[Bioperl-pipeline] Need help on installing the BioPipe 1

[Jason Stajich]

Are you trying to install it on mysql or postgres?

On Wed, 18 Dec 2002, Jia, Shuang wrote:

> Hey, everyone:
>
> I am installing the BioPipe in our system, I experienced some problems.
> Could anyone help me out?
>
> *	Follow the /biosql-schema/README, I should run '$
> scripts/transform_sql -target pg biosqldb-mysql.sql > biosqldb-pg.sql'. I
> changed biosqldb-mysql.sql to biopipelinedb-mysql.sql, whole command changed
> to '$ scripts/transform_sql -target pg biopipelinedb-mysql.sql>
> biopipelinedb-mysql.sql'. The system said "no biopipelinedb-mysql.sql such
> file". How could I run this for the biopipeline?
>
> *	Follow the /bioperl-pipeline/INSTALL, I should populate the database
> with the schema from the biosql-schema cvs modules: mysql -u root biopipe <
> ../biosql-schema/sql/biopipelinedb-mysql.sql. The system said 'bash:
> ../biosql-schema/sql/biopipelinedb-mysql.sql: No such file or directory'.
>
> I think this two problem is the same one, could someone tell me how to do
> it? Thanks very much.
>
> Another one is:
> *	After I installed bioperl-db, I tried to run test. I got the
> following message:
> 	Run test as the root user:
> 	[root@jupiter bioperl-db]# make test_dblink
> 	PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib
> -I/usr/lib/perl5/5.8.0/i386-linux-thread-multi -I/usr/lib/perl5/5.8.0 -e
> 'use Test::Harness qw(&runtests
> 	$verbose); $verbose=0; runtests @ARGV;' t/dblink.t
> 	t/dblink....driver not set at t/DBTestHarness.pm line 106
> 	        DBTestHarness::driver('DBTestHarness=HASH(0x804c0c0)')
> called at t/DBTestHarness.pm line 204
> 	        DBTestHarness::create_db('DBTestHarness=HASH(0x804c0c0)')
> called at t/DBTestHarness.pm line 94
> 	        DBTestHarness::new('DBTestHarness','biosql') called at
> t/dblink.t line 21
> 	t/dblink....dubious
> 	        Test returned status 255 (wstat 65280, 0xff00)
> 	DIED. FAILED tests 1-18
> 	        Failed 18/18 tests, 0.00% okay
> 	Failed Test Stat Wstat Total Fail  Failed  List of Failed
>
> ----------------------------------------------------------------------------
> ---
> 	t/dblink.t   255 65280    18   18 100.00%  1-18
> 	Failed 1/1 test scripts, 0.00% okay. 18/18 subtests failed, 0.00%
> okay.
> 	make: *** [test_dblink] Error 2
>
> 	Change user to myself:
> 	[sjia@jupiter bioperl-db]$ make test_dblink
> 	PERL_DL_NONLAZY=1 /usr/bin/perl -Iblib/arch -Iblib/lib
> -I/usr/lib/perl5/5.8.0/i386-linux-thread-multi -I/usr/lib/perl5/5.8.0 -e
> 'use Test::Harness qw(&runtests
> 	$verbose); $verbose=0; runtests @ARGV;' t/dblink.t
> 	No -I allowed while running setuid.
> 	make: *** [test_dblink] Error 29
>
>
>
> Shuang
>
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu