On 4-Mar-08, at 6:35 PM, Emmanuel Levy wrote:
Dear All,
I'd like to install BioMart to automate some queries with Ensembl. For
this I don't really understand why I need apache - so is there a way
to install the BioMart perl module without apache?
Hi Emmanuel,
if you are not interested in serving your own data but just automating
access to third party data you have two options there (neither of them
requires apache):
1. Web service access - this is by far the easiest and most flexible
- no installation of anything required you only need one script
without any modifications. All you have to do is to:
a. create your XML query (you can use MartView XML button to automate
this process)
b. run this query using our webExample.pl script (no modification
required) - just copy it and save
http://cvs.sanger.ac.uk/cgi-bin/viewcvs.cgi/*checkout*/biomart-perl/scripts/webExample.pl?content-type=text%2Fplain&rev=1.3&root=BioMart
For more info see http://www.biomart.org/martservice.html
(ignore the paragraph about meta data)
2. Install BioMart in the API mode - follow installation instructions
for biomart-perl only as in our documentation
(http://www.biomart.org/install.html - you probably only need the
quick install at http://www.biomart.org/install-overview.html)
and when prompted during installation say 'yes' to 'do you want to
install BioMart in the API mode' - this will install perl API with a
limited
number of CPAN dependencies only
let me know if you need more info,
a.
So far I've installed all the dependencies and when I run BioMart I've
got the following message:
----------------------------------------------------------------------------
mkdir: cannot create directory `PATH': File exists
mkdir: cannot create directory `TO': File exists
mkdir: cannot create directory `YOU': File exists
mkdir: cannot create directory `REGISTRY': File exists
mkdir: cannot create directory `FILE': File exists
mkdir: cannot create directory `UNDER': File exists
mkdir: cannot create directory `biomart-perl/conf/cachedRegistries':
No such file or directory
cp: `to': specified destination directory does not exist
Try `cp --help' for more information.
sh: line 1: http://www.biomart.org/biomart/martservice?type=registry:
No such file or directory
Unsuccessful stat on filename containing newline at
old/biomart-perl/lib//BioMart/Initializer.pm line 310.
Cached Registry Unavailable...
Unsuccessful stat on filename containing newline at
old/biomart-perl/lib//BioMart/Initializer.pm line 328.
Unsuccessful stat on filename containing newline at
old/biomart-perl/lib//BioMart/Initializer.pm line 334.
Running Complete Clean...
Unable to open configuration file 'PATH TO YOU REGISTRY FILE UNDER
biomart-perl/conf/. For Biomart Central Registry navigate to
http://www.biomart.org/biomart/martservice?type=registry', check file
existence and permissions
Is that normal?
----------------------------------------------------
Thanks for your help,
Best wishes,
Emmanuel
