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[basedb-cvs] basedb/documentation/faq Makefile,NONE,1.1 developer.tex,NONE,1.1 faq.tex,NONE,1.1 firstpage.tex,NONE,1.1 general.tex,NONE,1.1 installation.tex,NONE,1.1 introduction.tex,NONE,1.1 usage.tex,NONE,1.1
Update of /cvsroot/basedb/basedb/documentation/faq
In directory usw-pr-cvs1:/tmp/cvs-serv14533
Added Files:
Makefile developer.tex faq.tex firstpage.tex general.tex
installation.tex introduction.tex usage.tex
Log Message:
Adding first version of FAQ.
--- NEW FILE: Makefile ---
# $Id: Makefile,v 1.1 2002/10/02 15:16:20 kurri Exp $
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installation.tex introduction.tex usage.tex
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--- NEW FILE: developer.tex ---
% $Id: developer.tex,v 1.1 2002/10/02 15:16:21 kurri Exp $
\section{Developer}
\subsection{How do I write plug-ins?}
See {\tt exec/source/README.basefile} and/or read the information
below.
What a plug-in needs to know is this: It's run in a directory where
it's allowed to create files. Things written to {\tt stdout} will end
up in a file called {\tt stdout.txt} (in the current
directory). Errors and other information can be written to {\tt
stderr}. On {\tt stdin} the plug-in will get the data to be processed,
in the rather badly documented {\it BASEfile format}. When the plug-in
has terminated, {\tt jobController.php} will scan the output directory
(recursively) and add information about all files it finds to the
database. If if finds what it believes to be valid BASEfiles,
additional information about these will be stored, and if they contain
a few predefined things (bioassays, reporter lists) {\it
[...78 lines suppressed...]
BASEfile with one {\tt assays} section per assay in the input, have
only one assay per such section (that is, make it the ``serial''
version of this format), and put the same id for the assay as you got
in the input. You need to pass the position and molecule columns
through unchanged, and output the normalised values in columns called
{\tt intensity1} and {\tt intensity2}. Have a look at a {\tt
stdout.txt} from {\it lowess} to see what I mean.
To have a {\it genelist} ({\it reporter} list) created by {\tt
jobController.php}, output a section {\tt genelist} with columns {\tt
cloneId} and {\tt value}, where the cloneId is passed through from the
input {\it BASEfile} and {\tt value} is a value to be associated with
the gene. If there is no such value or you just want the rank of the
gene (the position in the genelist), leave out the {\tt value} column
altogether.
\noindent The BaseFileReader class: \\ In exec/source there is a C++ class
called {\it BaseFileReader}. This class is used by the plug-ins
provided with BASE, and in the source for those you can see how it can
be used to parse BASEfiles.
--- NEW FILE: faq.tex ---
% $Id: faq.tex,v 1.1 2002/10/02 15:16:21 kurri Exp $
\documentclass[10pt]{article}
\usepackage{html}
\evensidemargin 0pt
\flushbottom
\footskip 10mm
%\headheight 0pt
%\headsep 0pt
\oddsidemargin 0pt
%\pagestyle{empty}
\parindent 10pt
\parskip 1ex
\textheight 235mm
\textwidth 165mm
\topmargin -5mm
\begin{document}
\input{firstpage}
\input{introduction}
\input{general}
\input{installation}
\input{usage}
\input{developer}
\end{document}
--- NEW FILE: firstpage.tex ---
% $Id: firstpage.tex,v 1.1 2002/10/02 15:16:21 kurri Exp $
\begin{htmlonly}
\begin{verbatim}
$Date: 2002/10/02 15:16:21 $
\end{verbatim}
\end{htmlonly}
Created \today.
\begin{htmlonly}
This document is also available in \htmladdnormallink{postscript
format}{base_faq.ps} or \htmladdnormallink{portable document format
(pdf)}{base_faq.pdf}.
\end{htmlonly}
--- NEW FILE: general.tex ---
% $Id: general.tex,v 1.1 2002/10/02 15:16:21 kurri Exp $
\section{General}
\begin{htmlonly}
\begin{verbatim}
$Date: 2002/10/02 15:16:21 $
\end{verbatim}
\end{htmlonly}
\subsection{What is BASE?}
BASE is short for BioArray Software Environment.
BASE is a comprehensive database server to manage the massive amounts
of data generated by microarray analysis. In short, it manages
biomaterial information, raw data and images, and provides integrated
and ``plug-in''-able normalisation, data viewing and analysis
tools. Additionally, for labs that make their own in-house arrays or
for labs that wish to track probe information, the system also has
array production LIMS features which can be integrated with the data
[...90 lines suppressed...]
\end{itemize}
\subsection{Working browsers list}
Christopher Faulk, Fa...@pb..., and others have compiled a list of working
browsers. Remember, cookies {\em must} be turned on.
\begin{itemize}
\item IE v 6.0 on Windows 98, 2k, NT
\item IE v 5.0 on Windows 98, 2k, NT, Mac OS 9
\item Opera v 6.01 on windows2k
\item Netscape v 4.7 on Mac OS 9
\item Netscape v 6.1 on Windows 2k
\item Mozilla v 0.9.8 on Linux Mandrake 8.2 i586
\end{itemize}
\noindent These browser do not work, and you should not expect
support for them.
\begin{itemize}
\item links and lynx.
\item Konqueror 2.1.1
\end{itemize}
--- NEW FILE: installation.tex ---
% $Id: installation.tex,v 1.1 2002/10/02 15:16:21 kurri Exp $
\section{Installation}
\begin{htmlonly}
\begin{verbatim}
$Date: 2002/10/02 15:16:21 $
\end{verbatim}
\end{htmlonly}
\subsection{General}
\subsubsection{Where can I find the installation documentation?}
README in the distribution. Proper documentation are under construction. Make
sure you are using the recommended operating system, PHP, and
web server versions. Please use the mailing list if you need
additional help.
\subsection{Apache}
\subsubsection{Apache does not recognise my php.ini changes.}
You must restart Apache after changing {\tt php.ini}.
\subsubsection{Apache version 2 cannot locate files.}
The problem is that the PHP module defaults to {\it AcceptPathInfo}
off, so you'll need an explicit {\tt AcceptPathInfo on} in your {\tt
httpd.conf}. Cf. documentation at
\htmladdnormallink{http://httpd.apache.org}{http://httpd.apache.org/docs-2.0/mod/core.html\#acceptpathinfo}.
\subsubsection{File and Directory Permissions Problems}
You must set the proper permissions for the BASE upload directory. The
httpd process user id must have the right to write stuff to the
directory.
\subsection{MySQL}
\subsubsection{MySQL doesn't allow LOCAL at LOAD DATA INFILE}
You need to compile MySQL with {\tt --enable-local-infile} or start
{\tt safe\_mysqld} with {\tt --local-infile}.
\subsubsection{Can't connect to [local] MySQL server Error}
Please read the \htmladdnormallink{MySQL
documentation}{http://www.mysql.com/doc/en/Can_not_connect_to_server.html}.
\subsection{PHP}
\subsubsection{What version of PHP must I run?}
You should run the latest 4.2 version (at least version 4.2.2).
\subsubsection{PHP path problem; Plug-ins do not run}
Make sure your PHP scripts contain the correct path to the PHP
binary. The default is {\tt /usr/local/bin}, but your installation
might have another location for {\tt php}. Use the command {\tt which
php} to find out where the PHP binary is located.
\subsubsection{Can't login as root to BASE; Undefined variable \_SERVER}
This is a very clear indication that you are not running PHP 4.2.2, as
\_SERVER is one of the predefined ever-global variables since 4.1.
Point your browser to test.phtml (which does a phpinfo() to show PHP
setup info), and see what version it reports. It could be that your
standalone PHP and the apache module have different versions.
\subsubsection{PHP does not cooperate with MySQL}
PHP must be configured with MySQL support, e.g. \\ \indent {\tt ./configure
--with-mysql [other options]} \\ or \\ \indent {\tt ./configure
--with-mysql=/path/to/mysql/installation [...]}
\subsubsection{Magic quotes must be off}
I'm getting the message {\em PHP misconfigured - BASE can't
run. (magic quotes)}. {\tt magic\_quotes\_gpc} and {\tt
magic\_quotes\_runtime} must be set to {\tt "= Off"}
--- NEW FILE: introduction.tex ---
% $Id: introduction.tex,v 1.1 2002/10/02 15:16:21 kurri Exp $
\section*{BASE Frequently Asked Questions, FAQ}
\begin{htmlonly}
\begin{verbatim}
$Date: 2002/10/02 15:16:21 $
\end{verbatim}
\end{htmlonly}
--- NEW FILE: usage.tex ---
% $Id: usage.tex,v 1.1 2002/10/02 15:16:21 kurri Exp $
\section{Using BASE}
\begin{htmlonly}
\begin{verbatim}
$Date: 2002/10/02 15:16:21 $
\end{verbatim}
\end{htmlonly}
\subsubsection{Where can I find user documentation?}
We recommend the novice user read the Quick Start Guide, aka ``BASE
v1.0 instruction manual''. It can be found on the
\htmladdnormallinkfoot{Download page}{http://base.thep.lu.se} at the
BASE web site (you have to enter your personal registration code to
get in). This guide contains a step-by-step walk through of most of
the functionality in BASE v1.0 (there have been improvements in newer
versions of BASE but most of the guide is still very relevant).
\subsection{Must I use the Array LIMS part of BASE?}
[...107 lines suppressed...]
384-well, and its position was stored in the 'position' column. As
people desired to be able to reuse 96-wells on multiple 384-wells and
also to be able to pick probes from several plates to create new
plates, we wanted a more general many-to-many relationship. This has
been implemented, but there is as of yet no way to create 96-wells
from multiple 96-wells.
Another thing that I've considered is the possibility to define new
plate geometries and mappings from one to another. Right now the four
96-wells used on a 384 are assumed to be arranged in a pre- defined
manner:
\begin{verbatim}
121212
434343
121212
434343
etc.
\end{verbatim}
For labs with an other way of doing this step, flexibility is
needed.
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