[ensembl-dev] Ensembl API Version 72: Supported Species
Alexander Pico
apico at gladstone.ucsf.edu
Mon Sep 9 19:19:19 BST 2013
Great. I figured you meant something else… The verbose flag lists the loaded species as 'solanum_lycopersicum', while I was calling it without the underscore, which works in most cases. Why do only certain species require this underscore? Makes scripting across multiple species awkward. Is there a consistent pattern/rule here?
In any case, I've now got tomato running smoothly. Thanks!
- Alex
On Sep 9, 2013, at 1:22 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> Hi there,
>
> Sorry I couldn't be a bit more specific but typing isn't the easiest on a phone. You should add the -VERBOSE flag to your Registry call e.g.
>
> Bio::EnsEMBL::Registry->load_registry_from_db(
> -HOST => 'host', -PORT => 3306, -USER => 'user',
> -VERBOSE => 1,
> );
>
> This should print a lit of the species the registry is considering to load. Could you also send a copy of your Perl script in as there may be a configuration issue we can't diagnose without seeing the full story. As a little aside can you connect directly to the instance using Perl? For instance the following script will connect to the release 19 tomato DB on Ensembl Genomes' servers and do a quick ping:
>
> use strict;
> use warnings;
> use DBI;
> my $dbh = DBI->connect('dbi:mysql:database=solanum_lycopersicum_core_19_72_240;host=mysql.ebi.ac.uk;port=4157', 'anonymous');
> my $sth = $dbh->prepare("SELECT count(*) FROM meta");
> $sth->execute;
> my ($count) = @{$sth->fetchrow_arrayref()};
> $sth->finish;
> warn $count;
>
> Substitute for your connection details. When run against the live tomato server we get a row count of 116.
>
> Andy
>
> ------------
> Andrew Yates - Ensembl Core Software Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> Tel: +44-(0)1223-492538
> Fax: +44-(0)1223-494468
> http://www.ensembl.org/
>
> On 9 Sep 2013, at 03:22, Alexander Pico <apico at gladstone.ucsf.edu> wrote:
>
>> Hi Andy,
>>
>> I'm working with a local copy (i.e., solanum_lycopersicum_core_19_72_240). I added the flag to the launch of my Perl script and it generated a lot of output, but nothing I could read as being relevant. Is this what you meant?
>>
>> Summary of my perl5 (revision 5 version 10 subversion 1) configuration:
>> Platform:
>> osname=linux, osvers=2.6.18-348.2.1.el5, archname=x86_64-linux-thread-multi
>> uname='linux x86-001.build.bos.redhat.com 2.6.18-348.2.1.el5 #1 smp fri feb 8 01:01:24 est 2013 x86_64 x86_64 x86_64 gnulinux '
>> config_args='-des -Doptimize=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -DDEBUGGING=-g -Dversion=5.10.1 -Dmyhostname=localhost -Dperladmin=root at localhost -Dcc=gcc -Dcf_by=Red Hat, Inc. -Dprefix=/usr -Dvendorprefix=/usr -Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl5 -Dsitearch=/usr/local/lib64/perl5 -Dprivlib=/usr/share/perl5 -Darchlib=/usr/lib64/perl5 -Dvendorlib=/usr/share/perl5/vendor_perl -Dvendorarch=/usr/lib64/perl5/vendor_perl -Dinc_version_list=5.10.0 -Darchname=x86_64-linux-thread-multi -Dlibpth=/usr/local/lib64 /lib64 /usr/lib64 -Duseshrplib -Dusethreads -Duseithreads -Duselargefiles -Dd_dosuid -Dd_semctl_semun -Di_db -Ui_ndbm -Di_gdbm -Di_shadow -Di_syslog -Dman3ext=3pm -Duseperlio -Dinstallusrbinperl=n -Ubincompat5005 -Uversiononly -Dpager=/usr/bin/less -isr -Dd_gethostent_r_proto -Ud_endhostent_r_proto -Ud_sethostent_r_proto -Ud_endprotoent_r_proto -Ud_setprotoent_r_proto -U
>> d_endservent_r_proto -Ud_setservent_r_proto -Dscriptdir=/usr/bin -Dusesitecustomize'
>> hint=recommended, useposix=true, d_sigaction=define
>> useithreads=define, usemultiplicity=define
>> useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
>> use64bitint=define, use64bitall=define, uselongdouble=undef
>> usemymalloc=n, bincompat5005=undef
>> Compiler:
>> cc='gcc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
>> optimize='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic',
>> cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
>> ccversion='', gccversion='4.4.7 20120313 (Red Hat 4.4.7-3)', gccosandvers=''
>> intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
>> d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
>> ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
>> alignbytes=8, prototype=define
>> Linker and Libraries:
>> ld='gcc', ldflags =' -fstack-protector'
>> libpth=/usr/local/lib64 /lib64 /usr/lib64
>> libs=-lresolv -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread -lc
>> perllibs=-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
>> libc=, so=so, useshrplib=true, libperl=libperl.so
>> gnulibc_version='2.12'
>> Dynamic Linking:
>> dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E -Wl,-rpath,/usr/lib64/perl5/CORE'
>> cccdlflags='-fPIC', lddlflags='-shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic'
>>
>>
>> Characteristics of this binary (from libperl):
>> Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
>> PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP USE_64_BIT_ALL
>> USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
>> USE_PERLIO USE_REENTRANT_API USE_SITECUSTOMIZE
>> Built under linux
>> Compiled at Apr 4 2013 08:10:40
>> @INC:
>> /usr/local/lib64/perl5
>> /usr/local/share/perl5
>> /usr/lib64/perl5/vendor_perl
>> /usr/share/perl5/vendor_perl
>> /usr/lib64/perl5
>> /usr/share/perl5
>>
>>
>> - Alex
>>
>> On Sep 7, 2013, at 12:50 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
>>
>>> Hi there
>>>
>>> This normally means the registry has been unable to load the tomato database from the database server. If you run the loading code with a -VERBOSE flag it will give you a bit more information about what it's loading. Are you trying to load the species from ensembl genomes' public service or from a local copy?
>>>
>>> Andy
>>>
>>> Sent from my mobile.
>>>
>>> On 7 Sep 2013, at 02:04, Alexander Pico <apico at gladstone.ucsf.edu> wrote:
>>>
>>>> I'm receiving an error for just 2 species (out of list of 31) against version 72 of your Perl API:
>>>> * Solanum lycopersicum
>>>> * Glycine Max
>>>>
>>>> Here's an example:
>>>>
>>>> -------------------- WARNING ----------------------
>>>> MSG: Solanum lycopersicum is not a valid species name (check DB and API version)
>>>> FILE: Bio/EnsEMBL/Registry.pm LINE: 1188
>>>> CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 973
>>>> Date (localtime) = Fri Sep 6 17:14:51 2013
>>>> Ensembl API version = 72
>>>> ---------------------------------------------------
>>>>
>>>> -------------------- EXCEPTION --------------------
>>>> MSG: Can not find internal name for species 'Solanum lycopersicum'
>>>> STACK Bio::EnsEMBL::Registry::get_adaptor /***/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:975
>>>> STACK toplevel Ensembl_ETL_Device_v18_local.pl:437
>>>> Date (localtime) = Fri Sep 6 17:14:51 2013
>>>> Ensembl API version = 72
>>>> ---------------------------------------------------
>>>>
>>>> I know these worked in earlier API versions. Any guesses?
>>>> - Alex
>>>>
>>>>
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>>
>>
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