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<script src="http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js" type="text/javascript"></script>

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## Prerequisites
# Latest Xcode
# Latest Apple command line utilities
# Homebrew (check 'brew doctor')
# 20+ minutes (new machine with SSD – hours on our lab's 2008 Mac Pro)
 
## Commands (instead install scipy superpack?)
brew install python # Symlinking may well be problematic – use 'brew link --overwrite python' if necessary)
pip install virtualenv
pip install virtualenvwrapper

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# Resilio, Dropbox, JupyterLab, Firefox, Sublime, Atom, Zotero, VPNs,
# Slack, Bitwarden, Office, Sketch, Typora
# Brew, Miniconda, Jupyterlab, RStudio, Docker
# Install custom jupyterlab envs https://ipython.readthedocs.io/en/latest/install/kernel_install.html#kernels-for-different-environments
# Create /opt/ and /opt/bin, place nextflow inside latter.
# Put toggle-able symlinks to brewed GCC inside here, prepend to path in .bashrc (`gcc_links_on`, `gcc_links_off`)
# Nextflow
# .ssh
# Generate keys
# Create /opt and opt/bin, add to path

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bede-rmbp:~ bede$ brew update && brew upgrade && brew doctor
Already up-to-date.
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.

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<?php
// Send basic email alerts from cURL etc.
// Usage: curl domain.com/email_alert.php?script-ran-successfully

mail('mail@domain.com', 'Alert: ' . $_SERVER['QUERY_STRING'], 'Request origin: ' . $_SERVER['SERVER_ADDR']);
?>

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bede-rmbp:www bede$ foundation new project --libsass
Creating ./project
      create  project
Cloning into 'project'...
remote: Counting objects: 173, done.
remote: Total 173 (delta 0), reused 0 (delta 0), pack-reused 173
Receiving objects: 100% (173/173), 235.17 KiB | 436.00 KiB/s, done.
Resolving deltas: 100% (63/63), done.
Checking connectivity... done.
Installing dependencies with bower...

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#!/usr/bin/env python3

import io
import sys
import time
import datetime
import requests

from Bio import SeqIO

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# SAM to consensus FASTA code golf, inspired by http://lab.loman.net/2015/07/28/calling-haploid-consensus-sequence/

# Starting with a SAM:
samtools view -bS seqs.sam | samtools sort - seqs # Generate and sort BAM
samtools index seqs.bam # Index BAM

# Starting with an indexed BAM:
samtools mpileup -ud 1000 -f seqs_ref.fasta seqs.bam | bcftools call -c | vcfutils.pl vcf2fq | seqtk seq -a - > seqs.consensus.fa # Generate pileup, call variants, convert to fq, convert to fa

# Who can do better? The bar is set low...

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Bede$ brew install spades
==> Installing spades from homebrew/homebrew-science
==> Downloading https://homebrew.bintray.com/bottles-science/spades-3.6.1.yosemite.bottle.tar.gz

curl: (22) The requested URL returned error: 404 Not Found
Error: Failed to download resource "spades"
Download failed: https://homebrew.bintray.com/bottles-science/spades-3.6.1.yosemite.bottle.tar.gz
Warning: Bottle installation failed: building from source.
==> Downloading http://spades.bioinf.spbau.ru/release3.6.0/SPAdes-3.6.1.tar.gz
Already downloaded: /Library/Caches/Homebrew/spades-3.6.1.tar.gz

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class Spades < Formula
  desc "SPAdes: de novo genome assembly"
  homepage "http://bioinf.spbau.ru/spades/"
  bottle do
    cellar :any
    sha256 "9d69a98a442701f818df56325beeb1ddc8457da5932da172706becf18f6d3fed" => :yosemite
    sha256 "89ff010f4542bb2f63144c642a125fdedee8367a14410bfd3b30c6b27caeb1c9" => :mavericks
    sha256 "834d20f5a8b812cdb8c1e2b9c36a8baf35b5f6e5d7f3af910350713a3357ae5e" => :mountain_lion
  end