Thank you all,
Yes Junjun it is the same coding, but I have changed the Registry file, Here
is the new one
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<MartURLLocation
database="cosp"
default="1"
displayName="COSMIC (SANGER UK)"
host="www.sanger.ac.uk"
includeDatasets=""
martUser=""
name="CosmicMart"
path="/genetics/CGP/cosmic/biomart/martservice"
port="80"
redirect="1"
serverVirtualSchema="default"
visible="1"
/>
</MartRegistry>
Here is what I get at the console;
cygwin warning:
MS-DOS style path detected: C:/Users/Manjula/workspace/
TestMart/registry_DOM_XML
Preferred POSIX equivalent is: /cygdrive/c/Users/Manjula/
workspace/TestMart/registry_DOM_XML
CYGWIN environment variable option "nodosfilewarning" turns off this
warning.
Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
Connection parameters of [COSMIC (SANGER UK)] [ OK ]
Use of uninitialized value in lc at C:/Perl64/lib/BioMart/Initializer.pm
line 1135.
could not load module BioMart::Dataset::Vary: Accept-Encoding: syntax error
at (eval 103) line 1, near "require BioMart::Dataset::Vary:"
Trace begun at C:\Perl64\site\lib\BioMart\Root.pm line 191
BioMart::Root::loadModule('BioMart::Initializer=HASH(0x162da60)',
'BioMart::Dataset::Vary: Accept-Encoding') called at
C:\Perl64\lib\BioMart\Initializer.pm
line 1162
BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x162da60)')
called at C:\Perl64\lib\BioMart\Initializer.pm line 228
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x162da60)',
'registryFile', 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml',
'action', 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 377
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x162da60)',
'registryFile', 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml',
'action', 'clean') called at C:\Perl64\lib\BioMart\Initializer.pm line 144
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x162da60)',
'registryFile', 'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml',
'action', 'clean') called at C:\Perl64\site\lib\BioMart\RootI.pm line 64
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'C:/Users/Manjula/workspace/TestMart/cosmicRegistry.xml', 'action', 'clean')
called at C:\Users\Manjula\workspace\TestMart\Q1.pl line 22
When I change the path to the registry file as "/cygdrive/c/......" I get a
con not find the file error.
Strange thing is that, If I give the relative path to the registry file, I
get a different error. i.e;
Use of uninitialized value $1 in concatenation (.) or string at
C:/Perl64/lib/BioMart/Initializer.pm line 114.
Use of uninitialized value $1 in concatenation (.) or string at
C:/Perl64/lib/BioMart/Initializer.pm line 116.
Use of uninitialized value $1 in concatenation (.) or string at
C:/Perl64/lib/BioMart/Initializer.pm line 123.
Use of uninitialized value $1 in concatenation (.) or string at
C:/Perl64/lib/BioMart/Initializer.pm line 125.
Use of uninitialized value in concatenation (.) or string at
C:/Perl64/lib/BioMart/Initializer.pm line 134.
Use of uninitialized value $1 in concatenation (.) or string at
C:/Perl64/lib/BioMart/Initializer.pm line 143.
Connection parameters of [COSMIC (SANGER UK)] [ OK ]
Use of uninitialized value in lc at C:/Perl64/lib/BioMart/Initializer.pm
line 1135.
could not load module BioMart::Dataset::Vary: Accept-Encoding: syntax error
at (eval 103) line 1, near "require BioMart::Dataset::Vary:"
Trace begun at C:\Perl64\site\lib\BioMart\Root.pm line 191
BioMart::Root::loadModule('BioMart::Initializer=HASH(0x38da60)',
'BioMart::Dataset::Vary: Accept-Encoding') called at
C:\Perl64\lib\BioMart\Initializer.pm line 1162
BioMart::Initializer::_populateRegistry('BioMart::Initializer=HASH(0x38da60)')
called at C:\Perl64\lib\BioMart\Initializer.pm line 228
BioMart::Initializer::_init('BioMart::Initializer=HASH(0x38da60)',
'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at
C:\Perl64\lib\BioMart\Initializer.pm line 377
BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x38da60)',
'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at
C:\Perl64\lib\BioMart\Initializer.pm line 144
BioMart::Initializer::_new('BioMart::Initializer=HASH(0x38da60)',
'registryFile', 'cosmicRegistry.xml', 'action', 'clean') called at
C:\Perl64\site\lib\BioMart\RootI.pm line 64
BioMart::RootI::new('BioMart::Initializer', 'registryFile',
'cosmicRegistry.xml', 'action', 'clean') called at
C:\Users\Manjula\workspace\TestMart\Q1.pl line 22
Any help is greatly appreciated!
Thank you!
Regards,
Manjula
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