[BioMart Users] FW: [Ensembl #228924] Set up environment for Ensembl BioMart Perl API

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[BioMart Users] FW: [Ensembl #228924] Set up environment for Ensembl BioMart Perl API

Elena Rivkin

On 11-08-19 11:25 AM, "Dirk Paul" <[hidden email]> wrote:

>Hi Elena,
>
>Thanks for your email!
>
>I would like to use the Biomart Perl API. I followed the installation as
>described here: http://www.biomart.org/user-docs.pdf. I tried to install
>Apache, but I got an error message:
>
>wget http://www.apache.org/dist/httpd/httpd-2.2.14.tar.gz
>--2011-08-19 15:52:20--
>http://www.apache.org/dist/httpd/httpd-2.2.14.tar.gz
>Resolving wwwcache.sanger.ac.uk... 172.18.24.2, 172.18.24.1 Connecting
>to wwwcache.sanger.ac.uk|172.18.24.2|:3128... connected.
>Proxy request sent, awaiting response... 404 Not Found
>2011-08-19 15:52:20 ERROR 404: Not Found.
>
>Maybe I don't need to install this part and ModPerl? Anyways, when I try
>to install the Perl API and MartView together, I got the following error
>message (see below). Please advise!
>
>Many thanks, Dirk.
>
>***
>
>perl bin/configure.pl -r conf/registryURLPointer.xml
>
>Do you want to install in API only mode [y/n] [n]: n
>
>Checking prerequisites ...[Looks good]
>Use of uninitialized value in string ne at
>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/configureBioMart.pl line 111.
>Use of uninitialized value in regexp compilation at
>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/configureBioMart.pl line 113.
>
>rm /nfs/users/nfs_d/dp5/src/biomart-perl/conf/templates/default/*.ttcrm:
>cannot remove
>`/nfs/users/nfs_d/dp5/src/biomart-perl/conf/templates/default/*.ttc': No
>such file or directory
>
>APACHE: /usr/sbin/httpd
>HOST: test.biomart.org
>PORT: 9002
>PROXY:
>LOCATION: biomart
>APXS/2:
>
>You can change the above configuration by editing
>"biomart-perl/conf/settings.conf"
>
>
>
>No valid httpd binary specified, skipping Apache version and mod_perl
>checks. No
>                httpd.conf will be generated.
>Use of uninitialized value in string eq at
>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/configureBioMart.pl line 212.
>Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC Libdir
>/nfs/users/nfs_d/dp5/src/biomart-perl/lib is not in @INC, adding to @INC
>Use of uninitialized value in string eq at bin/ConfBuilder.pm line 89.
>Use of uninitialized value in string eq at bin/ConfBuilder.pm line 133.
>Use of uninitialized value in string eq at bin/ConfBuilder.pm line 225.
>Use of uninitialized value in string eq at bin/ConfBuilder.pm line 225.
>
>Cached Registry Unavailable...
>
>Running Complete Clean...
>
>
>Problems with the web server: 403 Proxy Configuration required
>
>
>
>
>ERROR something wrong with your registry:  Problems with the retrieval
>of dataset configuration
>               Please check:
>               that your mart Registry files contains correct connection
>params,
>               that you are using the correct version on XML::Simple,
>               that BioMart  databases contain a populated meta_conf
>tables and
>               that you have set martUser correctly if you are running
>in restricted data
>               access mode (populated meta_conf__user__dm)
>
>
>
>Trace begun at
>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/../lib/BioMart/Initializer.pm
>line 254
>BioMart::Initializer::_init('BioMart::Initializer=HASH(0x2551670)',
>'registryFile',
>'/nfs/users/nfs_d/dp5/src/biomart-perl/conf/registryURLPointer.xml',
>'action', 'cached', 'mode', 'memory') called at
>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/../lib/BioMart/Initializer.pm
>line 377
>BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x2551670)',
>'registryFile',
>'/nfs/users/nfs_d/dp5/src/biomart-perl/conf/registryURLPointer.xml',
>'action', 'cached', 'mode', 'memory') called at
>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/../lib/BioMart/Initializer.pm
>line 328
>BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x2551670)'
>, 'registryFile',
>'/nfs/users/nfs_d/dp5/src/biomart-perl/conf/registryURLPointer.xml',
>'action', 'cached', 'mode', 'memory') called at
>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/../lib/BioMart/Initializer.pm
>line 168
>BioMart::Initializer::_new('BioMart::Initializer=HASH(0x2551670)',
>'registryFile',
>'/nfs/users/nfs_d/dp5/src/biomart-perl/conf/registryURLPointer.xml',
>'action', 'cached', 'mode', 'memory') called at
>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/../lib/BioMart/RootI.pm line
>64 BioMart::RootI::new('BioMart::Initializer', 'registryFile',
>'/nfs/users/nfs_d/dp5/src/biomart-perl/conf/registryURLPointer.xml',
>'action', 'cached', 'mode', 'memory') called at
>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/configureBioMart.pl line 332
>eval {...} at
>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/configureBioMart.pl line 331
>
>
>
>-----Original Message-----
>From: Elena Rivkin [mailto:[hidden email]]
>Sent: 19 August 2011 16:19
>To: Dirk Paul
>Subject: Re: [Ensembl #228924] Set up environment for Ensembl BioMart
>Perl API
>
>Can you please post your question again?
>Thank you.
>Elena Rivkin, PhD
>Outreach and Training Coordinator, Informatics and Bio-computing
>
>Ontario Institute for Cancer Research
>MaRS Centre, South Tower
>101 College Street, Suite 800
>Toronto, Ontario, Canada M5G 0A3
>
>Tel: 647-258-4316
>Toll-free: 1-866-678-6427
>www.oicr.on.ca
>
>This message and any attachments may contain confidential and/or
>privileged information for the sole use of the intended recipient. Any
>review or distribution by anyone other than the person for whom it was
>originally intended is strictly prohibited. If you have received this
>message in error, please contact the sender and delete all copies.
>Opinions, conclusions or other information contained in this message may
>not be that of the organization.
>
>
>
>
>
>
>On 11-08-19 11:05 AM, "Bert Overduin via RT" <[hidden email]>
>wrote:
>
>>Hello Dirk Paul,
>>
>>I am forwarding your question to the BioMart group at OICR, as we are
>not
>>the right people to ask these technical questions, I am afraid.
>>
>>--
>>With kind regards,
>>Bert Overduin, Ph.D.
>>(Ensembl Helpdesk)
>>
>>Mailing lists: http://www.ensembl.org/info/about/contact/mailing.html
>>Blog: http://www.ensembl.info
>>YouTube: http://www.youtube.com/user/EnsemblHelpdesk
>>Facebook: http://www.facebook.com/Ensembl.org
>>Twitter: http://twitter.com/Ensembl
>>
>>
>>
>>--
>> The Wellcome Trust Sanger Institute is operated by Genome Research
>> Limited, a charity registered in England with number 1021457 and a
>> company registered in England with number 2742969, whose registered
>> office is 215 Euston Road, London, NW1 2BE.
>
>
>
>--
> The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.

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Re: [BioMart Users] FW: [Ensembl #228924] Set up environment for Ensembl BioMart Perl API

Junjun Zhang
Hi Dirk,

Apache httpd 2.2.14 is no longer available for downloading from the
specified path. Below is the most recent stable release:

http://www.apache.org/dist/httpd/httpd-2.2.19.tar.gz


Rather than installing Apache from source yourself, you could
alternatively ask your system admin team to install it for you.

Once Apache is installed, please follow the BioMart 0.7 user doc to
continue the BioMart installation.

Hope this helps, let us know if you need further assistance.

Best regards,

Junjun


On 11-08-19 11:26 AM, "Elena Rivkin" <[hidden email]> wrote:

>
>On 11-08-19 11:25 AM, "Dirk Paul" <[hidden email]> wrote:
>
>>Hi Elena,
>>
>>Thanks for your email!
>>
>>I would like to use the Biomart Perl API. I followed the installation as
>>described here: http://www.biomart.org/user-docs.pdf. I tried to install
>>Apache, but I got an error message:
>>
>>wget http://www.apache.org/dist/httpd/httpd-2.2.14.tar.gz
>>--2011-08-19 15:52:20--
>>http://www.apache.org/dist/httpd/httpd-2.2.14.tar.gz
>>Resolving wwwcache.sanger.ac.uk... 172.18.24.2, 172.18.24.1 Connecting
>>to wwwcache.sanger.ac.uk|172.18.24.2|:3128... connected.
>>Proxy request sent, awaiting response... 404 Not Found
>>2011-08-19 15:52:20 ERROR 404: Not Found.
>>
>>Maybe I don't need to install this part and ModPerl? Anyways, when I try
>>to install the Perl API and MartView together, I got the following error
>>message (see below). Please advise!
>>
>>Many thanks, Dirk.
>>
>>***
>>
>>perl bin/configure.pl -r conf/registryURLPointer.xml
>>
>>Do you want to install in API only mode [y/n] [n]: n
>>
>>Checking prerequisites ...[Looks good]
>>Use of uninitialized value in string ne at
>>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/configureBioMart.pl line 111.
>>Use of uninitialized value in regexp compilation at
>>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/configureBioMart.pl line 113.
>>
>>rm /nfs/users/nfs_d/dp5/src/biomart-perl/conf/templates/default/*.ttcrm:
>>cannot remove
>>`/nfs/users/nfs_d/dp5/src/biomart-perl/conf/templates/default/*.ttc': No
>>such file or directory
>>
>>APACHE: /usr/sbin/httpd
>>HOST: test.biomart.org
>>PORT: 9002
>>PROXY:
>>LOCATION: biomart
>>APXS/2:
>>
>>You can change the above configuration by editing
>>"biomart-perl/conf/settings.conf"
>>
>>
>>
>>No valid httpd binary specified, skipping Apache version and mod_perl
>>checks. No
>>                httpd.conf will be generated.
>>Use of uninitialized value in string eq at
>>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/configureBioMart.pl line 212.
>>Have auxiliary Perl libdirs in $PERL5LIB, adding to @INC Libdir
>>/nfs/users/nfs_d/dp5/src/biomart-perl/lib is not in @INC, adding to @INC
>>Use of uninitialized value in string eq at bin/ConfBuilder.pm line 89.
>>Use of uninitialized value in string eq at bin/ConfBuilder.pm line 133.
>>Use of uninitialized value in string eq at bin/ConfBuilder.pm line 225.
>>Use of uninitialized value in string eq at bin/ConfBuilder.pm line 225.
>>
>>Cached Registry Unavailable...
>>
>>Running Complete Clean...
>>
>>
>>Problems with the web server: 403 Proxy Configuration required
>>
>>
>>
>>
>>ERROR something wrong with your registry:  Problems with the retrieval
>>of dataset configuration
>>               Please check:
>>               that your mart Registry files contains correct connection
>>params,
>>               that you are using the correct version on XML::Simple,
>>               that BioMart  databases contain a populated meta_conf
>>tables and
>>               that you have set martUser correctly if you are running
>>in restricted data
>>               access mode (populated meta_conf__user__dm)
>>
>>
>>
>>Trace begun at
>>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/../lib/BioMart/Initializer.pm
>>line 254
>>BioMart::Initializer::_init('BioMart::Initializer=HASH(0x2551670)',
>>'registryFile',
>>'/nfs/users/nfs_d/dp5/src/biomart-perl/conf/registryURLPointer.xml',
>>'action', 'cached', 'mode', 'memory') called at
>>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/../lib/BioMart/Initializer.pm
>>line 377
>>BioMart::Initializer::init_clean('BioMart::Initializer=HASH(0x2551670)',
>>'registryFile',
>>'/nfs/users/nfs_d/dp5/src/biomart-perl/conf/registryURLPointer.xml',
>>'action', 'cached', 'mode', 'memory') called at
>>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/../lib/BioMart/Initializer.pm
>>line 328
>>BioMart::Initializer::init_cached('BioMart::Initializer=HASH(0x2551670)'
>>, 'registryFile',
>>'/nfs/users/nfs_d/dp5/src/biomart-perl/conf/registryURLPointer.xml',
>>'action', 'cached', 'mode', 'memory') called at
>>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/../lib/BioMart/Initializer.pm
>>line 168
>>BioMart::Initializer::_new('BioMart::Initializer=HASH(0x2551670)',
>>'registryFile',
>>'/nfs/users/nfs_d/dp5/src/biomart-perl/conf/registryURLPointer.xml',
>>'action', 'cached', 'mode', 'memory') called at
>>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/../lib/BioMart/RootI.pm line
>>64 BioMart::RootI::new('BioMart::Initializer', 'registryFile',
>>'/nfs/users/nfs_d/dp5/src/biomart-perl/conf/registryURLPointer.xml',
>>'action', 'cached', 'mode', 'memory') called at
>>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/configureBioMart.pl line 332
>>eval {...} at
>>/nfs/users/nfs_d/dp5/src/biomart-perl/bin/configureBioMart.pl line 331
>>
>>
>>
>>-----Original Message-----
>>From: Elena Rivkin [mailto:[hidden email]]
>>Sent: 19 August 2011 16:19
>>To: Dirk Paul
>>Subject: Re: [Ensembl #228924] Set up environment for Ensembl BioMart
>>Perl API
>>
>>Can you please post your question again?
>>Thank you.
>>Elena Rivkin, PhD
>>Outreach and Training Coordinator, Informatics and Bio-computing
>>
>>Ontario Institute for Cancer Research
>>MaRS Centre, South Tower
>>101 College Street, Suite 800
>>Toronto, Ontario, Canada M5G 0A3
>>
>>Tel: 647-258-4316
>>Toll-free: 1-866-678-6427
>>www.oicr.on.ca
>>
>>This message and any attachments may contain confidential and/or
>>privileged information for the sole use of the intended recipient. Any
>>review or distribution by anyone other than the person for whom it was
>>originally intended is strictly prohibited. If you have received this
>>message in error, please contact the sender and delete all copies.
>>Opinions, conclusions or other information contained in this message may
>>not be that of the organization.
>>
>>
>>
>>
>>
>>
>>On 11-08-19 11:05 AM, "Bert Overduin via RT" <[hidden email]>
>>wrote:
>>
>>>Hello Dirk Paul,
>>>
>>>I am forwarding your question to the BioMart group at OICR, as we are
>>not
>>>the right people to ask these technical questions, I am afraid.
>>>
>>>--
>>>With kind regards,
>>>Bert Overduin, Ph.D.
>>>(Ensembl Helpdesk)
>>>
>>>Mailing lists: http://www.ensembl.org/info/about/contact/mailing.html
>>>Blog: http://www.ensembl.info
>>>YouTube: http://www.youtube.com/user/EnsemblHelpdesk
>>>Facebook: http://www.facebook.com/Ensembl.org
>>>Twitter: http://twitter.com/Ensembl
>>>
>>>
>>>
>>>--
>>> The Wellcome Trust Sanger Institute is operated by Genome Research
>>> Limited, a charity registered in England with number 1021457 and a
>>> company registered in England with number 2742969, whose registered
>>> office is 215 Euston Road, London, NW1 2BE.
>>
>>
>>
>>--
>> The Wellcome Trust Sanger Institute is operated by Genome Research
>> Limited, a charity registered in England with number 1021457 and a
>> company registered in England with number 2742969, whose registered
>> office is 215 Euston Road, London, NW1 2BE.
>
>_______________________________________________
>Users mailing list
>[hidden email]
>https://lists.biomart.org/mailman/listinfo/users

_______________________________________________
Users mailing list
[hidden email]
https://lists.biomart.org/mailman/listinfo/users