[InterMine Dev] Building Intermine for GBrowse

Julie Sullivan julie at flymine.org
Tue Nov 27 16:11:59 GMT 2012



On 26/11/12 08:05, Allan Kamau wrote:
> 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?

I can't imagine why it would? I'll take a look and see if I can figure out 
what's going on.

>
> 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/>
> ".

thanks! I'll update our script.

>
> Allan.
>
>
>
>
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