% -*- mode: noweb; noweb-default-code-mode: R-mode; -*-
%\VignetteIndexEntry{annmap installation instruction}
%\VignetteKeywords{}
%\VignetteDepends{}
%\VignettePackage{annmap}
%documentclass[12pt, a4paper]{article}
\documentclass[12pt]{article}

\usepackage{amsmath,pstricks}
\usepackage{hyperref}
\usepackage[authoryear,round]{natbib}
\usepackage{color}
\usepackage{wrapfig}
\usepackage[scaled]{helvet}
\renewcommand*\familydefault{\sfdefault}

\definecolor{NoteGrey}{rgb}{0.96,0.97,0.98}

\textwidth=6.2in
\textheight=9.5in
\parskip=.3cm
\oddsidemargin=.1in
\evensidemargin=.1in
\headheight=-1in

\newcommand{\scscst}{\scriptscriptstyle}
\newcommand{\scst}{\scriptstyle}
\newcommand{\Rfunction}[1]{{\texttt{#1}}}
\newcommand{\Robject}[1]{{\texttt{#1}}}
\newcommand{\Rpackage}[1]{{\textit{#1}}}
\newcommand{\code}[1]{{\texttt{#1}}}

\author{Tim Yates}
\begin{document}
\title{\code{annmap} installation instructions}

\maketitle

\tableofcontents

\section {Installation of the \code{annmap} database}

The R package requires access to a MySQL database server running a current version
of the \code{Annmap Database}. Database packs (complete with installation
instructions) may be downloaded from \url{http://annmap.cruk.manchester.ac.uk/download}.

\subsection{Pre-requisites}

The following are required for the Annmap Database installation:

\begin{itemize}
\item MySQL Server v5.0.27+
\item 20GB+ Free disk space
\end{itemize}

\subsection{Installation}

\begin{center}
\fcolorbox{black}{NoteGrey} {
\begin{minipage}{13.5cm}
\begin{center}
\textbf{ Important }
\end{center}
\begin{center}
\textbf{You do not need to pre-install Ensembl as you did before with the deprecated \code{exonmap} package}
\end{center}
\end{minipage}
}
\end{center}

  First, you will need to download and unzip the \code{annmap} database for the species and version of
Ensembl you are interested in studying.  This can be downloaded from \url{http://annmap.cruk.manchester.ac.uk/download}

  You will then need to create the database into which to load the data.  To do
this, simply log in to your MySQL server, and execute the following command\footnote{This obviously
assumes you are installing v56 of the homo\_sapiens database.  You'll need to replace the database
name with the one you have downloaded.}:

\begin{center}
\code{create database annmap\_homo\_sapiens\_66 ;}
\end{center}

  Then, we have prepared 2 installation scripts to import the annmap database
into your chosen MySQL server.  These can be found in the root folder of the database package
you first downloaded.

\begin{itemize}
\item Windows \code{importdb.bat}
\item OS X/Linux \code{importdb.sh}
\end{itemize}

  To utilise these files, you will need to edit them to set your username,
select your password preferences (no password, prompt for password, or hardcoded
password), and set the hostname of the server mysql is running on.  All of these
settings can be found towards the top of the installdb script.

  Once run, the script will import all of the data into your MySQL server (this
will take a few hours, due to the amount of data).

\pagebreak

\section {Database configuration}

\subsection{Setting up the configuration folder}

The \code{annmap} package requires a file called \code{databases.txt} to be
placed inside a known folder.  The package checks for this file in the following
locations, and uses the first file it locates:

\begin{enumerate}
  \item
    A location defined by the System Environment Variable \code{ANNMAP\_HOME}.
  \item
    A folder named \code{.annmap} inside the current user's home directory (On
    my OS X machine, this will be \code{/Users/tyates/.annmap/})\footnote{If
    you are not sure where your home directory is, you can find out through R by
    typing \code{Sys.getenv( "HOME" )} into an R console.}.
\end{enumerate}

\subsection{Setting up the \code{databases.txt} file}

The \code{databases.txt} file is a tab-delimited file (a comma-delimited file is also accepted) in which each row defines a
particular instance of an annmap database.  The first row is always a list of
tab-delimited column headings.

The columns; \code{port} and \code{password} may be left blank if you are using
the default MySQL port (3306), or have a user account with no password required.
Password can also be set to \code{<ASK>}, in which case, the system will ask you to
enter your password before it connects to the server.

An example follows;

\fcolorbox{black}{NoteGrey} {
  \begin{tabular}{ l l l l l l l }
    \code{name}  & \code{host}          & \code{species}       & \code{version} & \code{port} & \code{username}  & \code{password} \\
    \code{hs}    & \code{localhost}     & \code{homo\_sapiens} & \code{66}      & \code{4406} & \code{dbuser}    & \code{dbpwd} \\
    \code{mouse} & \code{anotherserver} & \code{mus\_sapiens}  & \code{66}      &             & \code{userNoPwd} & \\
  \end{tabular}
}

This example file (when put in the correct location) would set up two databases:
one called '\code{hs}' pointing to a v66 Homo Sapiens database running on the local
machine (on a different port to the default); and another running v66 Mus Musculus
on '\code{anotherserver}'.

When you run \code{annmapConnect()} inside R, you should see both these appearing
in a list for you to select which database to attach to.  Or you can skip the
menu by entering the database of choice into the command as a parameter: 
\code{annmapConnect('mouse')}.

\end{document}
