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EMBOSS FAQ (Frequently Asked Questions)
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Q) Problems finding PHYLIP acd files ?
A) The 1.0 release of EMBOSS should be able to find the acd files
in the install directory or in the original source directory.
If you have copied the phylip binaries to another location and
removed these files you can still point to the new ACD directory.
If you have installed PHYLIP to the same top directory as EMBOSS
i.e. by default this is usually /usr/local/ (via make install)
then if you set the following in your .embossrc file then your
PHYLIP acd files will be found in
/usr/local/share/EMBOSS/acd/
if you have not installed PHYLIP then you will can set
emboss_acdroot to the directory containing the acd files or
copy them to the emboss/acd directory.
To tell EMBOSS where to find the files, specify the full path
of the ACD directory in your ~/.embossrc file, or in the
emboss.default file.
env emboss_acdroot /usr/local/share/EMBOSS/acd/
Q) What benefits do i gain from using the associated versions of
software.
A) a) You can read any sequence type that emboss can handle.
b) the associated software will use the emboss acd files so the
naming of output/input files is taken care of and will check all
values before the program is run. Command line arguments are used
instead interactive menu based ones.
Q) I have Emboss installed on our development server and I'm preparing a
dispatch which will send it out to about 20 remote sites.
I ran the configure with the --prefix option to install to a private
directory. I also collected all the data files (rebase, transfac etc.) to
another directory and extracted the information from them with the relevant
programs.
My intention was to simply transfer the Emboss install directory and the
Data directory to all sites, using symlinks where necessary so that the
directory paths corresponded.
However, when testing this I have found a couple of problems;
1) Although the Emboss programs work, I can't see any of the extracted
data.
For instance remap gives the error;
EMBOSS An error in remap.c at line 167:
Cannot locate enzyme file. Run REBASEEXTRACT
This is despite the fact that I have both the Emboss install and the Data
directories in the same place as on the development machine (which works).
2) The other major problem is that I can no longer see my databases defined
in emboss.default. Again, the file exists, and is in the same place as on
the development machine, but the box it is transferred to gives an empty
list from showdb.
Does anyone know where Emboss stores the information about the location of
these files? It can't have installed anything outside the original
installation directory (wasn't installed as root), so I'm guessing that the
problem stems from the program resolving symlinks at some point.
A) It is inside the binaries ...
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