173 lines
6.2 KiB
TeX
173 lines
6.2 KiB
TeX
\documentstyle[a4,11pt]{article}
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\title{Installing the Staden Package}
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\author{Simon Dear}
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\date{21 May 1993}
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\begin{document}
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\maketitle
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\section{Introduction}
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On the accompanying tape you will find executables for
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one of SunOS 4.x, Sun
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Solaris 2.x, DEC Ultrix, DEC OSF/1 and Silicon Graphics SGI operating systems.
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Also there are sources for all the programs in the Staden package.
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Programs in the package are:
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\begin{description}
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\item[mep and xmep] Motif exploration program.
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\item[nip and xnip] Nucleotide interpretation program.
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\item[nipl] Nucleotide interpretation program (library).
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Searches nucleotide libraries for patterns of motifs.
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\item[pip and xpip] Protein interpretation program.
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\item[pipl] Protein interpretation program (library).
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Searches protein libraries for patterns of motifs.
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\item[sip and xsip] Similarity investigation program.
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\item[sipl] Similarity investigation program (library).
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Compares a probe protein or nucleic acid sequence against
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a library of sequences.
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\item[sap and xsap] The original sequence assembly program.
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\item[bap and xbap] Our latest, most advanced sequence assembly program.
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\item[dap and xdap] An obsolete assembly program, superceded by {\em bap}.
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\item[lip] Library interface program.
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\item[rep] Repeat examination program.
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\item[ted] X windows utility for displaying and editing
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fluorescent sequencing machine traces.
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\item[splitp1, splitp2 and splitp3] Refer to help/SPLITP.MEM.
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\item[sethelp] Builds online help files.
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\item[gip] Gel input program.
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\item[convert] Converts between {\em xdap\/} and {\em xbap\/} databases.
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\item[cop and cop-bap] Checks completed {\em xdap\/} and {\em xbap\/}
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databases for editing errors.
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\item[trace2seq] Extracts sequence from trace files.
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\item[getABISampleName] Extracts sample names from ABI trace files.
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\item[makeSCF] Converts existing trace files to the compact
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SCF format.
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\item[alfsplit] Splits the Pharmacia A.L.F. gel
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file into multiple files, one for each sample.
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\item[frog] Relabels lanes in ABI trace files.
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\item[+ numerous scripts (including {\em squirrel (v1.4)\/})]
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\end{description}
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\section{Requirements}
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You will need a tape drive to read the software off the distribution
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tape (QIC-150, TK50, or Exabyte). You will also need a large amount of
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disk storage to accommodate the whole package. For release
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version-1993.0, requirements were
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31Mb (SunOS 4.x),
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36Mb (Sun Solaris 2.x)
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30Mb (DEC Ultrix)
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37Mb (DEC OSF/1)
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and
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27Mb (Silicon Graphics SGI.)
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To compile the Staden package you will require:
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\begin{itemize}
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\item An ANSI C compiler.
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\item A FORTRAN-77 compiler.
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\item X11 (Release 4 or 5).
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\item GNU make (except with SunOS and Solaris 2.x.)
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\end{itemize}
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\section{Installation}
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To install the package,
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\begin{enumerate}
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\item Create a directory for where you would like the software to be
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placed. You may have to be superuser to do this.
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\begin{verbatim} mkdir /home/Staden\end{verbatim}
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\item Change to this directory.
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\begin{verbatim} cd /home/Staden\end{verbatim}
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\item Place the tape into the tape unit.
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\item Extract the software off the distribution tape (NOTE: the device name may be
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different on your machine):
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\begin{verbatim} tar xvf /dev/rst0\end{verbatim}
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\item C shell users should set the environment variable {\bf STADENROOT}
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to be the directory where the package is installed and source the file
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{\em staden.login} found there. This is best done by adding lines to their
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{\em .login} file:
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\begin{verbatim}
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setenv STADENROOT /home/Staden
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source $STADENROOT/staden.login
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\end{verbatim}
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Users of the Bourne shell, sh, should similarly add lines their {\em .profile} file:
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\begin{verbatim}
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STADENROOT=/home/Staden
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export STADENROOT
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. $STADENROOT/staden.profile
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\end{verbatim}
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The startup routines set environment variables and modify the shell's
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search path so that it can find the programs in the Staden Package.
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When users next log on to the system, they will be able to use the
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programs.
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\end{enumerate}
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\section {Installation on Unsupported Platforms}
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Install the software as you would for a supported machine. You will
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need to remake all executables. The script {\em Staden\_install} can
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be used to help recompile the package. A large number of
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assumptions have been made, and you may need to change the makefiles
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to suit your system.
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The sources have been organised into subdirectories of the directory
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{\bf src}. In {\bf Misc} are routines common to many programs. They
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should be made first. In {\bf staden} are all the programs of the
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Staden suite ({\em mep}, {\em nip}, {\em pip}, {\em sap}, {\em sip},
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{\em dap}, {\em gip}, {\em vep}, {\em lip} and {\em rep}) with the
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exception of {\em bap}. Code for our latest sequence assembly program
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{\em bap} is in directories {\bf bap} and {\bf bap/osp-bits}. Make
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the objects in {\bf staden} first, then the ones in {\bf
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bap/osp-bits}, and finally the ones in {\bf bap}. In {\bf ted} is the
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trace editing program.
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\section {Other Software Provided}
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Other software and scripts can be found in the {\bf alf\/}, {\bf
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abi\/}, {\bf cop\/}, {\bf getMCH\/}, {\bf scf\/}, {\bf frog\/} and {\bf
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scripts}
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directories.
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Each directory contains documentation describing the programs
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contained.
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Since release version-1993.0 we have distributed the {\em squirrel (v1.4)}
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package. Please read the disclaimer that accompanies this software.
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Additional sources and scripts can be found in {\bf expGetSeq}, {\bf vepe},
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{\bf newted} and {\bf squirrel-1.4} directories.
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Many scripts (including {\em squirrel}) and filters were developed at the MRC-LMB for
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{\bf INTERNAL USE ONLY}.
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We are aware that people elsewhere will want to develop
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similar software.
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We include them in the Staden Package merely as {\bf EXAMPLES} of
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what has been achieved elsewhere.
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{\bf THESE SCRIPTS WILL NOT WORK ON YOUR SYSTEM WITHOUT MODIFICATION.}
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\section {When All Else Fails...}
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If you have any problems please contact the authors,
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\mbox{Rodger Staden}
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\mbox{(\em rs@mrc-lmba.cam.ac.uk\/)},
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\mbox{Simon Dear}
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\mbox{(\em sd@mrc-lmba.cam.ac.uk\/)}
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and
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\mbox{James Bonfield}
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\mbox{(\em jkb@mrc-lmba.cam.ac.uk\/)},
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by email or by writing to us at:
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MRC Laboratory of Molecular Biology, Hills Road, Cambridge, \mbox{CB2 2QH}, U.K.
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We also welcome general comments on the package.
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\end{document}
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