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Dear Gbrowse
by Luis.Delaye
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Dear Gbrowse, Im trying to install gbrowse ona Windows XP, I followed all installation steps and Im right now in the tutorial. However, I was not able to see the page: http://localhost/cgi-bin/gbrowse/volvox I check for the following instructions in the section: If You are Having Problems... and everything seems to be ok.. I check the Apache server error log and I found this message: [Sat Jun 07 12:17:25 2008] [error] [client 127.0.0.1] script not found or unable to stat: C:/Archivos de programa/Apache Software Foundation/Apache2.2/cgi-bin/gbrowse If you could help me I will appreciate a lot! Best regards! Luis Delaye ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Dear Gbrowse
by Scott Cain-3
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Hi Luis,
Is there a file at the location that the error log reported? If the gbrowse script is not there, where is it? I'm wondering if this is a language problem. I suspect that the installer doesn't know that your application folder is called "Archivos de programa" as opposed to "Program Files". Scott On Sat, 2008-06-07 at 12:28 +0200, Luis.Delaye@... wrote: > Dear Gbrowse, > > I’m trying to install gbrowse ona Windows XP, I followed all > installation steps and I’m right now in the tutorial. However, I was > not able to see the page: > > http://localhost/cgi-bin/gbrowse/volvox > > I check for the following instructions in the section: “If You are > Having Problems...” and everything seems to be ok.. > > I check the Apache server error log and I found this message: > > [Sat Jun 07 12:17:25 2008] [error] [client 127.0.0.1] script not found > or unable to stat: C:/Archivos de programa/Apache Software > Foundation/Apache2.2/cgi-bin/gbrowse > > If you could help me I will appreciate a lot! > > Best regards! > > Luis Delaye > > > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > ------------------------------------------------------------------------ Scott Cain, Ph. D. cain@... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Dear Gbrowse
by Luis.Delaye
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Hi Scott, It works! Thanks. I suscribed to the mailing list. Best! Luis > Hi Luis, > > Please keep your responses on the mailing list so that the conversation > can be archived, and people who are more familiar with Windows can help > when we need it. > > I doubt that C:\usr\local\apache\htdocs exists on your computer (or at > least it didn't before you tried this install). Much more likely is > that the gff files should go in sub-directories of > > C:\Archivos de programa\Apache Software Foundation\Apache2.2 \htdocs\gbrowse\databases > > for use with gbrowse, and the tutorial files will start out in > > C:\Archivos de programa\Apache Software Foundation\Apache2.2 \htdocs\gbrowse\tutorial\data_files > > or via the webserver at > > http://localhost/gbrowse/tutorial/data_files/elegans_sts.gff > > I am pretty sure I know what happened with your install, by the way: the > installer looks first for various Apache directories in C:\Program files > and then when it doesn't find them, use the "default" location > of /usr/local/apache for everything. This could be fixed by rerunning > the install and typing in the full path of the cgi, htdocs and conf > directories instead of accepting the defaults (which are clearly wrong > in this instance). This should fix your tutorial as well, as it has its > paths set when the installation happens. > > Scott > > On Tue, 2008-06-10 at 17:59 +0200, Luis.Delaye@... wrote: > > Hi Scott, > > > > Now I'm able to use GBrowse in my laptop (but with somehow limited > > capabilities). I put the following files: > > > > das > > gbrowse > > gbrowse_details > > gbrowse_est > > gbrowse_img > > gbrowse_moby > > moby_server > > printenv.pl > > tutorial_test.pl > > > > in the directory: > > > > C:\Archivos de programa\Apache Software Foundation\Apache2.2\cgi- > > > > But it I try to see the file: > > > > elegans_sts.gff > > > > in the directory: > > > > C:\usr\local\apache\htdocs > > > > and, following the tutorial, I try to look for it using the web > > browser (http://localhost/elegans_sts.gff) I got an HTTP 404 error. > > > > Mabe this could help to figure out. > > > > Thanks for your time! > > > > best! > > > > PD If there is a language problem maybe I can fix it... > > Luis > > > > > Hi Luis, > > > > > > Is there a file at the location that the error log reported? If > > > gbrowse script is not there, where is it? I'm wondering if this is a > > > language problem. I suspect that the installer doesn't know that > > your > > > application folder is called "Archivos de programa" as opposed to > > > "Program Files". > > > > > > Scott > > > > > > > > > On Sat, 2008-06-07 at 12:28 +0200, Luis.Delaye@... wrote: > > > > Dear Gbrowse, > > > > > > > > Iââ¬â¢m trying to install gbrowse ona Windows XP, I > > > > installation steps and Iââ¬â¢m right now in the tutorial. However, I > > was > > > > not able to see the page: > > > > > > > > http://localhost/cgi-bin/gbrowse/volvox > > > > > > > > I check for the following instructions in the section: â â¬ÅIf You > > are > > > > Having Problems...ââ¬Â and everything seems to be ok.. > > > > > > > > I check the Apache server error log and I found this message: > > > > > > > > [Sat Jun 07 12:17:25 2008] [error] [client 127.0.0.1] script not > > found > > > > or unable to stat: C:/Archivos de programa/Apache Software > > > > Foundation/Apache2.2/cgi-bin/gbrowse > > > > > > > > If you could help me I will appreciate a lot! > > > > > > > > Best regards! > > > > > > > > Luis Delaye > > > > > > > > > > > > > > > > --------------------------------------------------------------- > > ------ > > > > Check out the new SourceForge.net Marketplace. > > > > It's the best place to buy or sell services for > > > > just about anything Open Source. > > > > http://sourceforge.net/services/buy/index.php > > > > _______________________________________________ > > > > Gmod-gbrowse mailing list > > > > Gmod-gbrowse@... > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > > > > > -- > > > ----------------------------------------------------------------- > > --- > > > Scott Cain, Ph. D. > > cain@... > > > GMOD Coordinator (http://www.gmod.org/) 216- 392- > > 3087 > > > Cold Spring Harbor Laboratory > > > > > > > > > > > > > > -- > --------------------------------------------------------------------- --- > Scott Cain, Ph. D. cain.cshl@... > GMOD Coordinator (http://www.gmod.org/) 216-392- 3087 > Cold Spring Harbor Laboratory > > > > ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Dear Gbrowse
by Luis.Delaye
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Dear Scott, I have one more problem, I have been looking in the mailinglist for its solution without being succesfull. This is the problem: GBrowser, and it works fine with the examples. But when I try to use my own files.gff, all the features (images in tracks) dissapear. The same in windows and linux. Thanks! Luis Delaye > > Hi Scott, > > It works! Thanks. I suscribed to the mailing list. > > Best! > > Luis > > > Hi Luis, > > > > Please keep your responses on the mailing list so that the > conversation > > can be archived, and people who are more familiar with Windows can > help > > when we need it. > > > > I doubt that C:\usr\local\apache\htdocs exists on your computer > at > > least it didn't before you tried this install). Much more likely is > > that the gff files should go in sub-directories of > > > > C:\Archivos de programa\Apache Software Foundation\Apache2.2 > \htdocs\gbrowse\databases > > > > for use with gbrowse, and the tutorial files will start out in > > > > C:\Archivos de programa\Apache Software Foundation\Apache2.2 > \htdocs\gbrowse\tutorial\data_files > > > > or via the webserver at > > > > http://localhost/gbrowse/tutorial/data_files/elegans_sts.gff > > > > I am pretty sure I know what happened with your install, by the > the > > installer looks first for various Apache directories in C:\Program > files > > and then when it doesn't find them, use the "default" location > > of /usr/local/apache for everything. This could be fixed by > rerunning > > the install and typing in the full path of the cgi, htdocs and conf > > directories instead of accepting the defaults (which are clearly > wrong > > in this instance). This should fix your tutorial as well, as it > its > > paths set when the installation happens. > > > > Scott > > > > On Tue, 2008-06-10 at 17:59 +0200, Luis.Delaye@... wrote: > > > Hi Scott, > > > > > > Now I'm able to use GBrowse in my laptop (but with somehow limited > > > capabilities). I put the following files: > > > > > > das > > > gbrowse > > > gbrowse_details > > > gbrowse_est > > > gbrowse_img > > > gbrowse_moby > > > moby_server > > > printenv.pl > > > tutorial_test.pl > > > > > > in the directory: > > > > > > C:\Archivos de programa\Apache Software Foundation\Apache2.2\cgi- > bin > > > > > > But it I try to see the file: > > > > > > elegans_sts.gff > > > > > > in the directory: > > > > > > C:\usr\local\apache\htdocs > > > > > > and, following the tutorial, I try to look for it using the web > > > browser (http://localhost/elegans_sts.gff) I got an HTTP 404 > > > > > > Mabe this could help to figure out. > > > > > > Thanks for your time! > > > > > > best! > > > > > > PD If there is a language problem maybe I can fix it... > > > Luis > > > > > > > Hi Luis, > > > > > > > > Is there a file at the location that the error log reported? > the > > > > gbrowse script is not there, where is it? I'm wondering if this > is a > > > > language problem. I suspect that the installer doesn't know > that > > > your > > > > application folder is called "Archivos de programa" as opposed to > > > > "Program Files". > > > > > > > > Scott > > > > > > > > > > > > On Sat, 2008-06-07 at 12:28 +0200, Luis.Delaye@... wrote: > > > > > Dear Gbrowse, > > > > > > > > > > Iââ¬â¢m trying to install gbrowse ona Windows XP, I > followed all > > > > > installation steps and Iââ¬â¢m right now in the tutorial. > However, I > > > was > > > > > not able to see the page: > > > > > > > > > > http://localhost/cgi-bin/gbrowse/volvox > > > > > > > > > > I check for the following instructions in the section: â > â¬ÅIf You > > > are > > > > > Having Problems...ââ¬Â and everything seems to be ok.. > > > > > > > > > > I check the Apache server error log and I found this message: > > > > > > > > > > [Sat Jun 07 12:17:25 2008] [error] [client 127.0.0.1] script > not > > > found > > > > > or unable to stat: C:/Archivos de programa/Apache Software > > > > > Foundation/Apache2.2/cgi-bin/gbrowse > > > > > > > > > > If you could help me I will appreciate a lot! > > > > > > > > > > Best regards! > > > > > > > > > > Luis Delaye > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------- > ---- > > > ------ > > > > > Check out the new SourceForge.net Marketplace. > > > > > It's the best place to buy or sell services for > > > > > just about anything Open Source. > > > > > http://sourceforge.net/services/buy/index.php > > > > > _______________________________________________ > > > > > Gmod-gbrowse mailing list > > > > > Gmod-gbrowse@... > > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > > > > > > > > -- > > > > --------------------------------------------------------------- > ---- > > > --- > > > > Scott Cain, Ph. D. > > > cain@... > > > > GMOD Coordinator (http://www.gmod.org/) 216- > 392- > > > 3087 > > > > Cold Spring Harbor Laboratory > > > > > > > > > > > > > > > > > > > > -- > > ------------------------------------------------------------------- > --- > > Scott Cain, Ph. D. > cain.cshl@... > > GMOD Coordinator (http://www.gmod.org/) 216- 392- > 3087 > > Cold Spring Harbor Laboratory > > > > > > > > > > > > --------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php > _______________________________________________ > Gmod-gbrowse mailing list > Gmod-gbrowse@... > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse > > ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://sourceforge.net/services/buy/index.php _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Dear Gbrowse
by Scott Cain-3
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Luis,
Did you ever sort this out? I was obviously stumped but I will still try to help. Scott On Fri, Jun 13, 2008 at 2:29 PM, <Luis.Delaye@...> wrote: > > Dear Scott, > > I have one more problem, I have been looking in the mailinglist for > its solution without being succesfull. > > This is the problem: > > GBrowser, and it works fine with the examples. But when I try to use > my own files.gff, all the features (images in tracks) dissapear. The > same in windows and linux. > > Thanks! > > Luis Delaye > >> >> Hi Scott, >> >> It works! Thanks. I suscribed to the mailing list. >> >> Best! >> >> Luis >> >> > Hi Luis, >> > >> > Please keep your responses on the mailing list so that the >> conversation >> > can be archived, and people who are more familiar with Windows can >> help >> > when we need it. >> > >> > I doubt that C:\usr\local\apache\htdocs exists on your computer > (or >> at >> > least it didn't before you tried this install). Much more likely > is >> > that the gff files should go in sub-directories of >> > >> > C:\Archivos de programa\Apache Software Foundation\Apache2.2 >> \htdocs\gbrowse\databases >> > >> > for use with gbrowse, and the tutorial files will start out in >> > >> > C:\Archivos de programa\Apache Software Foundation\Apache2.2 >> \htdocs\gbrowse\tutorial\data_files >> > >> > or via the webserver at >> > >> > http://localhost/gbrowse/tutorial/data_files/elegans_sts.gff >> > >> > I am pretty sure I know what happened with your install, by the > way: >> the >> > installer looks first for various Apache directories in C:\Program >> files >> > and then when it doesn't find them, use the "default" location >> > of /usr/local/apache for everything. This could be fixed by >> rerunning >> > the install and typing in the full path of the cgi, htdocs and conf >> > directories instead of accepting the defaults (which are clearly >> wrong >> > in this instance). This should fix your tutorial as well, as it > has >> its >> > paths set when the installation happens. >> > >> > Scott >> > >> > On Tue, 2008-06-10 at 17:59 +0200, Luis.Delaye@... wrote: >> > > Hi Scott, >> > > >> > > Now I'm able to use GBrowse in my laptop (but with somehow > limited >> > > capabilities). I put the following files: >> > > >> > > das >> > > gbrowse >> > > gbrowse_details >> > > gbrowse_est >> > > gbrowse_img >> > > gbrowse_moby >> > > moby_server >> > > printenv.pl >> > > tutorial_test.pl >> > > >> > > in the directory: >> > > >> > > C:\Archivos de programa\Apache Software Foundation\Apache2.2\cgi- >> bin >> > > >> > > But it I try to see the file: >> > > >> > > elegans_sts.gff >> > > >> > > in the directory: >> > > >> > > C:\usr\local\apache\htdocs >> > > >> > > and, following the tutorial, I try to look for it using the web >> > > browser (http://localhost/elegans_sts.gff) I got an HTTP 404 > error. >> > > >> > > Mabe this could help to figure out. >> > > >> > > Thanks for your time! >> > > >> > > best! >> > > >> > > PD If there is a language problem maybe I can fix it... >> > > Luis >> > > >> > > > Hi Luis, >> > > > >> > > > Is there a file at the location that the error log reported? > If >> the >> > > > gbrowse script is not there, where is it? I'm wondering if > this >> is a >> > > > language problem. I suspect that the installer doesn't know >> that >> > > your >> > > > application folder is called "Archivos de programa" as opposed > to >> > > > "Program Files". >> > > > >> > > > Scott >> > > > >> > > > >> > > > On Sat, 2008-06-07 at 12:28 +0200, Luis.Delaye@... wrote: >> > > > > Dear Gbrowse, >> > > > > >> > > > > I’m trying to install gbrowse ona Windows XP, I >> followed all >> > > > > installation steps and I’m right now in the tutorial. >> However, I >> > > was >> > > > > not able to see the page: >> > > > > >> > > > > http://localhost/cgi-bin/gbrowse/volvox >> > > > > >> > > > > I check for the following instructions in the section: â >> €œIf You >> > > are >> > > > > Having Problems...†and everything seems to be ok.. >> > > > > >> > > > > I check the Apache server error log and I found this message: >> > > > > >> > > > > [Sat Jun 07 12:17:25 2008] [error] [client 127.0.0.1] script >> not >> > > found >> > > > > or unable to stat: C:/Archivos de programa/Apache Software >> > > > > Foundation/Apache2.2/cgi-bin/gbrowse >> > > > > >> > > > > If you could help me I will appreciate a lot! >> > > > > >> > > > > Best regards! >> > > > > >> > > > > Luis Delaye >> > > > > >> > > > > >> > > > > >> > > > > ------------------------------------------------------------- > -- >> ---- >> > > ------ >> > > > > Check out the new SourceForge.net Marketplace. >> > > > > It's the best place to buy or sell services for >> > > > > just about anything Open Source. >> > > > > http://sourceforge.net/services/buy/index.php >> > > > > _______________________________________________ >> > > > > Gmod-gbrowse mailing list >> > > > > Gmod-gbrowse@... >> > > > > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> > > > > >> > > > -- >> > > > --------------------------------------------------------------- > -- >> ---- >> > > --- >> > > > Scott Cain, Ph. D. >> > > cain@... >> > > > GMOD Coordinator (http://www.gmod.org/) > 216- >> 392- >> > > 3087 >> > > > Cold Spring Harbor Laboratory >> > > > >> > > > >> > > > >> > > >> > > >> > -- >> > ------------------------------------------------------------------- > -- >> --- >> > Scott Cain, Ph. D. >> cain.cshl@... >> > GMOD Coordinator (http://www.gmod.org/) 216- > 392- >> 3087 >> > Cold Spring Harbor Laboratory >> > >> > >> > >> > >> >> >> >> --------------------------------------------------------------------- > ---- >> Check out the new SourceForge.net Marketplace. >> It's the best place to buy or sell services for >> just about anything Open Source. >> http://sourceforge.net/services/buy/index.php >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > > > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. cain.cshl@... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Dear Gbrowse
by Lincoln Stein-3
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Hi Luis,
Something is wrong with the way your gff files are formatted (or possibly something wrong with the config file). Could you send some examples? Lincoln On Fri, Jun 13, 2008 at 2:29 PM, <Luis.Delaye@...> wrote:
-- Lincoln D. Stein Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Stacey Fairfield <Stacey.Fairfield@...> Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 USA (516) 367-8380 Assistant: Sandra Michelsen <michelse@...> ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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