[ensembl-dev] Problems installing Ensembl mirror

[Youens-Clark, Ken]

So I've been trying for a few days to set up a local Ensembl installation with the plant dbs, and I'm having a lot of problems.  

One annoying bit was that Apache2::SizeLimit doesn't like OSX/darwin, so "EnsEMBL::Web::Apache::Handlers" won't work.  I had to hack the source of Apache2::SizeLimit to get it not to complain about my OS.  I wonder if you could find some workaround for this?  Perhaps not use the module if the user is on OSX?  

Anyway, I've followed all the installation instructions as closely as I can, but I still cannot get my local server running.  I've tried to set up myself with the "mirror" plugins in "conf/Plugins.pm" like so:

> $SiteDefs::ENSEMBL_PLUGINS = [
>   'EnsEMBL::Mirror'    => $SiteDefs::ENSEMBL_SERVERROOT.'/public-plugins/mirror',
> #  'EnsEMBL::Ensembl'   => $SiteDefs::ENSEMBL_SERVERROOT.'/public-plugins/ensembl'
> ];

But not the "Ensembl" plugin as that just causes problems as I don't have (or want) all those dbs.

I set "public-plugins/mirror/conf/SiteDefs.pm" to load just rice:

>   sub update_conf {
>     $SiteDefs::ENSEMBL_PRIMARY_SPECIES    = 'Oryza_sativa';
>     $SiteDefs::ENSEMBL_SECONDARY_SPECIES  = 'Oryza_sativa';
>     $SiteDefs::__species_aliases{ 'Oryza_sativa' } = [qw(rice )];
>   ...

I set up an ini file for that species:

> $ cat Oryza_sativa.ini 
> [general]
> ENSEMBL_CHROMOSOMES     = [ 1 2 3 4 5 6 7 8 9 10 ];
> 
> [databases]
> DATABASE_CORE            = oryza_sativa_core_15_68_6;


My DEFAULTS.ini has the settings that match the MySQL permissions I created:

> [general]
> DATABASE_HOST       = localhost;
> DATABASE_HOST_PORT  = 3306
> DATABASE_WRITE_USER = ens_rw
> DATABASE_WRITE_PASS = ensembl
> DATABASE_DBUSER     = ens_rw
> DATABASE_DBPASS     = ensembl


I start up and get this output:

> [byrne@/usr/local/ensembl/public-plugins/mirror/conf]$ estart
> hostname: illegal option -- -
> usage: hostname [-fs] [name-of-host]
> 
> Starting up Ensembl server on host: byrne
>  Executing perl startup file
> ------------------------------------------------------------------------------
> -  INFO :    0.000 :    0.000 : Parser     >> Starting to parse tree
> ------------------------------------------------------------------------------
> -  INFO :    0.000 :    0.000 : Parser     >> Child objects attached
> -  INFO :    0.002 :    0.002 : Filesystem >> Trawled web tree
> ------------------------------------------------------------------------------
> -  INFO :    0.002 :    0.000 : Parser     >> Parsing ini files and munging dbs
> ------------------------------------------------------------------------------
> -  INFO :    0.008 :    0.006 : Parsing    >> DEFAULTS ini file
> -  INFO :    0.009 :    0.000 : Parsing    >> Oryza_sativa ini file
> -  INFO :    0.012 :    0.004 : Retrieve   >> Oryza_sativa database
> -  INFO :    0.014 :    0.002 : Retrieve   >> Oryza_sativa DAS sources
> -  INFO :    0.024 :    0.009 : Parsing    >> MULTI ini file
> -  INFO :    0.028 :    0.004 : Retrieve   >> MULTI ini file
> ------------------------------------------------------------------------------
> -  INFO :    0.028 :    0.001 : Parser     >> Post processing ini files
> ------------------------------------------------------------------------------
> -  INFO :    0.029 :    0.000 : munging    >> Oryza_sativa config
> -  INFO :    0.029 :    0.000 : munging    >> MULTI config
> --------------------------------------------------------------------------------------
> Placing .cvsignore and robots.txt into /usr/local/ensembl/public-plugins/mirror/htdocs
> --------------------------------------------------------------------------------------
> 
> ==============================================================================
>  Server information:
> ==============================================================================
> 
>  Ensembl version:    69
> 
>  Database Host:      localhost;
> 
>  External address:   http://localhost:8000/
>  Real address:       http://192.168.1.101:8000
> 
>  Cache namespace:    http://localhost:8000
> 
>  Server root:        /usr/local/ensembl
> 
>  PID file:           /usr/local/ensembl/logs/192.168.1.101.httpd.pid
>  Access logs:        /usr/local/ensembl/logs/192.168.1.101.access_log ensembl_extended
>  Error logs:         /usr/local/ensembl/logs/192.168.1.101.error_log
> 
>  CSS file:           http://localhost:8000/minified/d67f93dc569ac1397c0ef4be98acfa4f.css
>  JavaScript file:    http://localhost:8000/minified/d473830c62631f8e306e2b38f8cc0b16.js
> 
>  Plugins installed:  EnsEMBL::Mirror
>                      
> 
> ==============================================================================
> 
> ENSEMBL_BLAST_METHODS config unavailable at /usr/local/ensembl/modules/EnsEMBL/Web/BlastView/BlastDefs.pm line 66.

(BTW, I'd love to know why I'm getting that initial "hostname" error.)

When I request "http://localhost:8000/Oryza_sativa," I get a 404 with the following in my error log:

> [Mon Oct 29 16:42:58 2012] [error] [client ::1] File does not exist: /usr/local/ensembl/htdocs/Oryza_sativa
> Use of uninitialized value in lc at /Library/Perl/5.12/Class/DBI.pm line 196.
> [Mon Oct 29 16:42:58 2012] [error] [client ::1] Cannot include virtual file: does not exist or permission denied /ssi/species/ERROR_4xx.html
> SCRIPT: byrne    19614 2012-10-29 16:42:58 /Oryza_sativa 
> ENDSCR: byrne    19614 2012-10-29 16:42:58 /Oryza_sativa      0.001


Can someone help me with this?

--
Ken Youens-Clark
kclark at cshl.edu
Ware Lab/CSHL/USDA-ARS