297 lines
10 KiB
Plaintext
297 lines
10 KiB
Plaintext
General Information
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(Not for the faint hearted)
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30 September 1992
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0. Introduction
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---------------
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This document contains information on the following subjects:
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1. Installing the Staden Package on SPARCstations and DECstations
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2. Installing the Staden Package on Other Machines
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3. A Quick Guide to What's on the Release Tape
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4. Overview of Data Flow During Sequence Assembly
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5. Acknowledgements
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1. Installing the Staden Package on SPARCstations and DECstations
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-----------------------------------------------------------------
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We are endeavouring to make the installation of the Staden Package as
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quick and as easy as possible. In this current release we provide
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statically linked sparc and mips executables as well as all sources.
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To install the package:
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1) Create a new directory for the software. You may have to log on as
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superuser to do this.
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% mkdir -p /home/BioSW/staden
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2) Place the distribution tape in the drive and down load the package:
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-sun-
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% tar xvf /dev/rst0
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...system messages...
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-dec-
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% tar xvf /dev/rmt0h
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...system messages...
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3) Users of the C Shell should add the following to his/her .login
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file:
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setenv STADENROOT /home/BioSW/staden
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source $STADENROOT/staden.login
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Users of the Bourne shell should add the following to their .profile
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file:
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STADENROOT=/home/BioSW/staden
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export STADENROOT
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. $STADENROOT/staden.profile
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4) When the user next logs onto the work station the required
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initialisation will automatically be performed, and the programs in
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the Staden package can be run. Refer to the help/*.MEM files for
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information on the various program. (eg help on xdap is in
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help/DAP.MEM)
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2. Installing the Staden Package on Other Machines
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--------------------------------------------------
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This is a little more difficult as you will need to remake all the
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executables. Your system configuration may also mean that some changes
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will need to be made, though hopefully only to makefiles. We provide
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a script to aid installation (we hope!), but you may prefer to make
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all the components manually.
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To remake the Staden package you will require the following:
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1) A Fortran77 compiler
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2) An ANSI C compiler
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3) X11 Release 4, including the Athena Widget libraries.
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Start by following step 1 through 3 above, to unload the sources and
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perform initialisations. Read the rest of this document and the other
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help files. Look at the make files. Follow your nose!
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If you have any problems or successes porting our software to other
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platforms we would love to hear from you. We would also appreciate
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receiving your general comments on the package.
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Rodger Staden (principle author)
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phone: +44 223 402389 email: rs@mrc-lmba.cam.ac.uk
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post: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, U.K.
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Simon Dear:
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phone: +44 223 402266 email: sd@mrc-lmba.cam.ac.uk
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post: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, U.K.
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James Bonfield:
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phome: +44 223 402499 email: jkb@mrc-lmba.cam.ac.uk
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post: MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, U.K.
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3. A Quick Guide to What's on the Release Tape
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----------------------------------------------
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The directory structure on this tape is very important. Once set up, the Staden
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package expects things to be in a predefined place. The root directory
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of the structure is referred to by the environment variable
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STADENROOT. Below this there should be at least the following:
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1) bin/
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All executable files and scripts should be in this directory.
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$STADENROOT/bin is added to the search path by the script staden.login
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(or staden.profile if you are using the Bourne Shell). Though you are
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not forced to keep programs here, we find it is the simplest place to
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keep them.
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2) help/
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All on-line help files are in this directory. Files of the form *.MEM
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or *.mem are formatted ascii files and can be printed for personal
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reference. The script staden.login sets up many environment variables
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that refer to files in this directory, as well as modifying
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XFILESEARCHPATH, which is used by X programs.
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3) manl/
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Local manual pages for ted and the staden package are in this directory. The
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environment variable MANPATH is modified in staden.login to search
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here too.
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4) staden.login and staden.profile
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These two files are scripts to set up environment variables required
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by the Staden package. C Shell users should source staden.login from
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their .login file, and Bourne Shell users should "source" staden.profile
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from their .profile directory. See "Installing the Staden Package on
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SPARCstations and DECstations", Part 3.
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5) tables/
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Configuration files for the Staden package are in this directory.
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Various environment variables are set in staden.login to refer to
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files in this directory.
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Also of use are the following:
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doc/ - Miscellaneous documentation.
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userdata/ - Sample databases
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src/ - program sources
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ReleaseNotes - Notes on this and future releases
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Staden_install - Installation script
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SequenceLibraries - Notes on the use and installation of sequence libraries
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Program Sources
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---------------
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All the program sources are found in the directories in $STADENROOT/src:
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0) Misc/
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Sources for a library of useful routines used by the staden package.
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** Should be made before the programs in staden/ **
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1) staden/
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Sources for the Staden suite: mep, xmep, nip, xnip, nipl, pip, xpip,
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pipl, sap (now superseded by dap), xsap (now superceded by xdap), sip,
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xsip, sipl, dap, xdap, splitp1, splitp2, splitp3, gip and convert_project.
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2) ted/
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Sources for the trace display and sequence editing program ted.
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3) abi/
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Sample scripts and programs for handling ABI 373A data files.
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4) alf/
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Sample scripts and programs for handling Pharmacia A.L.F. data files.
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Each directory has appropriate makefiles and README files.
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4. Overview of Data Flow During Sequence Assembly
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-------------------------------------------------
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During a sequence assembly project the data can enter the sequence
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assembly program from various routes (See Figure below).
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Fluorescent Based
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Sequencing Machine
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Chromatogram Autoradiogram
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ABI 373A Pharmacia A.L.F. |
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| alfsplit |
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+--------+--------+ |
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ted (gip)
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+----------------+----------------+
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xdap
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Figure 1: Data Flow Through The Staden Suite
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The Pharmacia A.L.F. data files in their original format consist of
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one file for the (up to 10) samples that were on the gel. The program
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alfsplit divides the file up so that each sample is in a file of
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its own. From then on each gel reading can be handled individually.
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Whether these files can be transferred back to the Compaq for
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reprocessing is unknown.
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All data from fluorescent based sequencing machines must pass through
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the trace editing program ted. Ted allows data vector sequence at the
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5' end and unreliable data at the 3' end to be clipped. The sequence
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can be edited if desired, though we should stress that this is NOT
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RECOMMENDED when used in conjunction with xdap. Ted translates all
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Pharmacia A.L.F. uncertainty codes to a hyphen ("-") and outputs the
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clipped sequence, along with additional information on the position
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and content of cutoffs, to a file.
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People wanting to use xdap with ABI and Pharmacia files, but who have
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written their own trace clipping software should be aware that xdap
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requires information to be passed in the sequence file so that
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traces can be displayed. You may want to modify your software to be
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compatible with our file format. The file consists of four parts:
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1) Cut off information (Optional).
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Format is ";%6d%6d%6d%-4s%-16s", where
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field 1 = total number of bases called
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2 = number of bases in the clipped sequence at the 5' end
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3 = number of bases in the sequence in this file
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4 = type of trace file.
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"ALF " - Pharmacia A.L.F.
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"ABI " - ABI 373A
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"SCF " - SCF
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"PLN " - Text only
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5 = name of trace file.
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2) Content of the clipped sequence at the 5' end (Optional).
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The sequence can extend over several lines. Each line must
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begin with ";<" and should be less than 80 characters in
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length.
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3) Content of the clipped sequence at the 3' end (Optional).
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The sequence can extend over several lines. Each line must
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begin with ";>" and should be less than 80 characters in
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length.
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4) Initial tags for the sequence (Optional)
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Format is: ";;%4s %6d %6d %s\n", where
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field 1 = type of tag to be created (see $STADTABL/TAGDB)
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2 = position of tag
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3 = length of tag
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4 = annotation for tag (optional)
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This feature is only available in the program xbap, which
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at the time of writing is not yet being distributed with
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the package.
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5) The sequence, which can extend over several lines. Each
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line should be less than 80 characters in length.
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Here is a sample file:
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; 660 55 450ABI a21d12.s1RES
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;<AGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCCGGTTCCTTCTGG
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;<ATATC
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;>-GATAAGCTGATTTG-TTT-CCATTATGGC-GGTTTGAGCCTC-G-GGTC
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;>GACCACTCGGTGTGCCAGGAAGGGGTCTGAAATTGAATGGGTTATCACTA
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;>GGCGACGTTT--TTTTCAAATTCCGGGCTAAATTTTACGGC-GGA-CGGT
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;>TCCG-
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;;COMM 1 10 M13mp18 subclone
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CAAGACATTTTGAAATACTTGGAATACTGAATCCAAGATGTGGAACATTA
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GACATATCCGTGTGCTCAACAATCGACATTTGATCCACTGATGAAAATGT
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TCTTCGTTTAGAATTTCTCATAGCATCAGCCACTTTTGCATAATACTCGA
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TTGAAGGTTCATGGAAAAAGCTGCGTAGAAGGCATGTCATTGTGCTTACG
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AGCCATTTCGGATATCTTGTGAATTTAGCAGGAAGTTCTGTAACTGGTTG
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GAATTCAAATATATCAGTTCTTCTTCCTGGATCTCGTCCTTTTTGCACTA
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AAACCATTGCGATTGCATCCGGATTCTGAGTAAGAGCCACTACAGCTTTA
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TGATACAGGCTCTTGTTATTCCTTTCGTGCTCGAATGGGAACTTTCCAGT
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GGCACAAAAATATAGTGTACATCCCAGAGCCCATAGATCACATGTTCCGA
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5. Acknowledgements
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We would like to thank Applied Biosystems, Inc. and Pharmacia LKB
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Biotechnology for their cooperation in agreeing to our routines
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accessing the data files of their fluorescent sequencing machines.
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373A sequence data file formats are the exclusive property of Applied
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Biosystems, Inc.
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ALF sequence data file formats are the exclusive property of Pharmacia
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LKB Biotechnology, Inc.
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