Hi Jing
On 23/11/09 3:59 PM, "Jing, Rui" <rui_j...@dfci.harvard.edu> wrote: > 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. Hi Ray, Please refer to section 1.4.1.1 (Apache installation for MartView) of the quick install guide (http://www.biomart.org/install-overview.html) to check apxs2 availability A. > 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; mart-dev@ebi.ac.uk > 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:junjun.zh...@oicr.on.ca] > Sent: Fri 11/20/2009 2:54 PM > To: Jing, Rui; mart-dev@ebi.ac.uk > 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: owner-mart-...@ebi.ac.uk >> [mailto:owner-mart-...@ebi.ac.uk] On Behalf Of Jing, Rui >> Sent: Friday, November 20, 2009 11:34 AM >> To: mart-dev@ebi.ac.uk >> 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 >> >> >> >> The information in this e-mail is intended only for the >> person to whom it is >> addressed. If you believe this e-mail was sent to you in >> error and the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> http://www.partners.org/complianceline . If the e-mail was >> sent to you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> >> >
