffman

import requests

next_url = 'https://civicdb.org/api/variants?count=100'
variants = []

while next_url:
    response = requests.get(nextUrl)
    body = response.json()
    variants += body['records']
    next_url = body['_meta']['links']['next']

acoffman

OS X Command Line Tools

xcode-select --install

Homebrew (https://brew.sh/)

/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Ruby (https://www.ruby-lang.org)

brew update

brew install openssl libyaml libffi rbenv ruby-build

acoffman

Keybase proof

I hereby claim:

• I am acoffman on github.
• I am acoffman (https://keybase.io/acoffman) on keybase.
• I have a public key whose fingerprint is 3A64 D6BB 0521 3865 255C 4413 A2AA 59E5 20F4 063A

To claim this, I am signing this object:

acoffman

#tmux configure, updated libevent in /home/archive
LIBEVENT_CFLAGS="-I/home/archive/include" LIBEVENT_LIBS="-L/home/archive/lib -levent" ./configure --prefix=/home/archive

#vim configure, out of /home/archive
./configure --with-features=huge \
            --enable-rubyinterp \
            --enable-pythoninterp \
            --with-python-config-dir=/usr/lib/python2.7-config \
            --enable-perlinterp \
            --enable-luainterp \

acoffman

unless File.exist?('Gemfile')
  File.write('Gemfile', <<-GEMFILE)
    source 'https://rubygems.org'
    gem 'rails', github: 'rails/rails'
    gem 'arel', github: 'rails/arel'
    gem 'sqlite3'
  GEMFILE

  system 'bundle'
end

acoffman

make ycm_core
Scanning dependencies of target BoostParts
[  0%] Building CXX object BoostParts/CMakeFiles/BoostParts.dir/libs/date_time/src/gregorian/date_generators.cpp.o
In file included from /Users/acoffman/.vim/bundle/YouCompleteMe/cpp/BoostParts/libs/date_time/src/gregorian/date_generators.cpp:14:
In file included from /Users/acoffman/.vim/bundle/YouCompleteMe/cpp/BoostParts/boost/date_time/date_generators.hpp:16:
In file included from /usr/bin/../lib/c++/v1/stdexcept:46:
In file included from /usr/bin/../lib/c++/v1/exception:81:
/usr/bin/../lib/c++/v1/type_traits:737:2: error: #error is_base_of not implemented.
#error is_base_of not implemented.
 ^

acoffman

 cmake -G "Unix Makefiles" -DPATH_TO_LLVM_ROOT=~/ycm_temp/clang+llvm-3.2-x86_64-apple-darwin11 . ~/.vim/bundle/YouCompleteMe/cpp
-- The C compiler identification is Clang 3.1.0
-- The CXX compiler identification is Clang 3.1.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info

acoffman

Process:         postgres [834]
Path:            /Applications/Postgres.app/Contents/MacOS/bin/postgres
Identifier:      postgres
Version:         ??? (???)
Code Type:       X86-64 (Native)
Parent Process:  initdb [833]

Date/Time:       2012-12-06 17:09:06.342 -0600
OS Version:      Mac OS X 10.7.5 (11G63)
Report Version:  9

acoffman

12/6/12 5:09:06.248 PM Postgres: Existing PGVersion: (null)
12/6/12 5:09:06.248 PM Postgres: Installed PGVersion: 9.2
12/6/12 5:09:06.255 PM lsboxd: @AE relay 4755524c:4755524c
12/6/12 5:09:06.327 PM com.heroku.postgres-service: dyld: Symbol not found: _xmlStructuredErrorContext
12/6/12 5:09:06.327 PM com.heroku.postgres-service:   Referenced from: /Applications/Postgres.app/Contents/MacOS/bin/postgres
12/6/12 5:09:06.327 PM com.heroku.postgres-service:   Expected in: /usr/lib/libxml2.2.dylib
12/6/12 5:09:06.327 PM com.heroku.postgres-service:  in /Applications/Postgres.app/Contents/MacOS/bin/postgres
12/6/12 5:09:06.818 PM com.heroku.postgres-service: no data was returned by command ""/Applications/Postgres.app/Contents/MacOS/bin/postgres" -V"
12/6/12 5:09:06.820 PM Postgres: 833 /Applications/Postgres.app/Contents/MacOS/bin/initdb: Status 1
12/6/12 5:09:06.819 PM com.heroku.postgres-service: The program "postgres" is needed by initdb but was not found in the