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bionet.software.staden Frequently Asked Questions (FAQ)
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(last revised - 16-JAN-95)
Preface. The Explanation Of The "FAQ"
A FAQ is a way to explain the topic of discussion (bionet.software.staden)
and help avoid repetitive posts about a specific sub-topic. Before you post
a question about the Staden package, you should read this document to see
if your question has already been answered.
If you have corrections, additions, suggestions, or comments, send them
to Tim Littlejohn at tim at bch.umontreal.ca
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Table Of Contents
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1. What is the charter of this newsgroup?
2. Where can I find archives of previous postings to this newsgroup?
3. What is the Staden package?
4. Where do I get the Staden package from?
5. What tape formats are available?
6. Is it available by anonymous ftp?
7. How should I report problems I see with the package?
8. I'm running out of disk space. What can I do to make more room?
9. How do I contact the developers?
10. Where Can I find other information about the Staden package?
11. Credits
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bionet.software.staden : Frequently Asked Questions
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This Edition Overrides All Previous Editions
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1. What is the charter of this newsgroup?
The newsgroup serves as a communication forum for users of the Staden
Package for molecular sequence analysis. The package covers most sequence
analysis applications including DNA assembly, DNA analysis, protein sequence
analysis, sequence comparisons, library handling and searching. The assembly
program can handle input from ABI 373A, LI-COR, Pharmacia A.L.F. and Amersham
International BaseScanner instruments, plus digitizers. The package runs on
a large number of hardware/operating system platforms and is available for
a nominal fee.
The newsgroup has the following specific objectives:
1. to serve as a communication medium for announcing modifications
to the package;
2. to be a "self help" group, where users with problems can gain from
the experience of the rest of the user-community (and thereby reduce
the pressures of the developers to provide support). The newsgroup will
provide a forum for answers to frequently asked questions concerning the
package;
3. to exchange ideas and practical advice about getting the most from all
components of the package, from sequence assembly through to analysis;
4. to promote the continued growth and enhancement of the package.
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2. Where can I find archives of previous postings to this newsgroup?
Previous postings can be found at the following URLs:
gopher://megasun.bch.umontreal.ca:70/11/CMB/Stadengopher://gopher.bio.net:70/11/STADEN
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3. What is the Staden package?
The Staden Package is a software package to perform most aspects of
sequence analysis. Including DNA assembly; DNA analysis; protein sequence
analysis; sequence comparisons; library handling and searching.
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4. Where do I get the Staden package from?
Send you name and address together with a request for licence agreement
forms to:
Rodger Staden,
MRC Laboratory of Molecular Biology,
Hills Road,
Cambridge,
CB2 2QH,
United Kingdom.
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5. What tape formats are available?
QIC-150 and Exabyte (2.5Gb)
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6. Is it available by anonymous ftp?
No.
The developers say:
'In actual fact, the questions usually run along the lines of "What tape
formats are available?" [answer as above], followed by "Ok, I'll choose DAT
from that list" [pardon!? we didn't say DAT], followed by "Oh! In that case
how about ftp".'
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7. How should I report problems I see with the package?
Send a message to:
staden-package at mrc-lmb.cam.ac.uk
Stating:
1) Where did the problem occur?
2) Is the problem reproducable? If so what inputs were used? Is there
any test data available for us to use in debugging?
3) Was a core file produced? If so what do the following produce:
echo where | dbx `which xgap` core
echo where | gdb `which xgap` core
Obviously the above are for an example of a crash with xgap. I list both
dbx and gdb as one or the other may not be available.
For many core files will not be produced when a segmentation fault or bus
error occurs. To enable core files try "unlimit core" (csh and tcsh users)
or "ulimit -c unlimited" (bash and maybe sh).
4) Which version of the software do you have?
5) Which machine architecture are you running under and which operating
system are you using? (Eg a Sparcstation running SunOS 4.1.3)
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8. I'm running out of disk space. What can I do to make more room?
One trick is the "strip" the binary files. This can be done by using
the strip commant under unix. This will save you around 25 Meg of disk
space under the SunOS distribution, for example.
NOTE: "stripping" binaries removes their debugging information. If you
strip your files, you will not be able to perform a full debugging report
for the Staden developers.
The procedure for stripping binaries is as follows:
cd $STADENROOT
(cd bin; strip *)
(cd seqlibs-bin; strip *)
(cd squirrel/bin; strip *)
If you're still running short of disk space then maybe certain areas of the
package could be removed. The developers advise against this generally and
feel that obtaining more disk space is preferable. If you're removing files
from the disk please make sure you have a good copy of everything on tape.
Tapes don't last for ever and this naturally applies to the original tape
sent to you.
Large file collections that maybe considered 'unnecessary' (this obviously
depends on your desired uses for the package) are:
testpackage 13 Meg; Serves as an example (especially with gap) of
how to use the programs, but is not required
by any programs.
tables/prosite 10 Meg; The prosite library.
src 8 Meg; The source code. Nothing in this directory
is required for simply running the programs.
doc/manual.* 6 Meg; A PostScript and RTF form of the manual. A
very useful item, but not needed if you've
already printed it or if you use the version
on the Macintosh disk.
bin/??? Many of the binaries are large. The total
size of the bin directories is typically around
about 50 megs (77 for DEC Alpha systems). We
advise against removing binaries though. Many
programs are used in scripts (eg pregap) so it
is not immediately obvious which are required.
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9. How do I contact the developers?
For problems/bug reports:
staden-package at mrc-lmb.cam.ac.uk
For feature changes/additions:
staden-package-wishlist at mrc-lmb.cam.ac.uk
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10. Where Can I find other information about the Staden package?
Further information about the package can be obtained from the following
URLs:
gopher://megasun.bch.umontreal.ca:70/11/CMB/Staden
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11. Credits
This FAQ was written by Tim Littlejohn (tim at bch.umontreal.ca). Contributions
kindly made by James Bonfield (jkb at mrc-lmb.cam.ac.uk).
--
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Tim Littlejohn
E-mail: tim at bch.umontreal.ca
Snail Mail: Departement de biochimie Phone: (514) 343-6111, x5149
Universite de Montreal Fax: (514) 343-2210
C.P. 6128, Centre-ville
Montreal (Quebec), H3C 3J7
CANADA
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