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EMBOSS FAQ (Frequently Asked Questions)
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EMBOSS 'knows' the location of the files because it is picked up during the
configure, when you build your copy, and included in the binaries.
You can see it during compilation, especially of ajnam.c (where it is used):
-DAJAX_FIXED_ROOT=\"/full/source/path\" -DPREFIX=\"/install/prefix/path\"
To copy binaries, you need to define environment variable(s) to
override the compile-time definitions, unless you can make the path
(e.g. /usr/local) the same for the installations at each site.
emboss.default can set environment variables too, but you need to tell
EMBOSS where to find that file.
setenv EMBOSS_ROOT /dir/for/default/file
and then, in the emboss.default file you can set:
SET EMBOSS_ACDROOT /install/dir/share/EMBOSS/acd
or (this overrides it) you can use another environment variable:
SET EMBOSS_ACDROOT /install/dir/share/EMBOSS/acd
(Peter Rice 22 Nov 2000)
Q) I have downloaded the Emboss source and installed it for use at XYZ
University without any difficulty. The administration guide has advice
on configuring the software using emboss.default, and has examples for
allowing access to SRS indices. That appears to be done via the program
getz, which is not part of the Emboss package.
A) If you have SRS installed (so you have local SRS index files) you will
have a local copy of the getz program, which is part of SRS.
If you do not have SRS, you can build your own index files using dbiflat,
dbigcg (if you have GCG), dbiblast (if you have blast) and dbifasta. This is
the usual solution for sites that have no other database indexing in use.
You can also use SRS servers remotely, to get single entries, using their
URLs. No extra software is needed (EMBOSS just uses the HTTP protocol).
Of course, if you really need to build your own SRS indices you
could install it. SRS is a commercial product, but academic licences are
available. But as I now work for the developers of SRS, and this is
the EMBOSS bug mailing list, I shall say no more :-)
(Peter Rice 9 Jan 2001)
Q) I am not getting full static files even when I configure with
--disable-shared
A) This most often happens when using GNU LD. If both shared and
static versions of a library exist then GNU LD will take the
shared library as preferred. The root of this problem is libtool.
You can, however, force complete static images by adding a
definition to your "make" line:
make "LDFLAGS=-Wl,-static"
(Alan Bleasby 14 Feb 2001)
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