I can't find consistent or complete documentation on how to set up a config
file for communicating with a local ensembl database using exonmap.  The R
help page for xmapConnect says that the function uses a file called
"databases.txt", and points me to the package installation instructions to
find out how to set it up.  But the package (exonmap_1.0.07.tar.gz)
installation instructions only talk about config files called, for example,
"human.mycnf", and refer to example configuration files available at
http://xmap.picr.man.ac.uk, which I can't find.  In the INSTALL.txt that
came with xmap_homo_sapiens_core_50_36l.tgz<http://xmap.picr.man.ac.uk/downloads/xmap_homo_sapiens_core_50_36l.tgz>there
is no description of this file format either, though there was a
thread here suggesting that.

I have a working installation of ensembl's and xmap's human_core_50_36l, and
I've made a directory called ".exonmap" under my home directory, and in that
directory placed a file called "databases.txt" that looks like this:
'name'    'species'    'db.name'    'type'    'host'    'port'
'username'     'password'
'Human'    'human'    'homo_sapiens_core_50_36l'    '?'    '
myserver.correctlocation.edu'    '3306'    'correctuser'    'correctpasswd'

... with the correct host/user/pwd info ... and it's tab-separated, and
those single quotes are really in there (no quotes didn't any differently)
...
I tried a file called human.mycnf, but that didn't seem to make xmapConnect
happy.  I don't know what's really supposed to go in name, species, or type
... I assume name just dictates the argument you later give to xmapConnect,
but are species and type critical?
Right now, xmapConnect tells me this:

> xmapConnect("Human")
Error in if (v != "<ASK>") { : argument is of length zero


Did I entirely miss some set of documentation?


-- 
Joseph Fass
Bioinformatics Programmer
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com (professional)
970.227.5928 (c)  ||  530.752.2698 (w)

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