Gbrowse Installation And Setting Issue.
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Gbrowse Installation And Setting Issue.
by Giuseppe Calamita
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Hello,
I'm a webmaster for a Government Insitute about Plant Genetic tring to install and use for the first time your Gbrowse by following the available tutorials: http://gmod.org/wiki/GBrowse_Install_HOWTO#The_NetInstaller I'm on windows vista business and I have installed all the stuff needed to see working Gbrowse8 Activeperl, Bioperl, etc). The only weak point is about the installation folders of Gbrowse. Even if they are pointed out in the wiki I'm not sure about located them for installation. I have tried to install anyway and it seems the only thing does not work is when I click on the: "Example DatabaseAn example in-memory database for S. cerevisiae chromosomes 1 and 2 has been installed for you. Try it at this URL: http://localhost/cgi-bin/gbrowse/yeast "It simply does not work. The other folders seems ok. I have attched the Apache LOG file and it seems is something about GCI scripts lacking. These are the folders already verified as in your: http://localhost/genomes/gbrowse/tutorial/tutorial.html of the databases: C:\xampp\htdocs\genomes\gbrowse\databases\volvox and of the configurations: C:\xampp\htdocs\gbrowse.conf. This is the folder of the Apache root: C:\xampp\apache. This is the folder of the HTDOCS: C:\xampp\htdocs. Thank you in advance. mr. G. CALAMITA October, 7th 2009. ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Gbrowse Installation And Setting Issue.
by Scott Cain-4
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Hi Giuseppe,
This is a rather non-standard install of GBrowse on Windows, so it may be rather difficult to debug the installation remotely. I have two guesses: * your apache conf file, httpd.conf, does not know what you are using as a DOCROOT. What does httpd.conf have in it for DocumentRoot? What about cgi handling; how is it configured in your apache? * When you did the installation, you might not have set all of the paths to the various locations correctly. If that's the case, you may need to reinstall, making sure to get those right (they may need to be quoted if there are spaces in the paths). In any event, unless you have a compelling reason to use Windows, I would suggest a Linux server; significantly more people on the mailing list have experience with Linux installations than Windows. Scott On Oct 7, 2009, at 11:10 AM, Giuseppe Calamita wrote: > Hello, > > > > I'm a webmaster for a Government Insitute about Plant Genetic tring > to install and use for the first time your Gbrowse by following the > available tutorials: http://gmod.org/wiki/GBrowse_Install_HOWTO#The_NetInstaller > > I'm on windows vista business and I have installed all the stuff > needed to see working Gbrowse8 Activeperl, Bioperl, etc). The only > weak point is about the installation folders of Gbrowse. Even if > they are pointed out in the wiki I'm not sure about located them for > installation. > > I have tried to install anyway and it seems the only thing does not > work is when I click on the: > "Example Database > An example in-memory database for S. cerevisiae chromosomes 1 and 2 > has been installed for you. Try it at this URL: > > http://localhost/cgi-bin/gbrowse/yeast "It simply does not work. > > The other folders seems ok. > > I have attched the Apache LOG file and it seems is something about > GCI scripts lacking. > > These are the folders already verified as in your: http://localhost/genomes/gbrowse/tutorial/tutorial.html > of the databases: C:\xampp\htdocs\genomes\gbrowse\databases\volvox > and of the configurations: C:\xampp\htdocs\gbrowse.conf. > > This is the folder of the Apache root: C:\xampp\apache. > This is the folder of the HTDOCS: C:\xampp\htdocs. > > > > Thank you in advance. > > > > mr. G. CALAMITA > October, 7th 2009. > > > <Apache > LOG > .doc > > > ------------------------------------------------------------------------------ > Come build with us! The BlackBerry(R) Developer Conference in SF, CA > is the only developer event you need to attend this year. Jumpstart > your > developing skills, take BlackBerry mobile applications to market and > stay > ahead of the curve. Join us from November 9 - 12, 2009. Register now! > http://p.sf.net/sfu/devconference_______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse ----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Gbrowse Installation And Setting Issue.
by Scott Cain-4
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Hi Giuseppe,
I borrowed a Vista computer from a trusting friend and installed XAMPP. It doesn't appear to have libgd, or any way of installing libgd. Without that, you won't be able to use GBrowse. I would suggest dump XAMPP and getting ActiveState perl and the Apache installer from apache.org. As a side note, I did find php_gd2.dll, which is likely a library for php to use libgd, but is probably not general purpose (and the perl CPAN shell was unable to find it). Scott On Thu, Oct 8, 2009 at 11:30 AM, Scott Cain <scott@...> wrote: > Hello Giuseppe, > > Please hit "reply all" when replying so the GBrowse mailing list can stay in > the loop; I don't generally use Windows, so if someone else on the mailing > list is familiar with the set up you are describing, they can help too. > > Now I think we are starting to get somewhere, since I've realized at least > part of what I didn't understand: I've never heard of XAMPP, which means the > GBrowse installer doesn't know to look for it. It assumes that you > installed Apache via the installer that Apache provides, and puts the files > in C:\Program Files\. I still contend that installing using the Apache > installer might be a better way to go. > > About the installation, when it is asking you about your htdocs, cgi-bin and > conf directories, it is asking where they are, though if you give it > directories that don't exist, in most cases, it will create them for you. > That can cause some people confusion, as after they ran the installer once, > the directories may be there (since the installer created them), but they > may not be in the right place. My guess from the picture of your file > structure is that the apache root is C:\xampp\apache, and everything would > get installed relative to that: C:\xampp\apache\htdocs, > C:\xampp\apache\cgi-bin, C:\xampp\apache\conf (sorry I didn't see that image > in the last email you sent). > > I'm sorry that this has caused you problems; since GBrowse is a > cross-platform application, and platforms can vary widely, it is difficult > to anticipate what will happen in every instance. For that reason, it is > also not realistic for us to write an uninstaller. Just deleting the > folders that it creates is generally sufficient. > > Scott > > > On Oct 8, 2009, at 11:06 AM, Giuseppe Calamita wrote: > >> Hello, I do not know what do you mean by: "...to reinstall Apache and Perl >> in the default locations ..."; the situation is the following: >> • I have installed a XAMPP package which contains Apache (MySQL, >> PHP, etc.); it has been installed in the following: C:\XAMPP\Apache as you >> may see in the image with the folder ramification; >> • the Perl folder is: C.\Perl >> • yes I was using the gbrowse_netinstall.pl; I did not realize how >> to make a manual installation; >> "Apache root directory (enter '' for none)? >> Apache conf directory? [/usr/local/apache/conf] should probably be >> C:\xampp\conf (assuming that's where you put it) >> Apache htdocs directory? [/usr/local/apache/htdocs] C:\xampp\htdocs >> Apache cgibin directory? [/usr/local/apache/cgi-bin] C:\xampp\cgi-bin >> GBrowse root for static files? [gbrowse]" >> >> The question I keep on wondering is: all of the previous installation >> requests are about directory to be created in the installation process or >> are about directory already existing? Which are the existing ones and which >> have to be created? >> >> About my attached images has to be considered I have installed Gbrowse 2 >> or 3 times with gbrowse_netinstall.pl so it may be a little confused the >> folder ramification because some of them has been likely duplicated. >> >> Hence it is necessary an unistallation features of Gbrowse. >> >> >> Bye. >> >> >> mr. G. CALAMITA >> October 8th, 2009 >> >> P.S.: How ever the registration process does not send me the e-mail for >> the confirmation? >> >> >> On Thu, Oct 8, 2009 at 3:46 PM, Scott Cain <scott@...> wrote: >> Hi Giuseppe, >> >> In order for this to help anyone, you need to keep the GBrowse mailing >> list in the loop :-) >> >> First, I don't know if anyone has successfully installed GBrowse on Vista, >> so you may be breaking new ground. That's generally not a place you want to >> be when trying to learn about something. You might want to reinstall Apache >> and Perl in the default locations which should make installation of GBrowse >> quite a bit easier, since you won't have to know how to configure the >> installation process. Also, you haven't mentioned if you are using the net >> install script, gbrowse_netinstall.pl. If you aren't using the default >> installation locations for Apache and Perl, using it may hinder more than >> help. >> >> About the table you sent that lists and explains the various command line >> flags for directory settings you can use when installing GBrowse: The table >> already has descriptions of each of the items except for the last (BIN). Is >> the problem that you don't understand those descriptions (I'll attach it to >> my email so that it will go back to the mailing list)? That certainly will >> make it difficult for you to answer the installers questions (and to know >> when the installer isn't asking all the questions you need to answer). >> That's the reason for my suggestion about Apache and Perl above. The last >> option in that table, BIN, is the directory where utility scripts that get >> installed by GBrowse will go. These include a script call wiggle2gff.pl >> that converts wiggle files to GFF and WIG files as well as a utility to take >> UCSC gene table files and convert them to GFF. On Windows, that will >> typically be C:\perl\bin, assuming you've installed perl in the default >> location. >> >> Finally, about your httpd.conf file: it looks consistent with the way >> you've indicated that you want it set up. When you installed GBrowse, did >> you answer the questions about where to install things consistent with this? >> It would look something like this: >> >> Apache root directory (enter '' for none)? >> Apache conf directory? [/usr/local/apache/conf] should probably be >> C:\xampp\conf (assuming that's where you put it) >> Apache htdocs directory? [/usr/local/apache/htdocs] C:\xampp\htdocs >> Apache cgibin directory? [/usr/local/apache/cgi-bin] C:\xampp\cgi-bin >> GBrowse root for static files? [gbrowse] >> >> The other two can probably remain with the default (though I'm not >> positive about the apache root directory; you might want to answer >> C:\xampp). >> >> Good luck! >> Scott >> >> >> >> >> >> >> >> On Oct 8, 2009, at 6:31 AM, Giuseppe Calamita wrote: >> >> Hello, I have attached the httpd.conf and an image with the folder >> ramification where are the HTDOC, CGBIN folder and so on. >> >> There is also an image of the folders involved in the installation taken >> from the wiki; those folders confuse me because I do not know which I have >> to consider already existing (in my computer) and which do not. I would like >> you explain, folder per folder, the topic please. I hope my post would be >> useful for all of the windows vista users so those users will enlarge the >> base of the Gbrowse utilizers. >> >> >> Bye. >> >> >> mr. G. CALAMITA >> October, 8th 2009. >> >> >> On Wed, Oct 7, 2009 at 6:01 PM, Scott Cain <scott@...> wrote: >> Hi Giuseppe, >> >> This is a rather non-standard install of GBrowse on Windows, so it may be >> rather difficult to debug the installation remotely. I have two guesses: >> >> * your apache conf file, httpd.conf, does not know what you are using as a >> DOCROOT. What does httpd.conf have in it for DocumentRoot? What about cgi >> handling; how is it configured in your apache? >> >> * When you did the installation, you might not have set all of the paths >> to the various locations correctly. If that's the case, you may need to >> reinstall, making sure to get those right (they may need to be quoted if >> there are spaces in the paths). >> >> In any event, unless you have a compelling reason to use Windows, I would >> suggest a Linux server; significantly more people on the mailing list have >> experience with Linux installations than Windows. >> >> Scott >> >> >> >> On Oct 7, 2009, at 11:10 AM, Giuseppe Calamita wrote: >> >> Hello, >> >> >> >> I'm a webmaster for a Government Insitute about Plant Genetic tring to >> install and use for the first time your Gbrowse by following the available >> tutorials: http://gmod.org/wiki/GBrowse_Install_HOWTO#The_NetInstaller >> >> I'm on windows vista business and I have installed all the stuff needed to >> see working Gbrowse8 Activeperl, Bioperl, etc). The only weak point is about >> the installation folders of Gbrowse. Even if they are pointed out in the >> wiki I'm not sure about located them for installation. >> >> I have tried to install anyway and it seems the only thing does not work >> is when I click on the: >> "Example Database >> An example in-memory database for S. cerevisiae chromosomes 1 and 2 has >> been installed for you. Try it at this URL: >> >> http://localhost/cgi-bin/gbrowse/yeast "It simply does not work. >> >> The other folders seems ok. >> >> I have attched the Apache LOG file and it seems is something about GCI >> scripts lacking. >> >> These are the folders already verified as in your: >> http://localhost/genomes/gbrowse/tutorial/tutorial.html of the databases: >> C:\xampp\htdocs\genomes\gbrowse\databases\volvox >> and of the configurations: C:\xampp\htdocs\gbrowse.conf. >> >> This is the folder of the Apache root: C:\xampp\apache. >> This is the folder of the HTDOCS: C:\xampp\htdocs. >> >> >> >> Thank you in advance. >> >> >> >> mr. G. CALAMITA >> October, 7th 2009. >> >> >> <Apache >> LOG.doc>------------------------------------------------------------------------------ >> Come build with us! The BlackBerry(R) Developer Conference in SF, CA >> is the only developer event you need to attend this year. Jumpstart your >> developing skills, take BlackBerry mobile applications to market and stay >> ahead of the curve. Join us from November 9 - 12, 2009. Register now! >> >> http://p.sf.net/sfu/devconference_______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> ----------------------------------------------------------------------- >> Scott Cain, Ph. D. scott at scottcain dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> >> >> >> >> <httpdconf><tree.JPG><folderssetting.JPG> >> >> ----------------------------------------------------------------------- >> Scott Cain, Ph. D. scott at scottcain dot net >> GMOD Coordinator (http://gmod.org/) 216-392-3087 >> Ontario Institute for Cancer Research >> >> >> >> >> >> > > ----------------------------------------------------------------------- > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > > > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Gbrowse Installation And Setting Issue.
by Giuseppe Calamita
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Hello, strange thing; I have to tell you I did the same you did with vista, with Ubuntu.
About the Apache folders:
Anyway to see a Gbrowse working on vista is necessary for enlarge the base of utilizers and not to exclude all of those scientists or researchers compelled to use it. mr. G. CALAMITA October 9th, 2009. On Thu, Oct 8, 2009 at 8:33 PM, Scott Cain <scott@...> wrote: Hi Giuseppe, ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Gbrowse Installation And Setting Issue.
by Scott Cain-4
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Hi Giuseppe,
See my comments below. Scott On Oct 9, 2009, at 9:01 AM, Giuseppe Calamita wrote: > Hello, strange thing; I have to tell you I did the same you did with > vista, with Ubuntu. > About the Apache folders: > • I host a website and the folder where it is located in order to > be accessed via a browser is: c:\xampp\htdocs\www.mysite.it any > other locations will cause the browser a fault; (in the broser I > have to write: "localhost/www.mysite.it" to access it); Right, because in xampp, the webservers DOCROOT is C:\xampp\htdocs. If you take the contents of your www.mysite.it folder and move it up into the htdocs folder, you can get to it via http://localhost/. > • said that, I'm still confused about where the folder (cgi-bin, > htdocs, apache ...) location may be; there are more than one folder > related to cgi-bin (or BIN) for example and the problem is more > difficult because of all the previous installations (two); Don't pay much attention to BIN: the scripts that go there are only used for a small subset of things that people use GBrowse for, and none of it is needed for GBrowse's proper function. There are other directories than HTDOCS, CGI-BIN and CONF, which is where the perl libraries go, but generally the system default is the right thing to do (that is, they will go where perl wants them to go). > In UBUNTU I focused my attention on the folders ramification of the > Gbrowse installation - in order to attempt to understand something > more useful to fix my issue - and I noticed that: > • the folder where a website is rendered (accessed via browser) is > the following: ...\var\WWW\www.site.com In ubuntu the webservers DOCROOT is /var/www, so an index.html file that is put in that directory is what you will see if you go to http://localhost/ . > • there I found the index.html file and the Gbrowse folder with the > Databases, Contrib, Docs, Images, TMP, etc folders in it; Right, the default thing for GBrowse to do is to go into a directory under the DOCROOT so that the index.html file in the gbrowse directory is what you see when you go to http://localhost/gbrowse > Very intersting your attempt to use windows vista; from my side I'm > not a skilled developper so I will try to test if the issue may be > related to the folders or to the lacking of some packages/component > as you have noticed. > > Anyway to see a Gbrowse working on vista is necessary for enlarge > the base of utilizers and not to exclude all of those scientists or > researchers compelled to use it. > Again, I'm not saying Vista won't work (I don't know if it will), I'm saying: * XAMPP on Windows absolutely will not work unless you find a way to compile libgd and the GD perl module, which is not currently possible with the "out of the box" XAMPP. You may be able to run GBrowse on Vista with ActiveState perl and the Apache installer that comes from apache.org (you definitely can do that on XP). * The vast majority of users that run GBrowse do so on linux systems of some sort, and there are more MacOS X servers running GBrowse than Windows, so if you are trying to run GBrowse on Windows, you can expect some bumps and less help on the mailing list (because there are fewer people who know anything about it). Scott > > > mr. G. CALAMITA > October 9th, 2009. > > > > On Thu, Oct 8, 2009 at 8:33 PM, Scott Cain <scott@...> > wrote: > Hi Giuseppe, > > I borrowed a Vista computer from a trusting friend and installed > XAMPP. It doesn't appear to have libgd, or any way of installing > libgd. Without that, you won't be able to use GBrowse. I would > suggest dump XAMPP and getting ActiveState perl and the Apache > installer from apache.org. > > As a side note, I did find php_gd2.dll, which is likely a library for > php to use libgd, but is probably not general purpose (and the perl > CPAN shell was unable to find it). > > Scott > > > On Thu, Oct 8, 2009 at 11:30 AM, Scott Cain <scott@...> > wrote: > > Hello Giuseppe, > > > > Please hit "reply all" when replying so the GBrowse mailing list > can stay in > > the loop; I don't generally use Windows, so if someone else on the > mailing > > list is familiar with the set up you are describing, they can help > too. > > > > Now I think we are starting to get somewhere, since I've realized > at least > > part of what I didn't understand: I've never heard of XAMPP, which > means the > > GBrowse installer doesn't know to look for it. It assumes that you > > installed Apache via the installer that Apache provides, and puts > the files > > in C:\Program Files\. I still contend that installing using the > Apache > > installer might be a better way to go. > > > > About the installation, when it is asking you about your htdocs, > cgi-bin and > > conf directories, it is asking where they are, though if you give it > > directories that don't exist, in most cases, it will create them > for you. > > That can cause some people confusion, as after they ran the > installer once, > > the directories may be there (since the installer created them), > but they > > may not be in the right place. My guess from the picture of your > file > > structure is that the apache root is C:\xampp\apache, and > everything would > > get installed relative to that: C:\xampp\apache\htdocs, > > C:\xampp\apache\cgi-bin, C:\xampp\apache\conf (sorry I didn't see > that image > > in the last email you sent). > > > > I'm sorry that this has caused you problems; since GBrowse is a > > cross-platform application, and platforms can vary widely, it is > difficult > > to anticipate what will happen in every instance. For that > reason, it is > > also not realistic for us to write an uninstaller. Just deleting > the > > folders that it creates is generally sufficient. > > > > Scott > > > > > > On Oct 8, 2009, at 11:06 AM, Giuseppe Calamita wrote: > > > >> Hello, I do not know what do you mean by: "...to reinstall Apache > and Perl > >> in the default locations ..."; the situation is the following: > >> • I have installed a XAMPP package which contains Apache > (MySQL, > >> PHP, etc.); it has been installed in the following: C:\XAMPP > \Apache as you > >> may see in the image with the folder ramification; > >> • the Perl folder is: C.\Perl > >> • yes I was using the gbrowse_netinstall.pl; I did not > realize how > >> to make a manual installation; > >> "Apache root directory (enter '' for none)? > >> Apache conf directory? [/usr/local/apache/conf] should probably > be > >> C:\xampp\conf (assuming that's where you put it) > >> Apache htdocs directory? [/usr/local/apache/htdocs] C:\xampp > \htdocs > >> Apache cgibin directory? [/usr/local/apache/cgi-bin] C:\xampp > \cgi-bin > >> GBrowse root for static files? [gbrowse]" > >> > >> The question I keep on wondering is: all of the previous > installation > >> requests are about directory to be created in the installation > process or > >> are about directory already existing? Which are the existing ones > and which > >> have to be created? > >> > >> About my attached images has to be considered I have installed > Gbrowse 2 > >> or 3 times with gbrowse_netinstall.pl so it may be a little > confused the > >> folder ramification because some of them has been likely > duplicated. > >> > >> Hence it is necessary an unistallation features of Gbrowse. > >> > >> > >> Bye. > >> > >> > >> mr. G. CALAMITA > >> October 8th, 2009 > >> > >> P.S.: How ever the registration process does not send me the e- > mail for > >> the confirmation? > >> > >> > >> On Thu, Oct 8, 2009 at 3:46 PM, Scott Cain <scott@...> > wrote: > >> Hi Giuseppe, > >> > >> In order for this to help anyone, you need to keep the GBrowse > mailing > >> list in the loop :-) > >> > >> First, I don't know if anyone has successfully installed GBrowse > on Vista, > >> so you may be breaking new ground. That's generally not a place > you want to > >> be when trying to learn about something. You might want to > reinstall Apache > >> and Perl in the default locations which should make installation > of GBrowse > >> quite a bit easier, since you won't have to know how to configure > the > >> installation process. Also, you haven't mentioned if you are > using the net > >> install script, gbrowse_netinstall.pl. If you aren't using the > default > >> installation locations for Apache and Perl, using it may hinder > more than > >> help. > >> > >> About the table you sent that lists and explains the various > command line > >> flags for directory settings you can use when installing GBrowse: > The table > >> already has descriptions of each of the items except for the last > (BIN). Is > >> the problem that you don't understand those descriptions (I'll > attach it to > >> my email so that it will go back to the mailing list)? That > certainly will > >> make it difficult for you to answer the installers questions (and > to know > >> when the installer isn't asking all the questions you need to > answer). > >> That's the reason for my suggestion about Apache and Perl > above. The last > >> option in that table, BIN, is the directory where utility scripts > that get > >> installed by GBrowse will go. These include a script call > wiggle2gff.pl > >> that converts wiggle files to GFF and WIG files as well as a > utility to take > >> UCSC gene table files and convert them to GFF. On Windows, that > will > >> typically be C:\perl\bin, assuming you've installed perl in the > default > >> location. > >> > >> Finally, about your httpd.conf file: it looks consistent with the > way > >> you've indicated that you want it set up. When you installed > GBrowse, did > >> you answer the questions about where to install things consistent > with this? > >> It would look something like this: > >> > >> Apache root directory (enter '' for none)? > >> Apache conf directory? [/usr/local/apache/conf] should probably > be > >> C:\xampp\conf (assuming that's where you put it) > >> Apache htdocs directory? [/usr/local/apache/htdocs] C:\xampp > \htdocs > >> Apache cgibin directory? [/usr/local/apache/cgi-bin] C:\xampp > \cgi-bin > >> GBrowse root for static files? [gbrowse] > >> > >> The other two can probably remain with the default (though I'm not > >> positive about the apache root directory; you might want to answer > >> C:\xampp). > >> > >> Good luck! > >> Scott > >> > >> > >> > >> > >> > >> > >> > >> On Oct 8, 2009, at 6:31 AM, Giuseppe Calamita wrote: > >> > >> Hello, I have attached the httpd.conf and an image with the folder > >> ramification where are the HTDOC, CGBIN folder and so on. > >> > >> There is also an image of the folders involved in the > installation taken > >> from the wiki; those folders confuse me because I do not know > which I have > >> to consider already existing (in my computer) and which do not. I > would like > >> you explain, folder per folder, the topic please. I hope my post > would be > >> useful for all of the windows vista users so those users will > enlarge the > >> base of the Gbrowse utilizers. > >> > >> > >> Bye. > >> > >> > >> mr. G. CALAMITA > >> October, 8th 2009. > >> > >> > >> On Wed, Oct 7, 2009 at 6:01 PM, Scott Cain <scott@...> > wrote: > >> Hi Giuseppe, > >> > >> This is a rather non-standard install of GBrowse on Windows, so > it may be > >> rather difficult to debug the installation remotely. I have two > guesses: > >> > >> * your apache conf file, httpd.conf, does not know what you are > using as a > >> DOCROOT. What does httpd.conf have in it for DocumentRoot? What > about cgi > >> handling; how is it configured in your apache? > >> > >> * When you did the installation, you might not have set all of > the paths > >> to the various locations correctly. If that's the case, you may > need to > >> reinstall, making sure to get those right (they may need to be > quoted if > >> there are spaces in the paths). > >> > >> In any event, unless you have a compelling reason to use Windows, > I would > >> suggest a Linux server; significantly more people on the mailing > list have > >> experience with Linux installations than Windows. > >> > >> Scott > >> > >> > >> > >> On Oct 7, 2009, at 11:10 AM, Giuseppe Calamita wrote: > >> > >> Hello, > >> > >> > >> > >> I'm a webmaster for a Government Insitute about Plant Genetic > tring to > >> install and use for the first time your Gbrowse by following the > available > >> tutorials: http://gmod.org/wiki/GBrowse_Install_HOWTO#The_NetInstaller > >> > >> I'm on windows vista business and I have installed all the stuff > needed to > >> see working Gbrowse8 Activeperl, Bioperl, etc). The only weak > point is about > >> the installation folders of Gbrowse. Even if they are pointed out > in the > >> wiki I'm not sure about located them for installation. > >> > >> I have tried to install anyway and it seems the only thing does > not work > >> is when I click on the: > >> "Example Database > >> An example in-memory database for S. cerevisiae chromosomes 1 and > 2 has > >> been installed for you. Try it at this URL: > >> > >> http://localhost/cgi-bin/gbrowse/yeast "It simply does not work. > >> > >> The other folders seems ok. > >> > >> I have attched the Apache LOG file and it seems is something > about GCI > >> scripts lacking. > >> > >> These are the folders already verified as in your: > >> http://localhost/genomes/gbrowse/tutorial/tutorial.html of the > databases: > >> C:\xampp\htdocs\genomes\gbrowse\databases\volvox > >> and of the configurations: C:\xampp\htdocs\gbrowse.conf. > >> > >> This is the folder of the Apache root: C:\xampp\apache. > >> This is the folder of the HTDOCS: C:\xampp\htdocs. > >> > >> > >> > >> Thank you in advance. > >> > >> > >> > >> mr. G. CALAMITA > >> October, 7th 2009. > >> > >> > >> <Apache > >> > LOG > .doc > > > ------------------------------------------------------------------------------ > >> Come build with us! The BlackBerry(R) Developer Conference in SF, > CA > >> is the only developer event you need to attend this year. > Jumpstart your > >> developing skills, take BlackBerry mobile applications to market > and stay > >> ahead of the curve. Join us from November 9 - 12, 2009. Register > now! > >> > >> http://p.sf.net/sfu/devconference_______________________________________________ > >> Gmod-gbrowse mailing list > >> Gmod-gbrowse@... > >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > >> > >> > ----------------------------------------------------------------------- > >> Scott Cain, Ph. D. scott at scottcain dot net > >> GMOD Coordinator (http://gmod.org/) 216-392-3087 > >> Ontario Institute for Cancer Research > >> > >> > >> > >> > >> > >> <httpdconf><tree.JPG><folderssetting.JPG> > >> > >> > ----------------------------------------------------------------------- > >> Scott Cain, Ph. D. scott at scottcain dot net > >> GMOD Coordinator (http://gmod.org/) 216-392-3087 > >> Ontario Institute for Cancer Research > >> > >> > >> > >> > >> > >> > > > > > ----------------------------------------------------------------------- > > Scott Cain, Ph. D. scott at scottcain dot net > > GMOD Coordinator (http://gmod.org/) 216-392-3087 > > Ontario Institute for Cancer Research > > > > > > > > > > > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > ----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Gbrowse Installation And Setting Issue.
by Giuseppe Calamita
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* XAMPP on Windows absolutely will not work unless you find a way to compile libgd and the GD perl module, which is not currently possible with the "out of the box" XAMPP. You may be able to run GBrowse on Vista with ActiveState perl and the Apache installer that comes from apache.org (you definitely can do that on XP). From my Perl Package Manager I see already installed GD module; nothing there about libgd. Mine is ActiveState perl, as I installed it following the prerequisites to install Gbrowse in the wiki. Of vourse I'll try the attempt to install Apache, stopping the xampp Apache service before. A search in CPAN about libgd gave me GD as results. If you would have the chance to attempt all of those we said on your windows vista ...:-) Bye. mr. G. CALAMITA October, 9th 2009 On Fri, Oct 9, 2009 at 4:27 PM, Scott Cain <scott@...> wrote: Hi Giuseppe, ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Gbrowse Installation And Setting Issue.
by Scott Cain-4
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Ah, I see, you have both the perl installed by XAMPP and one from
ActiveState. That sounds like a recipe for disaster too, though it may work; I have no idea. When you install GD with ppm in ActiveState, it installs libgd for you. Scott On Oct 9, 2009, at 10:54 AM, Giuseppe Calamita wrote: > * XAMPP on Windows absolutely will not work unless you find a way to > compile libgd and the GD perl module, which is not currently > possible with the "out of the box" XAMPP. You may be able to run > GBrowse on Vista with ActiveState perl and the Apache installer that > comes from apache.org (you definitely can do that on XP). > > From my Perl Package Manager I see already installed GD module; > nothing there about libgd. Mine is ActiveState perl, as I installed > it following the prerequisites to install Gbrowse in the wiki. > > Of vourse I'll try the attempt to install Apache, stopping the xampp > Apache service before. > > A search in CPAN about libgd gave me GD as results. > If you would have the chance to attempt all of those we said on your > windows vista ...:-) > > Bye. > > > mr. G. CALAMITA > October, 9th 2009 > > > > On Fri, Oct 9, 2009 at 4:27 PM, Scott Cain <scott@...> > wrote: > Hi Giuseppe, > > See my comments below. > > Scott > > > > On Oct 9, 2009, at 9:01 AM, Giuseppe Calamita wrote: > > Hello, strange thing; I have to tell you I did the same you did with > vista, with Ubuntu. > About the Apache folders: > • I host a website and the folder where it is located in > order to be accessed via a browser is: c:\xampp\htdocs\www.mysite.it > any other locations will cause the browser a fault; (in the broser I > have to write: "localhost/www.mysite.it" to access it); > > Right, because in xampp, the webservers DOCROOT is C:\xampp\htdocs. > If you take the contents of your www.mysite.it folder and move it up > into the htdocs folder, you can get to it via http://localhost/. > > • said that, I'm still confused about where the folder (cgi- > bin, htdocs, apache ...) location may be; there are more than one > folder related to cgi-bin (or BIN) for example and the problem is > more difficult because of all the previous installations (two); > > Don't pay much attention to BIN: the scripts that go there are only > used for a small subset of things that people use GBrowse for, and > none of it is needed for GBrowse's proper function. There are other > directories than HTDOCS, CGI-BIN and CONF, which is where the perl > libraries go, but generally the system default is the right thing to > do (that is, they will go where perl wants them to go). > > > In UBUNTU I focused my attention on the folders ramification of the > Gbrowse installation - in order to attempt to understand something > more useful to fix my issue - and I noticed that: > • the folder where a website is rendered (accessed via > browser) is the following: ...\var\WWW\www.site.com > > In ubuntu the webservers DOCROOT is /var/www, so an index.html file > that is put in that directory is what you will see if you go to http://localhost/ > . > > • there I found the index.html file and the Gbrowse folder > with the Databases, Contrib, Docs, Images, TMP, etc folders in it; > > Right, the default thing for GBrowse to do is to go into a directory > under the DOCROOT so that the index.html file in the gbrowse > directory is what you see when you go to http://localhost/gbrowse > > > Very intersting your attempt to use windows vista; from my side I'm > not a skilled developper so I will try to test if the issue may be > related to the folders or to the lacking of some packages/component > as you have noticed. > > Anyway to see a Gbrowse working on vista is necessary for enlarge > the base of utilizers and not to exclude all of those scientists or > researchers compelled to use it. > > Again, I'm not saying Vista won't work (I don't know if it will), > I'm saying: > > * XAMPP on Windows absolutely will not work unless you find a way to > compile libgd and the GD perl module, which is not currently > possible with the "out of the box" XAMPP. You may be able to run > GBrowse on Vista with ActiveState perl and the Apache installer that > comes from apache.org (you definitely can do that on XP). > > * The vast majority of users that run GBrowse do so on linux systems > of some sort, and there are more MacOS X servers running GBrowse > than Windows, so if you are trying to run GBrowse on Windows, you > can expect some bumps and less help on the mailing list (because > there are fewer people who know anything about it). > > Scott > > > > > mr. G. CALAMITA > October 9th, 2009. > > > > On Thu, Oct 8, 2009 at 8:33 PM, Scott Cain <scott@...> > wrote: > Hi Giuseppe, > > I borrowed a Vista computer from a trusting friend and installed > XAMPP. It doesn't appear to have libgd, or any way of installing > libgd. Without that, you won't be able to use GBrowse. I would > suggest dump XAMPP and getting ActiveState perl and the Apache > installer from apache.org. > > As a side note, I did find php_gd2.dll, which is likely a library for > php to use libgd, but is probably not general purpose (and the perl > CPAN shell was unable to find it). > > Scott > > > On Thu, Oct 8, 2009 at 11:30 AM, Scott Cain <scott@...> > wrote: > > Hello Giuseppe, > > > > Please hit "reply all" when replying so the GBrowse mailing list > can stay in > > the loop; I don't generally use Windows, so if someone else on the > mailing > > list is familiar with the set up you are describing, they can help > too. > > > > Now I think we are starting to get somewhere, since I've realized > at least > > part of what I didn't understand: I've never heard of XAMPP, which > means the > > GBrowse installer doesn't know to look for it. It assumes that you > > installed Apache via the installer that Apache provides, and puts > the files > > in C:\Program Files\. I still contend that installing using the > Apache > > installer might be a better way to go. > > > > About the installation, when it is asking you about your htdocs, > cgi-bin and > > conf directories, it is asking where they are, though if you give it > > directories that don't exist, in most cases, it will create them > for you. > > That can cause some people confusion, as after they ran the > installer once, > > the directories may be there (since the installer created them), > but they > > may not be in the right place. My guess from the picture of your > file > > structure is that the apache root is C:\xampp\apache, and > everything would > > get installed relative to that: C:\xampp\apache\htdocs, > > C:\xampp\apache\cgi-bin, C:\xampp\apache\conf (sorry I didn't see > that image > > in the last email you sent). > > > > I'm sorry that this has caused you problems; since GBrowse is a > > cross-platform application, and platforms can vary widely, it is > difficult > > to anticipate what will happen in every instance. For that > reason, it is > > also not realistic for us to write an uninstaller. Just deleting > the > > folders that it creates is generally sufficient. > > > > Scott > > > > > > On Oct 8, 2009, at 11:06 AM, Giuseppe Calamita wrote: > > > >> Hello, I do not know what do you mean by: "...to reinstall Apache > and Perl > >> in the default locations ..."; the situation is the following: > >> • I have installed a XAMPP package which contains Apache > (MySQL, > >> PHP, etc.); it has been installed in the following: C:\XAMPP > \Apache as you > >> may see in the image with the folder ramification; > >> • the Perl folder is: C.\Perl > >> • yes I was using the gbrowse_netinstall.pl; I did not > realize how > >> to make a manual installation; > >> "Apache root directory (enter '' for none)? > >> Apache conf directory? [/usr/local/apache/conf] should probably > be > >> C:\xampp\conf (assuming that's where you put it) > >> Apache htdocs directory? [/usr/local/apache/htdocs] C:\xampp > \htdocs > >> Apache cgibin directory? [/usr/local/apache/cgi-bin] C:\xampp > \cgi-bin > >> GBrowse root for static files? [gbrowse]" > >> > >> The question I keep on wondering is: all of the previous > installation > >> requests are about directory to be created in the installation > process or > >> are about directory already existing? Which are the existing ones > and which > >> have to be created? > >> > >> About my attached images has to be considered I have installed > Gbrowse 2 > >> or 3 times with gbrowse_netinstall.pl so it may be a little > confused the > >> folder ramification because some of them has been likely > duplicated. > >> > >> Hence it is necessary an unistallation features of Gbrowse. > >> > >> > >> Bye. > >> > >> > >> mr. G. CALAMITA > >> October 8th, 2009 > >> > >> P.S.: How ever the registration process does not send me the e- > mail for > >> the confirmation? > >> > >> > >> On Thu, Oct 8, 2009 at 3:46 PM, Scott Cain <scott@...> > wrote: > >> Hi Giuseppe, > >> > >> In order for this to help anyone, you need to keep the GBrowse > mailing > >> list in the loop :-) > >> > >> First, I don't know if anyone has successfully installed GBrowse > on Vista, > >> so you may be breaking new ground. That's generally not a place > you want to > >> be when trying to learn about something. You might want to > reinstall Apache > >> and Perl in the default locations which should make installation > of GBrowse > >> quite a bit easier, since you won't have to know how to configure > the > >> installation process. Also, you haven't mentioned if you are > using the net > >> install script, gbrowse_netinstall.pl. If you aren't using the > default > >> installation locations for Apache and Perl, using it may hinder > more than > >> help. > >> > >> About the table you sent that lists and explains the various > command line > >> flags for directory settings you can use when installing GBrowse: > The table > >> already has descriptions of each of the items except for the last > (BIN). Is > >> the problem that you don't understand those descriptions (I'll > attach it to > >> my email so that it will go back to the mailing list)? That > certainly will > >> make it difficult for you to answer the installers questions (and > to know > >> when the installer isn't asking all the questions you need to > answer). > >> That's the reason for my suggestion about Apache and Perl > above. The last > >> option in that table, BIN, is the directory where utility scripts > that get > >> installed by GBrowse will go. These include a script call > wiggle2gff.pl > >> that converts wiggle files to GFF and WIG files as well as a > utility to take > >> UCSC gene table files and convert them to GFF. On Windows, that > will > >> typically be C:\perl\bin, assuming you've installed perl in the > default > >> location. > >> > >> Finally, about your httpd.conf file: it looks consistent with the > way > >> you've indicated that you want it set up. When you installed > GBrowse, did > >> you answer the questions about where to install things consistent > with this? > >> It would look something like this: > >> > >> Apache root directory (enter '' for none)? > >> Apache conf directory? [/usr/local/apache/conf] should probably > be > >> C:\xampp\conf (assuming that's where you put it) > >> Apache htdocs directory? [/usr/local/apache/htdocs] C:\xampp > \htdocs > >> Apache cgibin directory? [/usr/local/apache/cgi-bin] C:\xampp > \cgi-bin > >> GBrowse root for static files? [gbrowse] > >> > >> The other two can probably remain with the default (though I'm not > >> positive about the apache root directory; you might want to answer > >> C:\xampp). > >> > >> Good luck! > >> Scott > >> > >> > >> > >> > >> > >> > >> > >> On Oct 8, 2009, at 6:31 AM, Giuseppe Calamita wrote: > >> > >> Hello, I have attached the httpd.conf and an image with the folder > >> ramification where are the HTDOC, CGBIN folder and so on. > >> > >> There is also an image of the folders involved in the > installation taken > >> from the wiki; those folders confuse me because I do not know > which I have > >> to consider already existing (in my computer) and which do not. I > would like > >> you explain, folder per folder, the topic please. I hope my post > would be > >> useful for all of the windows vista users so those users will > enlarge the > >> base of the Gbrowse utilizers. > >> > >> > >> Bye. > >> > >> > >> mr. G. CALAMITA > >> October, 8th 2009. > >> > >> > >> On Wed, Oct 7, 2009 at 6:01 PM, Scott Cain <scott@...> > wrote: > >> Hi Giuseppe, > >> > >> This is a rather non-standard install of GBrowse on Windows, so > it may be > >> rather difficult to debug the installation remotely. I have two > guesses: > >> > >> * your apache conf file, httpd.conf, does not know what you are > using as a > >> DOCROOT. What does httpd.conf have in it for DocumentRoot? What > about cgi > >> handling; how is it configured in your apache? > >> > >> * When you did the installation, you might not have set all of > the paths > >> to the various locations correctly. If that's the case, you may > need to > >> reinstall, making sure to get those right (they may need to be > quoted if > >> there are spaces in the paths). > >> > >> In any event, unless you have a compelling reason to use Windows, > I would > >> suggest a Linux server; significantly more people on the mailing > list have > >> experience with Linux installations than Windows. > >> > >> Scott > >> > >> > >> > >> On Oct 7, 2009, at 11:10 AM, Giuseppe Calamita wrote: > >> > >> Hello, > >> > >> > >> > >> I'm a webmaster for a Government Insitute about Plant Genetic > tring to > >> install and use for the first time your Gbrowse by following the > available > >> tutorials: http://gmod.org/wiki/GBrowse_Install_HOWTO#The_NetInstaller > >> > >> I'm on windows vista business and I have installed all the stuff > needed to > >> see working Gbrowse8 Activeperl, Bioperl, etc). The only weak > point is about > >> the installation folders of Gbrowse. Even if they are pointed out > in the > >> wiki I'm not sure about located them for installation. > >> > >> I have tried to install anyway and it seems the only thing does > not work > >> is when I click on the: > >> "Example Database > >> An example in-memory database for S. cerevisiae chromosomes 1 and > 2 has > >> been installed for you. Try it at this URL: > >> > >> http://localhost/cgi-bin/gbrowse/yeast "It simply does not work. > >> > >> The other folders seems ok. > >> > >> I have attched the Apache LOG file and it seems is something > about GCI > >> scripts lacking. > >> > >> These are the folders already verified as in your: > >> http://localhost/genomes/gbrowse/tutorial/tutorial.html of the > databases: > >> C:\xampp\htdocs\genomes\gbrowse\databases\volvox > >> and of the configurations: C:\xampp\htdocs\gbrowse.conf. > >> > >> This is the folder of the Apache root: C:\xampp\apache. > >> This is the folder of the HTDOCS: C:\xampp\htdocs. > >> > >> > >> > >> Thank you in advance. > >> > >> > >> > >> mr. G. CALAMITA > >> October, 7th 2009. > >> > >> > >> <Apache > >> > LOG > .doc > > > ------------------------------------------------------------------------------ > >> Come build with us! The BlackBerry(R) Developer Conference in SF, > CA > >> is the only developer event you need to attend this year. > Jumpstart your > >> developing skills, take BlackBerry mobile applications to market > and stay > >> ahead of the curve. Join us from November 9 - 12, 2009. Register > now! > >> > >> http://p.sf.net/sfu/devconference_______________________________________________ > >> Gmod-gbrowse mailing list > >> Gmod-gbrowse@... > >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > >> > >> > ----------------------------------------------------------------------- > >> Scott Cain, Ph. D. scott at scottcain dot net > >> GMOD Coordinator (http://gmod.org/) 216-392-3087 > >> Ontario Institute for Cancer Research > >> > >> > >> > >> > >> > >> <httpdconf><tree.JPG><folderssetting.JPG> > >> > >> > ----------------------------------------------------------------------- > >> Scott Cain, Ph. D. scott at scottcain dot net > >> GMOD Coordinator (http://gmod.org/) 216-392-3087 > >> Ontario Institute for Cancer Research > >> > >> > >> > >> > >> > >> > > > > > ----------------------------------------------------------------------- > > Scott Cain, Ph. D. scott at scottcain dot net > > GMOD Coordinator (http://gmod.org/) 216-392-3087 > > Ontario Institute for Cancer Research > > > > > > > > > > > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at > scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > > ----------------------------------------------------------------------- > Scott Cain, Ph. D. scott at scottcain dot net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > > > > ----------------------------------------------------------------------- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Apache LOG.doc (17K) 
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