[InterMine Dev] Building Intermine for GBrowse

Allan Kamau kamauallan at gmail.com
Mon Nov 26 08:05:25 GMT 2012


We have been trying to get GBrowse to work with Intermine so far we have
made some progress and made a few observations.
We used the IntermineGbrowse docs and built a mysql database to hold the
data for GBrowse (since we prefer PostgreSQL we shall soon be moving away
from mySQL)

On running "ant load-gbrowse-data-mysql" after setting my umask to 0002, I
observed the following:
The error "[exec] Can't
open /usr/local/src/intermine1.1/mymine2_ak/gbrowse/build/gbrowse/data/*.{fa,gff}:
No such file or directory at /usr/local/bin/bp_bulk_load_gff.pl line 436."

Digging a little deeper it into the ../../imbuild/gbrowse.xml I see the
command being execute is as follows "bp_bulk_load_gff.pl --local
--maxfeature 1000000000 --create --database
dbi:mysql:gbrowse\;host=localhost --user me --password meagain
/usr/local/src/intermine1.1/mymine2_ak/gbrowse/build/gbrowse/data/*.{fa,gff}"
When I execute this command directly from the command line, the data are
loaded into the database and no errors are thrown. It looks like ant is
trying to access these files (the *.fa and *.gff) as some other user?



On running "ant install-gbrowse-conf", I observed the following:

The ant command completes without throwing any errors. However on accessing
the mine's GBrowse web resource directly "
http://myserver/cgi-bin/gbrowse/gbrowse/mymine2_ak/<http://pipeline01.cbrc.kaust.edu.sa/cgi-bin/gbrowse/gbrowse/test_cbrcredseamine2_ak/>"
the error 'Can't call method "segment" on an undefined value.' gets
displayed. After some googling I learn that my
"/etc/gbrowse/mymine2_ak.conf" may have been wrongly configured. When I
changed the current DB connection settings
in "/etc/gbrowse/mymine2_ak.conf" from

db_args     = -adaptor dbi::mysql
              -dsn dbi:mysql:gbrowse;host=localhost
host        = localhost
user        = me
pass        = meagain



to


db_args     = -adaptor dbi::mysql
              -dsn dbi:mysql:gbrowse;host=localhost
                -user me
                -pass meagain

The connection is established and I can access my mines data via GBrowse
when using the direct URL to GBrowse "
http://myserver/cgi-bin/gbrowse/gbrowse/mymine2_ak/<http://pipeline01.cbrc.kaust.edu.sa/cgi-bin/gbrowse/gbrowse/test_cbrcredseamine2_ak/>
".


Allan.
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