[InterMine Dev] "ant load-gbrowse-data-mysql" command "No such file or directory ..."

Allan Kamau kamauallan at gmail.com
Mon Nov 19 12:42:42 GMT 2012

While following the instructions on Intermine-GBrowse setup "
http://intermine.org/wiki/GBrowseConfiguration" we
experienced an error (shown at the end of this email) while loading data
into mysql using "ant load-gbrowse-data-mysql" command.
We managed to follow the previous steps outlined in the above document
successfully and the data were generated successfully and the files exist
and can be listed using
"ls /home/me/intermine/abc/gbrowse/build/gbrowse/data/*.{fa,gff}".

It is likely these data file are not been accessed by the user loading data
to mysql. To simply this loading of data, I copied the entire directory of
"/home/me/intermine" into "/tmp" directory and then executed the command
"chmod ugo+rwx /tmp/intermine". But some how an error similar to the one
below is been presented. Is there a way I could manually simulate the
loading of these data to mysql. Or since "bp_bulk_load_gff.pl" perl script
is been used in loading of the data (I think), kindly provide me with an
example command line usage of this script as "load-gbrowse-data-mysql" ant
task would execute it.

[exec] Can't open
/home/me/intermine/abc/gbrowse/build/gbrowse/data/*.{fa,gff}: No such file
or directory at /usr/local/bin/bp_bulk_load_gff.pl line 436.

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