[Bioperl-l] bioperl-db install

[Keith Allen]

Thanks for the pointers Elia.  I'm running mysql  Ver 11.15 Distrib 3.23.47,
for pc-linux-gnu (i686), so I went into the biosql cvs repository and got
what should be the latest code (biosqldb-mysql.sql version 1.6).  After
creating a new database, I ran the 1.6 code with the command line:

mysql -u <user> -p <database> < biosqldb_1.6

and I got the error:

ERROR 1072 at line 141: Key column 'dbxref_id' doesn't exist in table

which bothers me a little, because if you look at the code, it does too
exist ;-)   Line 141 is creating an index on TABLE bioentry_direct_links,
so in the spirit of academic curiosity, I commented it out, but now I get
the error:

ERROR 1061 at line 140: Duplicate key name 'bdl1'

which makes even less sense.  Line 140 is creating another index on
a different column of the bioentry_direct_links table.  I'm stumped,
but then I'm no mysql expert, as all present will attest.

Any pointers?

-Keith


Elia Stupka wrote:

> > and gcc 3.0.2.  The patient did more than burp, I'm afraid, in
> > fact, I'm going to spray the output from make test (make
>
> Hi Keith, just to make sure things are clear...
>
> bioperl-db at the moment works wonderfully, but forget about the test
> suite...
>
> In other words, after you follow the instructions and thus download the
> main trunk of bioperl-db, you should be able to use load_seqdatabase.pl
> without any problem, but don't try making tests.
>
> Also, you need to checkout the sql schema from biosql-schema cvs module in
> the biosql cvs repository. There is no more schema directly inside
> bioperl-db because the database is now being used across languages.
>
> But believe me, it's perfectly fine, I've loaded all of swissprot
> yesterday... ;)
>
> Elia
>
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