bmpvieira

JS Cube

Forked from Julian Mazzitelli's Pen JS Cube.

A Pen by Bruno Vieira on CodePen.

License.

bmpvieira

#!/bin/bash
# Docker running natively in OSX connected to daemon running inside Vagrant
#
# This allows to use Docker natively in an OSX terminal, connected to a docker
# daemon running inside a CoreOS VM in Vagrant. Shared folder enabled through NFS.
#
# I tried to use [dvm](https://github.com/fnichol/dvm) but got issues with
# networking (#4) and shared folder (#7), so I just switched to CoreOS and
# added the settings for it to work like dvm.

bmpvieira

app.get '/watable', (req, res, next) ->
  res.render 'watable'

app.get '/data.json', (req, res, next) ->
  UserModel.find {}, 'email firstname lastname', (err, users) ->
    return next err if err

    rows = []
    for user in users
      user = user.toObject()

bmpvieira

# blastXMLtoJSON.coffee | 2013 Bruno Vieira [mail@bmpvieira.com]
#
# This script converts NCBI's Blast XML results to JSON
#
# For small files, it parses everything into a object in memory and
# writes the result to the output file in the end.
# For big files, it will write each Blast “Iteration” object separately, 
# one per line, to avoid memory limits. 
#
# Usage: coffee blastXMLtoJSON.coffee blast_results.xml output.json

bmpvieira

# getMycorSequences.coffee
# This script fetches sequences from MycorWeb Blast result links.
#
# links file must be provided and can be obtained with getMycorLinks.coffee:
# https://gist.github.com/4683065
#
# Dependencies: casperjs
# Usage: casperjs getMycorSequences.coffee fileWithLinks
# Example: casperjs getMycorSequences.coffee sequencesLinks:0-4275.txt
# Author: Bruno Vieira (mail@bmpvieira.com)

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# getMycorLinks.coffee
# This script fetches all the sequences links from a MycorWeb Blast result.
#
# sequences can be fetched from these links with getMycorSequences.coffee:
# https://gist.github.com/4683075
# results can be splitted into multiple files to run multiple instances of
# getMycorSequences.coffee
#
# Dependencies: casperjs
# Usage: casperjs getMycorLinks.coffee numberOutputFiles URL

bmpvieira

/*
  author: bmpvieira
  license: WTFPL
  description: Simple Youtube playlist parser using https://github.com/dominictarr/JSONStream
  usage example: node youtubePlaylistParser.js PLt4dwg5cC5TSqHR44YK0UQ_8TSG8YtZtI | cclive -f best -c
*/

var request = require('request');
var JSONStream = require('JSONStream');

bmpvieira

(define-public python-cwltool
  (package
    (name "python-cwltool")
    (version "1.0.20150916041152")
    (source
      (origin
        (method url-fetch)
        (uri (string-append
               "https://pypi.python.org/packages/source/c/cwltool/cwltool-"
               version

bmpvieira

var fs = require('fs')
var ncbi = require('bionode-ncbi')
var request = require('request')
var through = require('through2')
var _ = require('lodash')

var property = 'README.txt'

var requestStream = through.obj(function(obj, enc, next) {
  var fileName = _.get(obj, property).split('/')[5]

bmpvieira

# Setup R with LEA package (because it segfaults on OSX)
# http://membres-timc.imag.fr/Olivier.Francois/LEA/software.htm
# Run one by one the following commands 
brew install boot2docker docker
boot2docker init
boot2docker up
docker run -it -v ~/Downloads:/Downloads r-base
docker run -it r-base
install.packages("/Downloads/LEA_0.2.tar", repos = NULL, type = "source")