Hi,
When I ran: perl bin/configure.pl -r conf/martDBLocation.xml --clean
meesage is the following:
Got usable Apache in /usr/sbin/httpd, probing for version & ModPerl
configuration
Can't exec "/usr/sbin/apxs2": No such file or directory at
/common/home/hge/software/biomart-perl/bin/configureBioMart.pl line 176.
Use of uninitialized value in scalar chomp at
/common/home/hge/software/biomart-perl/bin/configureBioMart.pl line 177.
Use of uninitialized value in concatenation (.) or string at
/common/home/hge/software/biomart-perl/bin/configureBioMart.pl line 179.
Libdir /common/home/hge/software/biomart-perl/lib is not in @INC, adding to @INC
Connection parameters of [My BioMart Database] [ OK ]
I thought it maybe need to install apache, then I tried to install apache under
/home/software/biomart-perl/apache/source/httpd-2.2.14/
cd /home/biomart/apache
mkdir source
cd source
wget http://www.apache.org/dist/httpd/httpd-2.2.14.tar.gz
tar zxvf httpd-2.2.14.tar.gz
cd httpd-2.2.14
./configure \
--enable-deflate \
--prefix=/home/software/biomart-perl/apache \
make install
the error messages like these:
> make install
configure: WARNING: you should use --build, --host, --target
configure: WARNING: you should use --build, --host, --target
checking for chosen layout... Apache
checking for working mkdir -p... yes
checking build system type... Invalid configuration `make': machine `make' not
recognized
configure: error: /bin/sh build/config.sub make failed
Could you please let me know how to solve the problem?
Thanks,
Ray
________________________________
From: Jing, Rui
Sent: Fri 11/20/2009 3:35 PM
To: Junjun Zhang; [email protected]
Subject: RE:
Hi Junjun,
yes, the following command line ran OK with no error messages.
perl bin/configure.pl -r conf/martDBLocation.xml --clean
But when I try to start with: /usr/local/apache/bin/httpd -d $PWD -f
$PWD/conf/httpd.conf
it does not work. I forget the error message. Could you please let me know how
to start apache ?
when apache is started, which link I can visit martview?
Thank you so much!
Ray
________________________________
From: Junjun Zhang [mailto:[email protected]]
Sent: Fri 11/20/2009 2:54 PM
To: Jing, Rui; [email protected]
Subject: RE: [mart-dev] Having problem with web service client access to biomart
Hi Ray,
We need a bit of clarification for the problem, please scroll down.
> -----Original Message-----
> From: [email protected]
> [mailto:[email protected]] On Behalf Of Jing, Rui
> Sent: Friday, November 20, 2009 11:34 AM
> To: [email protected]
> Subject: RE: [mart-dev] Having problem with web service
> client access to biomart
>
> Hello,
>
> I want to config biomart-perl. when I connect with martDBLocation:
> perl bin/configure.pl -r conf/martDBLocation.xml --clean ,
> it looks ok
What do you mean: it looks ok? Do you mean the above command line ran OK with no
error message? If so, after that, did you try start apache, and check martview?
>
> I changed settgins.conf and registryURLPointer.xml.
> v> $PWD/conf/httpd.conf
> It does not work.
Please do not use registryURLPointer, what you need is martDBLocation in order
to make martview work with your own data marts.
Best regards,
Junjun
Could you please let me know how to start
> biomart and make the
> link working
> http://localhost:80/biomart-perl/martview
<http://localhost/biomart-perl/martview>
>
> the followings are my conf (settings.conf and registryURLPointer.xml)
>
> 1. settings.conf
> ################ httpd.conf settings ####################
> [httpdSettings]
> apacheBinary=/usr/local/apache/bin/httpd
> serverHost=localhost
> port=80
> # 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-perl ( which I installed into
> /home/software/biomart-perl/ )
>
> 2. registryURLPointer.xml
>
> name = "central_server"
> host = "localhost"
> port = "80"
> path = ""
> includeMarts = "msd,uniprot"
>
> Thanks,
>
> Ray
>
>
>
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