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.profile in Mac OS X with MySQL

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Last Modified: 2013-11-12
Hi,

I'm trying to run BioSQL and load my first database with MySQL:

"Starting BioSQL and loading the first database
------------------------------------

You have to first choose the language or project you want to use in
to load your data. You currently have three options: Perl and BioPerl,
Java and BioJava and Python and BioPython. You will need to download
the schema, the same for all three languages, and the supporting modules
for each language. In each case the package is a mixture of generic
modules for database access and then the BioSQL binding code.


Schema Loading
-------------

The BioSQL schema is distributed separately from the language
bindings. Use the svn checkout from the anonymous server:
svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema
Create a database, which we'll call 'biosql', in the data instance:

For MySQL do:
mysqladmin -u root create biosql"





I am going with the perl-Bioperl route. I have MySQL already installed in usr/local/mysql and i'm  now wondering how i can use MySQL to create the database 'biosql'.

when i type in:
bash-3.2# mysqladmin -u root create biosql

i receive:
bash: mysqladmin: command not found


I have been advised to change the $PATH in my .profile... but have no idea where this is, and how to change it to configure it to usr/local/mysql.

Any advice on this would be much appreciated.

Thanks.
Comment
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Commented:
You can put the full path in the command:

/usr/bin/mysqladmin -u root create biosql


If you need to find a program which is not in your path, you can always use the "locate" command

eg

[localhost:~] user% locate mysqladmin
/usr/bin/mysqladmin
/usr/share/man/man1/mysqladmin.1


Cheers,

Joel

Author

Commented:
Hi Joel.

Since last posting.. i have changed my .profile to:

export PATH=/usr/local/mysql-5.1.35-osx10.5-x86/bin/:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin

my mysqladmin is located in:

 /usr/local/mysql-5.1.36-osx10.5-x86/bin/mysqladmin


So the guide says:

The BioSQL schema is distributed separately from the language
bindings. Use the svn checkout from the anonymous server:
svn co svn://code.open-bio.org/biosql/biosql-schema/trunk biosql-schema
Create a database, which we'll call 'biosql', in the data instance:

For MySQL do:
mysqladmin -u root create biosql"


i have tried firstly:

bash-3.2# /usr/local/mysql-5.1.36-osx10.5-x86/bin/mysqladmin -u root create biosql

which returned nothing? unless biosql has been made and i just can't see it?



and for the second attempt i tried going into bash-3.2# /usr/local/mysql-5.1.36-osx10.5-x86/bin/

and in this directory i entered "bash-3.2# mysqladmin -u root create biosql".
which gave: bash: mysqladmin: command not found

Stephen.


Commented:
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Author

Commented:
Hey Joel... one last thing :oP

I'm going to take it biosql has been created if no errors have come back, as you say.

The guide says:

For MySQL do:

  >mysqladmin -u root create biosql



To load the schema, use the appropiate SQL dialect in
biosql-schema/sql.

For mysql do:

  >mysql -u root biosql < biosqldb-mysql.sql


i have entered the following shown below receiving the error message:

bash-3.2# mysql -u root biosql < biosqldb-mysql.sql
bash-3.2# bash: biosqldb-mysql.sql: No such file or directory

Stephen





Author

Commented:
Sorry, to elaborate further:

As i have previously mentions, the guide i'm following states:

"To load the schema, use the appropiate SQL dialect in
biosql-schema/sql.

For mysql do:

  >mysql -u root biosql < biosqldb-mysql.sql"


I have the biosqldb-mysql.sql file saved in "/Users/stevey_mac2k2/Desktop/ExerciseTwo/biosql-1.0.1/sql/biosqldb-mysql.sql"

in Terminal, i have gone into the "/Users/stevey_mac2k2/Desktop/ExerciseTwo/biosql-1.0.1/sql/" directory and entered:

bash-3.2# mysql -u root biosql < biosqldb-mysql.sql
bash: mysql: command not found

bash-3.2# pwd
/Users/stevey_mac2k2/Desktop/ExerciseTwo/biosql-1.0.1/sql

Any idea what i'm doing wrong with this?

Thanks,

Stephen.



Commented:
This is the same issue, in that it can't find the binary mysql.

So, you would do

locate mysql

and then put in the full path to the command.

From your location before, I would guess that this would be

/usr/local/mysql-5.1.36-osx10.5-x86/bin/mysql < ./biosqldb-mysql.sql

assuming that you are in the directory where  biosqldb-mysql.sql is located.

Cheers,

Joel
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