Hi All,
I went ahead and decided to do away with Biomart 0.6 as advised and
started installing Biomart 0.7 on my 64 bit linux.
Now as i follow the "3.3 Setting up MartView" section of the user-docs
(after being referred to this section by the BioMart 0.7 Quick Install
Guide), i created my own registry file in the biomart-perl/conf directory
as specified in section 3.3 of that document and when i tried to configure
MartView, i got the error below:
I have checked that i have the DB_File module, that the DB_File.so exists
and that i have the XSLoader.pm in that path.
I already created the database and checked it exists in mysql. The .xml
file i used is shown below as well as the settings.conf file i edited.
I will greatly appreciate your assistance. Thanks
Nelson
The ERROR while configuring MartView:
[nndegwa biomart-perl]$ perl bin/configure.pl -r
conf/nelsonsReactomeRegistry.xml
Do you want to install in API only mode [y/n] [n]: n
Checking prerequisites ...[Looks good]
Can't load
'/homes/nndegwa/reactomes/Reactome/test/perl64/lib/auto/DB_File/DB_File.so'
for module DB_File: libdb-4.2.so: cannot open shared object file: No such
file or directory at
/homes/nndegwa/reactomes/Reactome/test/perl64/lib/XSLoader.pm line 70.
at /homes/nndegwa/reactomes/Reactome/test/perl64/lib/DB_File.pm line 252
Compilation failed in require at
/homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/CGI/Session/Driver/db_file.pm
line 8.
BEGIN failed--compilation aborted at
/homes/nndegwa/reactomes/Reactome/test/perl64/site/lib/CGI/Session/Driver/db_file.pm
line 8.
Compilation failed in require at
/automount/nas10b_vol-vol1-homes/nndegwa/reactomes/Reactome/test/Biomart_07_fresh/my_biomart-perl/biomart-perl/bin/../lib/BioMart/Web.pm
line 47.
BEGIN failed--compilation aborted at
/automount/nas10b_vol-vol1-homes/nndegwa/reactomes/Reactome/test/Biomart_07_fresh/my_biomart-perl/biomart-perl/bin/../lib/BioMart/Web.pm
line 47.
Compilation failed in require at (eval 17) line 3.
...propagated at
/homes/nndegwa/reactomes/Reactome/test/perl64/lib/base.pm line 94.
BEGIN failed--compilation aborted at
/automount/nas10b_vol-vol1-homes/nndegwa/reactomes/Reactome/test/Biomart_07_fresh/my_biomart-perl/biomart-perl/bin/../lib/BioMart/Web/TemplateBuilder.pm
line 53.
Compilation failed in require at
/automount/nas10b_vol-vol1-homes/nndegwa/reactomes/Reactome/test/Biomart_07_fresh/my_biomart-perl/biomart-perl/bin/configureBioMart.pl
line 39.
BEGIN failed--compilation aborted at
/automount/nas10b_vol-vol1-homes/nndegwa/reactomes/Reactome/test/Biomart_07_fresh/my_biomart-perl/biomart-perl/bin/configureBioMart.pl
line 39.
A copy of my registry: I modified the host, port database, schema, user
and password accordingly, and left the other fields as they are.
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<virtualSchema name="default">
<MartDBLocation
name = "example"
displayName = "My Example"
databaseType = "mysql"
host = "localhost"
port = "3306"
database = "mymart"
schema = "mymart"
user = "myusername"
password = "mypassword"
visible = "1"
default = ""
includeDatasets = ""
/>
</virtualSchema>
</MartRegistry>
I also did edit the settings.conf file under the conf folder to reflect my
customizations:
#########################################################
################ httpd.conf settings ####################
[httpdSettings]
apacheBinary=/homes/nndegwa/reactomes/Reactome/test/GKB/BioMart/apache/bin/httpd
serverHost=localhost
port=9002
# to use proxying set the proxy port below (even if its 80) and set
serverHost as your proxy host
proxy=
# if apxs or apxs2 is not in default directory where httpd lives, you may
set this param to point to apxs/2
apxs=
location=biomart
> Hi,
> I have been attempting to install Biomart 0.6 on a 64 bit linux machine
and i keep running into all sorts of problems as many of the libraries i
intend to use are 32 bit.
> Has anyone been able to successfully do this? Any ideas how i can go
about
> this please?
> I have installed a 32 bit perl (with the recommended tweaking to fool
the
> system) and but then getting Perl modules via CPAN fails to works and
manual module installation seems rather crude. Here is the error i get
from CPAN
>
>
> YAML Error: Invalid element in map
> Code: YAML_LOAD_ERR_BAD_MAP_ELEMENT
> Line: 3
> Document: 1
>
> CPAN by the way works fine with the 64 bit perl
>
> Thanks
> Nelson
>
