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

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Release Notes for Staden Package 1992.3
---------------------------------------
Installation guide
------------------
The file doc/install.PS contain installation instructions.
Manual for the Staden Package
-----------------------------
There is now a 135 page manual on the Staden Package. It is currently
being distributed on a Word4 document on a Macintosh floppy disk.
Feedback and bug reports
------------------------
We welcome comments and suggestions on all aspects of the package and are
best contacted by email: rs@uk.ac.cam.mrc-lmb and sd@uk.ac.cam.mrc-lmb.
All abnormal terminations are bugs and we would like to be told of them
so they can be fixed. We recommend that you request an update at least once
a year as the package is evolving very rapidly.
Note due to popular demand we have decided to release new routines earlier
than in the past so please report bugs. The documentation for additions may
be sparser than before, or non-existent, but if there is something with which
you need help, email us.
Changes this release
--------------------
The assembly programs bap and xbap heve several new functions:
1. Find single stranded regions and try to fill them with "hidden"
data from the adjacent readings.
2. Find single stranded regions (includes ends of contigs) and
select primers and templates for double stranding them (joining
them).
3. Pre assembly screening for readings to find those that align
best. Optionally the hidden data can also be included in the
comparison (part of assembly function).
4. Find pairs of readings taken from opposite ends of the same
template (ie forward and reverse read pairs). List or plot their
positions.
5. A new function to check that readings have been assembled into
the correct positions. It aligns the hidden (previously termed "unused")
parts of readings with the consensus they overlap to see how well
they align. Poor alignments are reported.
6. During assembly each reading is now allowed to match up to 100
different places.
It might be guessed from the above that we are trying to improve our
ability to deal with the assembly of human data. Hence, also the next
addition.
A new experimental program (rep) for screening readings for Alu
sequences prior to assembly. The Alu containing segments are tagged
so they can be seen in the contig editor. A library of Alu sequences
is included in /tables/alus. The program is quite slow as it compares
each reading in both orientations with all of the Alu sequences (126
of them) in order to find the best match. Only time and more data will
tell how sensitive it is, and whether the current default score 0f 0.6
is "correct". BEWARE rep modifies the original reading files to include
the tag information. The only information is in /help/alu.help
A new program for extracting sets of sequences and their annotations
from the sequence libraries (lip). The only information is in
/help/lip.help
Changes to the xterm userinterface. These routines have been completely
rewritten. One addition is that now ?? in response to a question will
allow the user to get help on any function in a program. help is also
improved in the x version.
Changes last release
--------------------
DAP, XDAP have been replaced by BAP and XBAP (see below)
A new function for examining repeats has been added to NIP
A new repeat search has been added to SIP
Some outputs have been changed to produce FASTA format files
instead of PIR.
MEP now allows searches for motifs in which any 8 out of a string
of 20 can be switched on.
The manual has been updated.
Keyword and author searches on sequence libraries
All programs that use the libraries can now perform author
and keyword searches on all libraries (only nip did so before).
Postscript output
All graphics can now be saved to disk in postscript form by
use of a sub-option in "Redirect output".
Sequence assembly
BAP, XBAP replace DAP and XDAP. A program to convert DAP databases to BAP
databases (convert) is included. BAP databases can contain up to 8000 readings
and a consensus of 500,000 bases. A minor edit and recompilation will allow
up to 99,999 readings. The space is used more efficiently now as the databases
grow as the number of readings increases. Reading names can be 16 characters
in length. In addition:
1) Assembly is 4 times as fast as in the DAP.
2) Find internal joins is 5 times as fast and now brings up the join editor
with the two contigs in the correct orientation and aligned.
3) The assembly routines align pads better, plus a new automatic function can
also be used to align them prior to editing.
4) The contig editor has been greatly speeded up and its functionality
has been enhanced.
5) A routine for selecting oligos for primer walking is included.
6) A new routine allows batches of readings to be removed from a database.
7) We have also included routines for making SCF files, for getting the
sequence from SCF files, and one for marking the poor quality data in
readings. See the manual.
Sequence library formats
The standard sequence library indexing method is now that used on the
EMBL CD-ROM. The libraries (EMBL nucleotide and SWISSPROT protein) can be
left on the CD-ROM or copied to disk. We include in the package programs
for creating this type of index for EMBL updates, PIR in codata format,
NRL3D and GenBank. If the indexes are created all programs can read all
these libraries. Programs and scripts for this task are contained in the
directory indexseqlibs.
The keyword and author searches are particularly fast and the
keyword index is based on ALL text in the files - not just the keywords.
Feature table formats
The programs now use the new feature table format common to EMBL
and GenBank, but retain the old format for SWISSPROT which has not yet
changed.
For details of the above see file SequenceLibraries.
Pattern searches
Pipl and Nipl now have the facility to find only the best scoring
match for each sequence. The prompt is "? report all matches", so typing
only return means all matches will be shown and typing n means only the
highest scoring will be reported. It is particularly useful when employed
to create alignments. The corresponding help file has not been updated.
Also to incorporate long unix file names the pattern files no longer include
the annotation "filename".
Nip
Option 38 in nip "translate and list" has been removed as the the
more flexible routines of option 39 incorporate all its functionality. Many
options that relate to feature tables have been modified but their help files
are not yet up to date.
Vep
A program (vep) for automatic excising of vector (either
sequencing vector or cosmid vector) sequences from readings is now
included in the package.
Rodger Staden, Simon Dear, James Bonfield

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Notes on library handling
-------------------------
Contents of this document:
I) Introduction
II) Details of file organisation and use
III) Options currently available
IV) Installation guide
V) New feature table handling routines
VI) Indexing the sequence libraries
Section I Introduction
----------------------
Available sequence libraries
There are a number of different sequence libraries for nucleotide and protein:
PIR, GenBank, EMBL, Swissprot, and the Japanese Databank. Even after all the
years of their existence they still use different formats for their data. This
provides tedious and unrewarding work for software developers. Recently EMBL
and GenBank agreed a new and common way of writing their feature tables, which
is great help, although the rest of their format is different. Swissprot still
uses the old embl style feature table format and PIR yet another.
All the libraries distribute their data on magnetic tapes and EMBL and GenBank
have started to distribute on cdrom. The EMBL cdrom also contains Swissprot.
The GenBank and EMBL cdroms use different formats and have different contents.
The EMBL cdrom has useful indexes sorted alphabetically: those for entry name
and accession number, brief descriptions, keywords and freetext indexes are
already available and others are expected. These indexes point to the data for
each entry, and can be used to extract the data for any entry quickly.
Moving to unix
The VAX version of our package used PIR format which meant reformatting all
libraries other than PIR into that format. This required, at least
temporarily, having space for two copies of the libraries, and quite a lot of
cpu time. The software for doing this was provided by PIR, and is very VAX
specific and hence will not run under unix. For the unix version of our package
I have decided to use the EMBL cdrom format and its indexes as the primary
format. The current programs also support the use of PIR format libraries
without indexes - ie just the sequence and annotation files.
Indexing GenBank, EMBL updates, PIR and NRL3D
We include programs to create indexes for the above libraries. See below and
the README file in indexseqlibs. The programs can read all the above libraries
once the indexes are created. The indexing programs index the data in its
distributed form: WE DO NOT REFORMAT OR COPY THE LIBRARIES but simply create
indexes to the original files. Obviously this saves a lot of disk space, and
for those content to use only embl and swissprot from the cdrom, almost no disk
space is required. We havent tried it yet, but for genbank on cdrom, the only
extra disk space required would be for the indexes.
---------------------------------------------------------------------------
Section II Details of file organisation and use
-----------------------------------------------
The following strategy has been used to try to deal with alternate
and changing sequence library formats.
1) libraries are described at several levels:
a) the top level file is a list of available libraries which contains:
the library type, the name of the file containing the name of
each libraries individual files, and the prompt to appear on
the users screen: LTYPE LOGNAM PROMPT
b) the file containing the names of the libraries individual files
contains flags to define the file types: FTYPE LOGNAM
c) the individual library files
2) libary types handled:
a) EMBL/SWISSPROT in distributed format with cdrom index format
LTYPE = 'A'
b) GenBank in distributed format with cdrom index format LTYPE = 'C'
c) PIR/NRL3D in CODATA format with cdrom index format LTYPE = 'B'
d) PIR/NBRF .seq files can be read sequentially as "personal files
in PIR format" and do not appear in the list of available libraries.
e) FASTA format files can be read sequentially as "personal files
in FASTA format" and do not appear in the list of available
libraries.
3) EMBL, SWISSPROT and other libraries for which EMBL-style indexes have been
created
current file types:
A division.lookup
B entryname.index
C accession.target
D accession.hits
E brief description
F freetext.target
G freetext.hits
H author.target
I author.hits
Library list
level 1
|
|
-----------------------------------------------------------
| | |
lib 1 file list lib 2 file list lib 3 file list
level 2
| |
-------- ---------
level 3
file 1 file 1
file 2 file 2
. .
file n file n
---------------------------------------------------------------------------
Example
-------
Level 1
File name: sequence.libs
Environment variable: SEQUENCELIBRARIES
Contents:
A EMBLFILES EMBL nucleotide library ! in cdrom format
C GENBFILES GenBank nucleotide library!
A SWISSFILES SWISSPROT protein library! in cdrom format
B PIRFILES PIR protein library!
B NRL3DFILES NRL3D protein library!
Notes:
The libraries have types A,B,C. The logical names are EMBLLIBDESCRP and
SWISSLIBDESCRP, etc and the prompts are 'EMBL nucleotide library' and
'SWISSPROT protein library', etc. Anything to the right of a ! is a comment.
Level 2: the list of library files (using embl as an example)
File name: embl.files
Environment variable: EMBLFILES
Contents:
A EMBLDIVPATH/embl_div.lkp
B EMBLINDPATH/entrynam.idx
C EMBLINDPATH/acnum.trg
D EMBLINDPATH/acnum.hit
E EMBLINDPATH/brief.idx
F EMBLINDPATH/freetext.trg
G EMBLINDPATH/freetext.hit
H EMBLINDPATH/author.trg
I EMBLINDPATH/author.hit
Level 3: the sequence and annotation files (eg 15 for embl, 1 for swissprot).
Paths and file names:
EMBLPATH/bb.dat
EMBLPATH/fun.dat
EMBLPATH/inv.dat
EMBLPATH/mam.dat
EMBLPATH/org.dat
EMBLPATH/patent.dat
EMBLPATH/phg.dat
EMBLPATH/pln.dat
EMBLPATH/pri.dat
EMBLPATH/pro.dat
EMBLPATH/rod.dat
EMBLPATH/syn.dat
EMBLPATH/una.dat
EMBLPATH/vrl.dat
EMBLPATH/vrt.dat
All files from the division lookup file down are exactly as they appear on the
cdrom. The division lookup file relates numbers stored in the indexes to
actual division (or data) files stored on the disk. We rewrite it so the
directory structure and file names can be chosen locally. Its format is
I6,1x,A. An example is given below.
Division lookup file
File name: STADTABL/embl_div.lkp
Environment variable path EMBLDIVPATH
Contents:
1 EMBLPATH/bb.dat
2 EMBLPATH/fun.dat
3 EMBLPATH/inv.dat
4 EMBLPATH/mam.dat
5 EMBLPATH/org.dat
6 EMBLPATH/patent.dat
7 EMBLPATH/phg.dat
8 EMBLPATH/pln.dat
9 EMBLPATH/pri.dat
10 EMBLPATH/pro.dat
11 EMBLPATH/rod.dat
12 EMBLPATH/syn.dat
13 EMBLPATH/una.dat
14 EMBLPATH/vrl.dat
15 EMBLPATH/vrt.dat
---------------------------------------------------------------------------
Section III Options currently available
---------------------------------------
Facilities currently offered in nip,pip,sip,nipl,pipl,sipl:
Get a sequence by knowing its entry name
Get a sequences' annotation by knowing its entry name
Get an entry name by knowing its accession number
Search the freetext index
Search the author index
Facilities currently offered in nipl,pipl,sipl:
Search whole library
Search only a list of entry names
Search all but a list of entry names
Outline of each type of operation
Looking for an entry by name: the programs will open the library description
file and read the names of its files and their file types. Then they will open
the entrynam.idx file, and find the sequence offset, annotation offset and
division number. Then open the division lookup file, find the file name for the
division required, open that file, seek to the required byte and get the data.
Looking for an entry by accession number: the programs will open the library
description file and read the names of its files and their file types. Then
they open the acnum.trg and acnum.hit files. The acnum.trg file is read to find
the accession number and a pointer to the acnum.hit file and the number of
hits. That file is read and the corresponding entry names displayed. At
present no further action is performed, although I expect to list out the
titles for the entries found.
Searching the whole of a library: the programs will open the library
description file and read the names of its files and their file types. Then
they open the division lookup file, read the names and numbers of the sequence
files, open all of them, then open the entryname file. Then the library is
processed sequentially by reading the entry names, their sequence offsets and
division numbers from the entry names file, and then the sequence from the
appropriate data file.
Searching the whole of a library using a list of entry names to include: the
programs will open the library description file and read the names of its files
and their file types. Then they open the division lookup file, read the names
and numbers of the sequence files, open all of them, then open the entryname
file. Then the library is processed by reading the list of entry names and
finding the names in the entry names file to get their sequence offsets and
division numbers, and then the sequence from the appropriate data file. It will
stop when it reaches the end of the list of entry names. The list of entry
names can be in any order.
Searching the whole of a library using a list of entry names to exclude: the
programs will open the library description file and read the names of its files
and their file types. Then they open the division lookup file, read the names
and numbers of the sequence files, open all of them, then open the entryname
file. Then the library is processed sequentially by reading the list of entry
names, reading the next entry in the entry names file to make sure it does not
match, then getting the sequence offsets and division numbers, and then the
sequence from the appropriate data file. If a the next name matches the name on
the list of entry names, it will be skipped, and the next name to exclude read.
If the list of excluded names is finished the rest of the library is searched
sequentially. The list of entry names must be in the same order as those in the
library (ie sorted alphabetically).
Searching a whole library using a PIR format file is performed by reading it
sequentially. If as list of entry names is used it must be in the same order as
the entries in the library file.
---------------------------------------------------------------------------
Section IV Installation guide
-----------------------------
EMBL CDROM
The data can be left on the cdrom or copied to hard disk. The files
staden.login and staden.profile source the file $STADTABL/libraries.config.csh
and $STADTABL/libraries.config.sh respectively. Refer to this file to see what
is required to install, add or move a sequence library that you want to be used
by the programs.
Other libraries (PIR, Genbank, EMBL updates)
Create the indexes then edit the files that tell the programs where the data is
stored. The files staden.login and staden.profile source the file
$STADTABL/libraries.config Refer to this file to see what is required to
install, add or move a sequence library that you want to be used by the
programs.
------------------------------------------------------------------------------
Section V New feature table handling facilities
-----------------------------------------------
As mentioned above EMBL and GenBank have recently introduced new feature tables
for annotating the sequences. They are a great improvement on the previous ones
and, among other things, now permit correct translation of spliced genes.
Various options within nip have been added or modified to take advantage of
these changes. The routine to translate DNA to protein and write the protein
to disk now gives correct results for spliced genes. The routine to translate
DNA to protein and display the two together now gives correct translations
except for the amino acids spanning intron/exon junctions. The routine to plot
maps from feature tables can use the new style. The open reading frame finding
routine writes out its results in the new style. The routine that finds open
reading frames and writes their translations to disk also writes a title in the
form of a new style feature table entry. The feature table format output from
the pattern searches in nip also uses the new style.
----------------------------------------------------------------------------
Section VI Indexing the sequence libraries
--------------------------------------------
We handle EMBL, SwissProt, and GenBank in their distributed format, plus
PIR and NRL3D in codata format. All programs and scripts are in directory
indexseqlibs.
Currently we produce entryname index, accession number index freetext index,
and brief index (brief index contains the entry name the primary accession
number the sequence length and an 80 character description).
To produce any of the indexes requires the creation of several intermediate
files and the indexing programs are written so that the intermediate files
are the same for all libraries. This means that only the programs that read
the distributed form of each library need to be unique to that library, and
all the other processing programs can be used for all libraries.
However even the though the indexes have the same format, programs (like nip)
that read the libraries need to treat each library separately because their
actual contents are written differently.
Making the entry name index
---------------------------
Common program entryname2
EMBL emblentryname1
SwissProt emblentryname1
GenBank genbentryname1
PIR pirentryname1
NRL3D pirentryname1
Making the accession number index
---------------------------------
Common programs access2 access3 access4
EMBL emblaccess1
SwissProt emblaccess1
GenBank genbaccess1
PIR piraccess1 piraccess2
NRL3D No accession numbers
Making the brief index
----------------------
Common program title2
EMBL embltitle1
SwissProt embltitle1
GenBank genbtitle1
PIR pirtitle1 pirtitle2 (pir3 has no accession numbers)
NRL3D pirtitle2
Scripts
-------
emblentryname.script
emblaccession.script
embltitle.script
swissentryname.script
swissaccession.script
swisstitle.script
genbentrynamescript
genbaccession.script
genbtitle.script
pirentryname.script
piraccession.script
pirtitle.script
nrl3dentryname.script
nrl3dtitle.script

453
Staden_install-alpha Normal file
View file

@ -0,0 +1,453 @@
#! /bin/csh -f
#
# staden_install - version 2.4
#
# This is a prototype installation program.
#
# 9 March 1992
# Modified for installation on Sun, Alliant, etc
# No longer install 2rs
#
# 20 November 1992
# Now includes convert, cop, frog, getMCH and scf
#
# 25 November 1992
# SGI supported
#
# 19 May 1993
# DEC Alpha, Solaris supported
#
# Written by sd@uk.ac.cam.mrc-lmb
#
# prelim
set prog = $0 ; set prog = $prog:t
# Machines supported: al sun dec sgi alpha solaris
#set MACHINE = `echo $prog | sed 's/.*-//'`
set MACHINE = alpha
# For local (MRC-LMB) setup only
#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
set LOCAL = NO
echo ""
echo -n "Staden Package installation procedure - "
switch (${MACHINE})
case "al":
echo "Alliant FX/2800 Concentrix version"
set MAKE = "make -sk"
breaksw
case "sun":
echo "SunOS version"
set MAKE = "make -sk"
breaksw
case "dec":
echo "DEC Ultrix (mips) version"
set MAKE = "gmake -sk"
breaksw
case "sgi":
echo "Silicon Graphics Iris version"
set MAKE = "gmake -sk"
breaksw
case "alpha":
echo "DEC Alpha OSF/1 version"
set MAKE = "gmake -sk"
breaksw
case "solaris":
echo "Solaris version"
set MAKE = "make -sk"
breaksw
default:
echo "Panic. Unknown version"
exit 1
endsw
echo ""
echo "* starting initialization...please wait."
echo ""
# Binary fork of source directory
if ($LOCAL == "YES") then
set DIR_BINARIES = ${MACHINE}-binaries
set DIR_PROGS = ${MACHINE}-bin
else
set DIR_BINARIES = .
set DIR_PROGS = bin
set MAKE = "$MAKE -f makefile-${MACHINE}"
endif
init:
# Set useful shell variables
set YES="YES";
set NO="NO"
# set/unset some .cshrc envs.
unset noclobber
set noglob
# set interrupt trap
onintr end_failure
# Make dir command
set MKDIR = "mkdir"
# Copy command
set CP = "cp -p"
# Install command
#set INSTALL = "install"
#set INSTALL = "mv"
set INSTALL = "cp"
# Set up default responses
set DEF_STADEN_ROOT = `pwd`
set DEF_REQ_NONX = "$YES"
set DEF_REQ_X = "$YES"
set DEF_REQ_TED = "$YES"
set DEF_REQ_MISC = "$YES"
# directories
set DIR_SRC = $DEF_STADEN_ROOT/src
set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
set DIR_MISC = $DIR_SRC/Misc
set DIR_STADEN = $DIR_SRC/staden
set DIR_TED = $DIR_SRC/ted
set DIR_ABI = $DIR_SRC/abi
set DIR_ALF = $DIR_SRC/alf
set DIR_BAP = $DIR_SRC/bap
set DIR_OSP = $DIR_SRC/bap/osp-bits
set DIR_CONVERT = $DIR_SRC/convert
set DIR_COP = $DIR_SRC/cop
set DIR_FROG = $DIR_SRC/frog
set DIR_GETMCH = $DIR_SRC/getMCH
set DIR_SCF = $DIR_SRC/scf
main:
preamble:
echo ""
echo ""
echo "* Please answer the following questions."
echo " Default answers to questions are given in square brackets."
echo " If you require help at any stage respond with a ? to the question."
echo ""
ask_staden_root:
set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
ask_require_nonx_progs:
echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
set ANS_REQ_NONX = $<
if ("$ANS_REQ_NONX" == "?") then
echo "* If you do not have X windows on your system you will require"
echo " these. However, you will require Tektronics terminal emulation."
echo " If you do not require all of the non-X programs, you should abort"
echo " and manually make the ones you require."
echo ""
goto ask_require_nonx_progs
else if ("$ANS_REQ_NONX" != "") then
if ("$ANS_REQ_NONX" =~ [yY]*) then
set ANS_REQ_NONX=$YES
else if ("$ANS_REQ_NONX" =~ [nN]*) then
set ANS_REQ_NONX=$NO
else
goto ask_require_nonx_progs
endif
else
set ANS_REQ_NONX=$DEF_REQ_NONX
endif
ask_require_x_progs:
echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
set ANS_REQ_X = $<
if ("$ANS_REQ_X" == "?") then
echo "* These are the programs that require X windows."
echo " If you do not require all of the X programs, you should abort"
echo " and manually make the ones you require."
echo ""
goto ask_require_x_progs
else if ("$ANS_REQ_X" != "") then
if ("$ANS_REQ_X" =~ [yY]*) then
set ANS_REQ_X=$YES
else if ("$ANS_REQ_X" =~ [nN]*) then
set ANS_REQ_X=$NO
else
goto ask_require_nonx_progs
endif
else
set ANS_REQ_X=$DEF_REQ_X
endif
ask_require_ted:
echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
set ANS_REQ_TED = $<
if ("$ANS_REQ_TED" == "?") then
echo "* This is the trace editor program. It allows you to look at"
echo " traces obtained from automated fluorescent sequencing machines."
echo ""
goto ask_require_ted
else if ("$ANS_REQ_TED" != "") then
if ("$ANS_REQ_TED" =~ [yY]*) then
set ANS_REQ_TED=$YES
else if ("$ANS_REQ_TED" =~ [nN]*) then
set ANS_REQ_TED=$NO
else
goto ask_require_ted
endif
else
set ANS_REQ_TED=$DEF_REQ_TED
endif
ask_require_misc:
echo -n "Compile other programs [$DEF_REQ_MISC]? "
set ANS_REQ_MISC = $<
if ("$ANS_REQ_MISC" == "?") then
echo "* Other programs include:"
echo " alfsplit"
echo " getABISampleName"
echo ""
goto ask_require_misc
else if ("$ANS_REQ_MISC" != "") then
if ("$ANS_REQ_MISC" =~ [yY]*) then
set ANS_REQ_MISC=$YES
else if ("$ANS_REQ_MISC" =~ [nN]*) then
set ANS_REQ_MISC=$NO
else
goto ask_require_misc
endif
else
set ANS_REQ_MISC=$DEF_REQ_MISC
endif
time_taken_warning:
echo ""
echo "The installation procedure is now ready to start."
echo ""
echo "**** Warning:"
echo " The installation will take considerable time to complete. If you"
echo " are installing the whole Staden Package from scratch it could"
echo " take as long as an hour for all exectuables to be compiled and"
echo " installed."
echo ""
ask_goahead:
echo -n "Proceed with the installation [YES]? "
set ANSWER=$<
if ("$ANSWER" == "?") then
echo "* Final confirmation to proceed with the installation. Answer"
echo " YES to proceed; otherwise, answer NO to abort the installation."
echo ""
goto ask_goahead
else if ("$ANSWER" != "") then
if ("$ANSWER" =~ [nN]*) then
goto chickens_exit
else if ("$ANSWER" !~ [yY]*) then
goto ask_goahead
endif
endif
installation_proper:
# make binaries directory if it doesn't exist
if (! -d $DIR_BIN) then
$MKDIR $DIR_BIN
endif
if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
echo ""
echo "+ Compiling miscellaneous library"
pushd $DIR_MISC > /dev/null
cd $DIR_BINARIES
$MAKE all
popd > /dev/null
endif
if ("$ANS_REQ_NONX" == "$YES") then
echo ""
echo "+ Installing non X programs"
pushd $DIR_STADEN > /dev/null
cd $DIR_BINARIES
$MAKE nprogs lprogs
$INSTALL mep $DIR_BIN
$INSTALL nip $DIR_BIN
$INSTALL pip $DIR_BIN
$INSTALL sap $DIR_BIN
$INSTALL sapf $DIR_BIN
$INSTALL sip $DIR_BIN
$INSTALL splitp1 $DIR_BIN
$INSTALL splitp2 $DIR_BIN
$INSTALL splitp3 $DIR_BIN
$INSTALL sethelp $DIR_BIN
$INSTALL gip $DIR_BIN
$INSTALL nipl $DIR_BIN
$INSTALL pipl $DIR_BIN
$INSTALL sipl $DIR_BIN
$INSTALL dap $DIR_BIN
$INSTALL nipf $DIR_BIN
$INSTALL vep $DIR_BIN
$INSTALL rep $DIR_BIN
$INSTALL lip $DIR_BIN
#$INSTALL convert_project $DIR_BIN
popd > /dev/null
pushd $DIR_OSP > /dev/null
cd $DIR_BINARIES
$MAKE
popd > /dev/null
pushd $DIR_BAP > /dev/null
cd $DIR_BINARIES
$MAKE bap
$INSTALL bap $DIR_BIN
popd > /dev/null
endif
if ("$ANS_REQ_TED" == "$YES") then
echo ""
echo "+ Installing Trace editor"
pushd $DIR_TED > /dev/null
cd $DIR_BINARIES
$MAKE ted
$INSTALL ted $DIR_BIN
popd > /dev/null
endif
if ("$ANS_REQ_X" == "$YES") then
echo ""
echo "+ Installing X programs"
pushd $DIR_STADEN > /dev/null
cd $DIR_BINARIES
$MAKE xprogs
$INSTALL xmep $DIR_BIN
$INSTALL xnip $DIR_BIN
$INSTALL xpip $DIR_BIN
$INSTALL xsap $DIR_BIN
$INSTALL xsip $DIR_BIN
$INSTALL xdap $DIR_BIN
popd > /dev/null
pushd $DIR_OSP > /dev/null
cd $DIR_BINARIES
$MAKE
popd > /dev/null
pushd $DIR_BAP > /dev/null
cd $DIR_BINARIES
$MAKE xbap
$INSTALL xbap $DIR_BIN
popd > /dev/null
endif
if ("$ANS_REQ_MISC" == "$YES") then
echo ""
echo "+ Installing miscellaneous programs"
pushd $DIR_ABI > /dev/null
cd $DIR_BINARIES
$MAKE all
$INSTALL getABISampleName $DIR_BIN
popd > /dev/null
pushd $DIR_ALF > /dev/null
cd $DIR_BINARIES
$MAKE alfsplit
$INSTALL alfsplit $DIR_BIN
popd > /dev/null
pushd $DIR_CONVERT > /dev/null
cd $DIR_BINARIES
$MAKE convert
$INSTALL convert $DIR_BIN
popd > /dev/null
pushd $DIR_COP > /dev/null
cd $DIR_BINARIES
$MAKE all
$INSTALL cop $DIR_BIN
$INSTALL cop-bap $DIR_BIN
popd > /dev/null
pushd $DIR_FROG > /dev/null
cd $DIR_BINARIES
$MAKE frog
$INSTALL frog $DIR_BIN
popd > /dev/null
pushd $DIR_GETMCH > /dev/null
cd $DIR_BINARIES
$MAKE trace2seq
$INSTALL trace2seq $DIR_BIN
popd > /dev/null
pushd $DIR_SCF > /dev/null
cd $DIR_BINARIES
$MAKE makeSCF
$INSTALL makeSCF $DIR_BIN
popd > /dev/null
endif
installation_done:
echo ""
echo "+ Installation completed"
echo ""
echo " Some further initialisation is required in order to use the"
echo " package. csh users should insert the following in their .login"
echo " files:"
echo " "
echo " setenv STADENROOT $ANS_STADEN_ROOT"
echo ' source $STADENROOT/staden.login'
echo " "
echo " Users of the Bourne shell, sh, should insert the following in"
echo " their .profile:"
echo " "
echo " STADENROOT=$ANS_STADEN_ROOT"
echo " export STADENROOT"
echo ' . $STADENROOT/staden.profile'
echo " "
echo " These initialisations will alter the shell's search path so that"
echo " it can find the programs in the STADEN Package"
echo " "
normal_exit:
exit 0
chickens_exit:
echo ""
echo "+ Installation cancelled"
echo ""
exit 0
end_failure:
unset noglob
echo ""
echo "Aborted STADEN Package installation on `date`"
echo ""
exit 1

453
Staden_install-dec Normal file
View file

@ -0,0 +1,453 @@
#! /bin/csh -f
#
# staden_install - version 2.4
#
# This is a prototype installation program.
#
# 9 March 1992
# Modified for installation on Sun, Alliant, etc
# No longer install 2rs
#
# 20 November 1992
# Now includes convert, cop, frog, getMCH and scf
#
# 25 November 1992
# SGI supported
#
# 19 May 1993
# DEC Alpha, Solaris supported
#
# Written by sd@uk.ac.cam.mrc-lmb
#
# prelim
set prog = $0 ; set prog = $prog:t
# Machines supported: al sun dec sgi alpha solaris
#set MACHINE = `echo $prog | sed 's/.*-//'`
set MACHINE = dec
# For local (MRC-LMB) setup only
#set LOCAL = `echo $prog | awk '/local/{print "YES";exit;}{print "NO";}'`
set LOCAL = NO
echo ""
echo -n "Staden Package installation procedure - "
switch (${MACHINE})
case "al":
echo "Alliant FX/2800 Concentrix version"
set MAKE = "make -sk"
breaksw
case "sun":
echo "SunOS version"
set MAKE = "make -sk"
breaksw
case "dec":
echo "DEC Ultrix (mips) version"
set MAKE = "gmake -sk"
breaksw
case "sgi":
echo "Silicon Graphics Iris version"
set MAKE = "gmake -sk"
breaksw
case "alpha":
echo "DEC Alpha OSF/1 version"
set MAKE = "gmake -sk"
breaksw
case "solaris":
echo "Solaris version"
set MAKE = "make -sk"
breaksw
default:
echo "Panic. Unknown version"
exit 1
endsw
echo ""
echo "* starting initialization...please wait."
echo ""
# Binary fork of source directory
if ($LOCAL == "YES") then
set DIR_BINARIES = ${MACHINE}-binaries
set DIR_PROGS = ${MACHINE}-bin
else
set DIR_BINARIES = .
set DIR_PROGS = bin
set MAKE = "$MAKE -f makefile-${MACHINE}"
endif
init:
# Set useful shell variables
set YES="YES";
set NO="NO"
# set/unset some .cshrc envs.
unset noclobber
set noglob
# set interrupt trap
onintr end_failure
# Make dir command
set MKDIR = "mkdir"
# Copy command
set CP = "cp -p"
# Install command
#set INSTALL = "install"
#set INSTALL = "mv"
set INSTALL = "cp"
# Set up default responses
set DEF_STADEN_ROOT = `pwd`
set DEF_REQ_NONX = "$YES"
set DEF_REQ_X = "$YES"
set DEF_REQ_TED = "$YES"
set DEF_REQ_MISC = "$YES"
# directories
set DIR_SRC = $DEF_STADEN_ROOT/src
set DIR_BIN = $DEF_STADEN_ROOT/$DIR_PROGS
set DIR_MISC = $DIR_SRC/Misc
set DIR_STADEN = $DIR_SRC/staden
set DIR_TED = $DIR_SRC/ted
set DIR_ABI = $DIR_SRC/abi
set DIR_ALF = $DIR_SRC/alf
set DIR_BAP = $DIR_SRC/bap
set DIR_OSP = $DIR_SRC/bap/osp-bits
set DIR_CONVERT = $DIR_SRC/convert
set DIR_COP = $DIR_SRC/cop
set DIR_FROG = $DIR_SRC/frog
set DIR_GETMCH = $DIR_SRC/getMCH
set DIR_SCF = $DIR_SRC/scf
main:
preamble:
echo ""
echo ""
echo "* Please answer the following questions."
echo " Default answers to questions are given in square brackets."
echo " If you require help at any stage respond with a ? to the question."
echo ""
ask_staden_root:
set ANS_STADEN_ROOT = $DEF_STADEN_ROOT
ask_require_nonx_progs:
echo -n "Compile all the non-X programs in the Staden Package [$DEF_REQ_NONX]? "
set ANS_REQ_NONX = $<
if ("$ANS_REQ_NONX" == "?") then
echo "* If you do not have X windows on your system you will require"
echo " these. However, you will require Tektronics terminal emulation."
echo " If you do not require all of the non-X programs, you should abort"
echo " and manually make the ones you require."
echo ""
goto ask_require_nonx_progs
else if ("$ANS_REQ_NONX" != "") then
if ("$ANS_REQ_NONX" =~ [yY]*) then
set ANS_REQ_NONX=$YES
else if ("$ANS_REQ_NONX" =~ [nN]*) then
set ANS_REQ_NONX=$NO
else
goto ask_require_nonx_progs
endif
else
set ANS_REQ_NONX=$DEF_REQ_NONX
endif
ask_require_x_progs:
echo -n "Compile all the X programs in the Staden Package [$DEF_REQ_X]? "
set ANS_REQ_X = $<
if ("$ANS_REQ_X" == "?") then
echo "* These are the programs that require X windows."
echo " If you do not require all of the X programs, you should abort"
echo " and manually make the ones you require."
echo ""
goto ask_require_x_progs
else if ("$ANS_REQ_X" != "") then
if ("$ANS_REQ_X" =~ [yY]*) then
set ANS_REQ_X=$YES
else if ("$ANS_REQ_X" =~ [nN]*) then
set ANS_REQ_X=$NO
else
goto ask_require_nonx_progs
endif
else
set ANS_REQ_X=$DEF_REQ_X
endif
ask_require_ted:
echo -n "Compile the trace editing program ted [$DEF_REQ_TED]? "
set ANS_REQ_TED = $<
if ("$ANS_REQ_TED" == "?") then
echo "* This is the trace editor program. It allows you to look at"
echo " traces obtained from automated fluorescent sequencing machines."
echo ""
goto ask_require_ted
else if ("$ANS_REQ_TED" != "") then
if ("$ANS_REQ_TED" =~ [yY]*) then
set ANS_REQ_TED=$YES
else if ("$ANS_REQ_TED" =~ [nN]*) then
set ANS_REQ_TED=$NO
else
goto ask_require_ted
endif
else
set ANS_REQ_TED=$DEF_REQ_TED
endif
ask_require_misc:
echo -n "Compile other programs [$DEF_REQ_MISC]? "
set ANS_REQ_MISC = $<
if ("$ANS_REQ_MISC" == "?") then
echo "* Other programs include:"
echo " alfsplit"
echo " getABISampleName"
echo ""
goto ask_require_misc
else if ("$ANS_REQ_MISC" != "") then
if ("$ANS_REQ_MISC" =~ [yY]*) then
set ANS_REQ_MISC=$YES
else if ("$ANS_REQ_MISC" =~ [nN]*) then
set ANS_REQ_MISC=$NO
else
goto ask_require_misc
endif
else
set ANS_REQ_MISC=$DEF_REQ_MISC
endif
time_taken_warning:
echo ""
echo "The installation procedure is now ready to start."
echo ""
echo "**** Warning:"
echo " The installation will take considerable time to complete. If you"
echo " are installing the whole Staden Package from scratch it could"
echo " take as long as an hour for all exectuables to be compiled and"
echo " installed."
echo ""
ask_goahead:
echo -n "Proceed with the installation [YES]? "
set ANSWER=$<
if ("$ANSWER" == "?") then
echo "* Final confirmation to proceed with the installation. Answer"
echo " YES to proceed; otherwise, answer NO to abort the installation."
echo ""
goto ask_goahead
else if ("$ANSWER" != "") then
if ("$ANSWER" =~ [nN]*) then
goto chickens_exit
else if ("$ANSWER" !~ [yY]*) then
goto ask_goahead
endif
endif
installation_proper:
# make binaries directory if it doesn't exist
if (! -d $DIR_BIN) then
$MKDIR $DIR_BIN
endif
if ("$ANS_REQ_MISC" == "$YES" || "$ANS_REQ_X" == "$YES" || "$ANS_REQ_NONX" == "$YES" ) then
echo ""
echo "+ Compiling miscellaneous library"
pushd $DIR_MISC > /dev/null
cd $DIR_BINARIES
$MAKE all
popd > /dev/null
endif
if ("$ANS_REQ_NONX" == "$YES") then
echo ""
echo "+ Installing non X programs"
pushd $DIR_STADEN > /dev/null
cd $DIR_BINARIES
$MAKE nprogs lprogs
$INSTALL mep $DIR_BIN
$INSTALL nip $DIR_BIN
$INSTALL pip $DIR_BIN
$INSTALL sap $DIR_BIN
$INSTALL sapf $DIR_BIN
$INSTALL sip $DIR_BIN
$INSTALL splitp1 $DIR_BIN
$INSTALL splitp2 $DIR_BIN
$INSTALL splitp3 $DIR_BIN
$INSTALL sethelp $DIR_BIN
$INSTALL gip $DIR_BIN
$INSTALL nipl $DIR_BIN
$INSTALL pipl $DIR_BIN
$INSTALL sipl $DIR_BIN
$INSTALL dap $DIR_BIN
$INSTALL nipf $DIR_BIN
$INSTALL vep $DIR_BIN
$INSTALL rep $DIR_BIN
$INSTALL lip $DIR_BIN
#$INSTALL convert_project $DIR_BIN
popd > /dev/null
pushd $DIR_OSP > /dev/null
cd $DIR_BINARIES
$MAKE
popd > /dev/null
pushd $DIR_BAP > /dev/null
cd $DIR_BINARIES
$MAKE bap
$INSTALL bap $DIR_BIN
popd > /dev/null
endif
if ("$ANS_REQ_TED" == "$YES") then
echo ""
echo "+ Installing Trace editor"
pushd $DIR_TED > /dev/null
cd $DIR_BINARIES
$MAKE ted
$INSTALL ted $DIR_BIN
popd > /dev/null
endif
if ("$ANS_REQ_X" == "$YES") then
echo ""
echo "+ Installing X programs"
pushd $DIR_STADEN > /dev/null
cd $DIR_BINARIES
$MAKE xprogs
$INSTALL xmep $DIR_BIN
$INSTALL xnip $DIR_BIN
$INSTALL xpip $DIR_BIN
$INSTALL xsap $DIR_BIN
$INSTALL xsip $DIR_BIN
$INSTALL xdap $DIR_BIN
popd > /dev/null
pushd $DIR_OSP > /dev/null
cd $DIR_BINARIES
$MAKE
popd > /dev/null
pushd $DIR_BAP > /dev/null
cd $DIR_BINARIES
$MAKE xbap
$INSTALL xbap $DIR_BIN
popd > /dev/null
endif
if ("$ANS_REQ_MISC" == "$YES") then
echo ""
echo "+ Installing miscellaneous programs"
pushd $DIR_ABI > /dev/null
cd $DIR_BINARIES
$MAKE all
$INSTALL getABISampleName $DIR_BIN
popd > /dev/null
pushd $DIR_ALF > /dev/null
cd $DIR_BINARIES
$MAKE alfsplit
$INSTALL alfsplit $DIR_BIN
popd > /dev/null
pushd $DIR_CONVERT > /dev/null
cd $DIR_BINARIES
$MAKE convert
$INSTALL convert $DIR_BIN
popd > /dev/null
pushd $DIR_COP > /dev/null
cd $DIR_BINARIES
$MAKE all
$INSTALL cop $DIR_BIN
$INSTALL cop-bap $DIR_BIN
popd > /dev/null
pushd $DIR_FROG > /dev/null
cd $DIR_BINARIES
$MAKE frog
$INSTALL frog $DIR_BIN
popd > /dev/null
pushd $DIR_GETMCH > /dev/null
cd $DIR_BINARIES
$MAKE trace2seq
$INSTALL trace2seq $DIR_BIN
popd > /dev/null
pushd $DIR_SCF > /dev/null
cd $DIR_BINARIES
$MAKE makeSCF
$INSTALL makeSCF $DIR_BIN
popd > /dev/null
endif
installation_done:
echo ""
echo "+ Installation completed"
echo ""
echo " Some further initialisation is required in order to use the"
echo " package. csh users should insert the following in their .login"
echo " files:"
echo " "
echo " setenv STADENROOT $ANS_STADEN_ROOT"
echo ' source $STADENROOT/staden.login'
echo " "
echo " Users of the Bourne shell, sh, should insert the following in"
echo " their .profile:"
echo " "
echo " STADENROOT=$ANS_STADEN_ROOT"
echo " export STADENROOT"
echo ' . $STADENROOT/staden.profile'
echo " "
echo " These initialisations will alter the shell's search path so that"
echo " it can find the programs in the STADEN Package"
echo " "
normal_exit:
exit 0
chickens_exit:
echo ""
echo "+ Installation cancelled"
echo ""
exit 0
end_failure:
unset noglob
echo ""
echo "Aborted STADEN Package installation on `date`"
echo ""
exit 1

453
Staden_install-sgi Normal file
View file

@ -0,0 +1,453 @@
#! /bin/csh -f
#
# staden_install - version 2.4
#
# This is a prototype installation program.
#
# 9 March 1992
# Modified for installation on Sun, Alliant, etc
# No longer install 2rs
#
# 20 November 1992
# Now includes convert, cop, frog, getMCH and scf
#
# 25 November 1992
# SGI supported
#
# 19 May 1993
# DEC Alpha, Solaris supported
#