[BioC] specifications for exonmap database config file?

Heidi Dvinge heidi at ebi.ac.uk
Mon Dec 8 23:57:32 CET 2008

Hi Joseph

> 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.

First of all, you'll want to update your exonmap package! The current
version is something like 2.0.01, and it's undergone fairly extensive
changes. One of those changes is how to connect to the database. It used
to be via an "human.mycnf" file in earlier versions of exonmap, but this
has now been replaced by "databases.txt". An example is given in
INSTALL.pdf at

> 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'
Close, but I think that you'll have to specify the "type", i.e. "core" or
"otherfeatures". I don't have access to my R-related folders at the
moment, but I think I have something along the lines of:

name    species db.name type    host    port    username        password
"human" "homo_sapiens"  "homo_sapiens_core_50_36l"      "core" 
"my-mysql-location" "4094"  "heidi" "my-password"

> ... 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
What does traceback() say? What's your sessionInfo?
You might also have to set Sys.setenv(R_XMAP_CONF_DIR="path/.exonmap")
depending on the location of your databases.txt file if this isn't already
done, although this error message seems to relate to something else.

> 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)
> 	[[alternative HTML version deleted]]
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