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Joseph Fass
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70
@joseph-fass-2739
Last seen 4.8 years ago
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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