[Bioperl-pipeline] Need help on installing the BioPipe 1
Jason Stajich
jason@cgt.mc.duke.edu
Sun, 22 Dec 2002 10:19:06 -0500 (EST)
On Fri, 20 Dec 2002, Jia, Shuang wrote:
> I am working on MySQL. I think I have done with the first two problems.
You do not need to run the previous transform step you listed.
* 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
>
> But for the last one, I did the following.
> 1. cd bioperl-db
> 2. cd t
> 3. cp DBHarness.conf.example DBTestHarness.biosql.conf
> 4. cp DBTestHarness.conf.example DBTestHarness.markerdb.conf
> 5. change this two .conf files at the following:
> 'driver' => 'mysql',
> 'host' => 'localhost',
> 'user' => 'sjia',
> 'port' => '3306'
> 'password' => jia123,
> #'schema_sql' => [ '../biosql-schema/sql/biosqldb-mysql.sql'],
> 'schema_sql' => [ './sql/markerdb-mysql.sql'],
> #'dbname' => 'biopipe',
> 'database' => 'biopipe',
>
You do not need to do anything with markerdb - this is not related to the
biosql db for storing sequences but a separate part of project. So ignore
those errors - in fact you don't want to have created a
DBTestHarness.markerdb.conf file - I don't think those instructions are at
all part of the biopipe installation on Shawn's HOWTO that is at
www.biopipe.org
You need to copy DBTestHarness.conf.example to DBTestHarness.conf and edit
this to contain the proper information. You also need to checkout
biosql-schema on the bioperl-release-1-1-0 branch when getting
biosql-schema.
> 6. perl Makefile.PL
> 7. make
> 8. make install
> 9. make test_comment
> 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); $verbose=0; runtests @ARGV;' t/comment.t
> t/comment....driver not set at t/DBTestHarness.pm line 106
> DBTestHarness::driver('DBTestHarness=HASH(0x804c0c0)') called at
> t/DBTestHarness.pm line 204
> DBTestHarness::create_db('DBTestHarness=HASH(0x804c0c0)') called at
> t/DBTestHarness.pm line 94
> DBTestHarness::new('DBTestHarness','biosql') called at t/comment.t
> line
> 20
> t/comment....dubious
> Test returned status 255 (wstat 65280, 0xff00)
> DIED. FAILED tests 1-11
> Failed 11/11 tests, 0.00% okay
> Failed Test Stat Wstat Total Fail Failed List of Failed
> ----------------------------------------------------------------------------
> ---
> t/comment.t 255 65280 11 11 100.00% 1-11
> Failed 1/1 test scripts, 0.00% okay. 11/11 subtests failed, 0.00% okay.
> make: *** [test_comment] Error 2
>
> What's wrong in my steps?
>
> Thanks.
>
>
> Shuang.
>
> -----Original Message-----
> From: Jason Stajich [mailto:jason@cgt.mc.duke.edu]
> Sent: Friday, December 20, 2002 10:12 AM
> To: Jia, Shuang
> Cc: 'bioperl-pipeline@bioperl.org'
> Subject: Re: [Bioperl-pipeline] Need help on installing the BioPipe 1
>
>
> Are you trying to install it on mysql or postgres?
>
> On Wed, 18 Dec 2002, Jia, Shuang wrote:
>
> > Hey, everyone:
> >
> > I am installing the BioPipe in our system, I experienced some problems.
> > Could anyone help me out?
> >
> > * Follow the /biosql-schema/README, I should run '$
> > 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
> >
> > _______________________________________________
> > bioperl-pipeline mailing list
> > bioperl-pipeline@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-pipeline
> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu