Gbrowse 2 installation in CentOS 5
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Gbrowse 2 installation in CentOS 5
by Bala Selvaraj
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Hi GMOD users, With installation of Gbrowse 2 not possible with windows, I am trying to install it in CentOS 5 using the Biopackages.net. However, I am facing issues with yum as it cannnot install Bio::Graphics or GMOD. Has anyone tried to install Gbrowse 2 using yum in CentOS 5. Thanks for your reply -Bala ------------------------------------------------------------------------------ OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Gbrowse 2 installation in CentOS 5
by Scott Cain-4
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Hi Bala,
Since GBrowse2 is still in development, there are no RPMs for it, so I don't see how you could use yum to install it. Additionally, since Bio::Graphics is under active development, RPM production for it is typically going to lag behind (in fact, I'd be surprised if Allen and Brian made an RPM for it yet at all). At best, you could get many of the prereqs with yum. Also, I don't know what you mean when you write you cannot install GMOD: do you mean GBrowse? What I would try for installing GBrowse is to use the cpan shell (after you use yum to install gd-dev/libgd): sudo cpan cpan> install LDS/GBrowse-1.994.tar.gz Scott On Thu, Jun 4, 2009 at 7:58 AM, Selvaraj, Balamuruganand (B) <BSelvaraj@...> wrote: > > Hi GMOD users, > > With installation of Gbrowse 2 not possible with windows, I am trying to > install it in CentOS 5 using the Biopackages.net. > > However, I am facing issues with yum as it cannnot install Bio::Graphics or > GMOD. > > Has anyone tried to install Gbrowse 2 using yum in CentOS 5. > > Thanks for your reply > > -Bala > > ------------------------------------------------------------------------------ > OpenSolaris 2009.06 is a cutting edge operating system for enterprises > looking to deploy the next generation of Solaris that includes the latest > innovations from Sun and the OpenSource community. Download a copy and > enjoy capabilities such as Networking, Storage and Virtualization. > Go to: http://p.sf.net/sfu/opensolaris-get > _______________________________________________ > 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 ------------------------------------------------------------------------------ OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Gbrowse 2 installation in CentOS 5
by Miquel Ramia
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Hi,
I'm trying to install GBrowse2 in CentOS5 (running Gbrowse 1.69 with no problems), but I tried CPAN and manually downloading the package, and allways get the same error in ./Build test, The process "crash" in: t/03.render.t ............. 114/138 (sometimes 112, sometimes 118) but it stops completely. Anyone with the same problem? I'll try installing GBrowse2 in another computer as well Scott Cain wrote: > Hi Bala, > > Since GBrowse2 is still in development, there are no RPMs for it, so I > don't see how you could use yum to install it. Additionally, since > Bio::Graphics is under active development, RPM production for it is > typically going to lag behind (in fact, I'd be surprised if Allen and > Brian made an RPM for it yet at all). At best, you could get many of > the prereqs with yum. Also, I don't know what you mean when you write > you cannot install GMOD: do you mean GBrowse? > > What I would try for installing GBrowse is to use the cpan shell > (after you use yum to install gd-dev/libgd): > > sudo cpan > cpan> install LDS/GBrowse-1.994.tar.gz > > Scott > > > > On Thu, Jun 4, 2009 at 7:58 AM, Selvaraj, Balamuruganand (B) > <BSelvaraj@...> wrote: > >> Hi GMOD users, >> >> With installation of Gbrowse 2 not possible with windows, I am trying to >> install it in CentOS 5 using the Biopackages.net. >> >> However, I am facing issues with yum as it cannnot install Bio::Graphics or >> GMOD. >> >> Has anyone tried to install Gbrowse 2 using yum in CentOS 5. >> >> Thanks for your reply >> >> -Bala >> >> ------------------------------------------------------------------------------ >> OpenSolaris 2009.06 is a cutting edge operating system for enterprises >> looking to deploy the next generation of Solaris that includes the latest >> innovations from Sun and the OpenSource community. Download a copy and >> enjoy capabilities such as Networking, Storage and Virtualization. >> Go to: http://p.sf.net/sfu/opensolaris-get >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> >> > > > > ------------------------------------------------------------------------------ OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Gbrowse 2 installation in CentOS 5
by Scott Cain-4
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Hi Miquel,
That happens to me occasionally as well. First, make sure you have the most current version of Bio::Graphics. If it still hangs during that test, you can do a force install, as I think the test failure has more to do with the test itself rather than how GBrowse works. Scott On Thu, Jun 4, 2009 at 11:31 AM, Miquel Ramia <miquel.ramia@...> wrote: > Hi, > > I'm trying to install GBrowse2 in CentOS5 (running Gbrowse 1.69 with no > problems), but I tried CPAN and manually downloading the package, and > allways get the same error in ./Build test, The process "crash" in: > > t/03.render.t ............. 114/138 > > (sometimes 112, sometimes 118) but it stops completely. > > Anyone with the same problem? > > I'll try installing GBrowse2 in another computer as well > > Scott Cain wrote: >> >> Hi Bala, >> >> Since GBrowse2 is still in development, there are no RPMs for it, so I >> don't see how you could use yum to install it. Additionally, since >> Bio::Graphics is under active development, RPM production for it is >> typically going to lag behind (in fact, I'd be surprised if Allen and >> Brian made an RPM for it yet at all). At best, you could get many of >> the prereqs with yum. Also, I don't know what you mean when you write >> you cannot install GMOD: do you mean GBrowse? >> >> What I would try for installing GBrowse is to use the cpan shell >> (after you use yum to install gd-dev/libgd): >> >> sudo cpan >> cpan> install LDS/GBrowse-1.994.tar.gz >> >> Scott >> >> >> >> On Thu, Jun 4, 2009 at 7:58 AM, Selvaraj, Balamuruganand (B) >> <BSelvaraj@...> wrote: >> >>> >>> Hi GMOD users, >>> >>> With installation of Gbrowse 2 not possible with windows, I am trying to >>> install it in CentOS 5 using the Biopackages.net. >>> >>> However, I am facing issues with yum as it cannnot install Bio::Graphics >>> or >>> GMOD. >>> >>> Has anyone tried to install Gbrowse 2 using yum in CentOS 5. >>> >>> Thanks for your reply >>> >>> -Bala >>> >>> >>> ------------------------------------------------------------------------------ >>> OpenSolaris 2009.06 is a cutting edge operating system for enterprises >>> looking to deploy the next generation of Solaris that includes the latest >>> innovations from Sun and the OpenSource community. Download a copy and >>> enjoy capabilities such as Networking, Storage and Virtualization. >>> Go to: http://p.sf.net/sfu/opensolaris-get >>> _______________________________________________ >>> 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 ------------------------------------------------------------------------------ OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Gbrowse 2 installation in CentOS 5
by Bala Selvaraj
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Scott, Finally, I got the Gbrowse2 installed. I get the automated page with http://localhost/gbrowse2 However, when I click the Example database I get a blank page I checked the configuration files both the Gbrowse.conf and yeast_simple.conf are present in locations as dictated by the Gbrowse.conf I am yet to check the Apache log file. ~Bala -----Original Message----- From: Scott Cain [mailto:scott@...] Sent: Thursday, June 04, 2009 9:53 AM To: Selvaraj, Balamuruganand (B) Cc: gmod-gbrowse@... Subject: Re: [Gmod-gbrowse] Gbrowse 2 installation in CentOS 5 Hi Bala, Since GBrowse2 is still in development, there are no RPMs for it, so I don't see how you could use yum to install it. Additionally, since Bio::Graphics is under active development, RPM production for it is typically going to lag behind (in fact, I'd be surprised if Allen and Brian made an RPM for it yet at all). At best, you could get many of the prereqs with yum. Also, I don't know what you mean when you write you cannot install GMOD: do you mean GBrowse? What I would try for installing GBrowse is to use the cpan shell (after you use yum to install gd-dev/libgd): sudo cpan cpan> install LDS/GBrowse-1.994.tar.gz Scott On Thu, Jun 4, 2009 at 7:58 AM, Selvaraj, Balamuruganand (B) <BSelvaraj@...> wrote: > > Hi GMOD users, > > With installation of Gbrowse 2 not possible with windows, I am trying to > install it in CentOS 5 using the Biopackages.net. > > However, I am facing issues with yum as it cannnot install Bio::Graphics or > GMOD. > > Has anyone tried to install Gbrowse 2 using yum in CentOS 5. > > Thanks for your reply > > -Bala > > ------------------------------------------------------------------------------ > OpenSolaris 2009.06 is a cutting edge operating system for enterprises > looking to deploy the next generation of Solaris that includes the latest > innovations from Sun and the OpenSource community. Download a copy and > enjoy capabilities such as Networking, Storage and Virtualization. > Go to: http://p.sf.net/sfu/opensolaris-get > _______________________________________________ > 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 ------------------------------------------------------------------------------ OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Gbrowse 2 installation in CentOS 5
by Bala Selvaraj
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Hi,
I know I must be doing something wrong. When I check the Apache Error Logs, I get this error [Thu Jun 04 17:59:20 2009] [error] [client 127.0.0.1] (13)Permission denied: exec of '/var/www/cgi-bin/gb2/gbrowse2' failed [Thu Jun 04 17:59:20 2009] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer http://localhost/gbrowse2 Although, the first log points towards Permission access :: My admin is also getting the same error. If anybody else, had same problem and solved it, Pl let me know. Thanks -Bala -----Original Message----- From: Selvaraj, Balamuruganand (B) Sent: Thursday, June 04, 2009 4:59 PM To: 'Scott Cain' Cc: gmod-gbrowse@... Subject: RE: [Gmod-gbrowse] Gbrowse 2 installation in CentOS 5 Scott, Finally, I got the Gbrowse2 installed. I get the automated page with http://localhost/gbrowse2 However, when I click the Example database I get a blank page I checked the configuration files both the Gbrowse.conf and yeast_simple.conf are present in locations as dictated by the Gbrowse.conf I am yet to check the Apache log file. ~Bala -----Original Message----- From: Scott Cain [mailto:scott@...] Sent: Thursday, June 04, 2009 9:53 AM To: Selvaraj, Balamuruganand (B) Cc: gmod-gbrowse@... Subject: Re: [Gmod-gbrowse] Gbrowse 2 installation in CentOS 5 Hi Bala, Since GBrowse2 is still in development, there are no RPMs for it, so I don't see how you could use yum to install it. Additionally, since Bio::Graphics is under active development, RPM production for it is typically going to lag behind (in fact, I'd be surprised if Allen and Brian made an RPM for it yet at all). At best, you could get many of the prereqs with yum. Also, I don't know what you mean when you write you cannot install GMOD: do you mean GBrowse? What I would try for installing GBrowse is to use the cpan shell (after you use yum to install gd-dev/libgd): sudo cpan cpan> install LDS/GBrowse-1.994.tar.gz Scott On Thu, Jun 4, 2009 at 7:58 AM, Selvaraj, Balamuruganand (B) <BSelvaraj@...> wrote: > > Hi GMOD users, > > With installation of Gbrowse 2 not possible with windows, I am trying to > install it in CentOS 5 using the Biopackages.net. > > However, I am facing issues with yum as it cannnot install Bio::Graphics or > GMOD. > > Has anyone tried to install Gbrowse 2 using yum in CentOS 5. > > Thanks for your reply > > -Bala > > ------------------------------------------------------------------------------ > OpenSolaris 2009.06 is a cutting edge operating system for enterprises > looking to deploy the next generation of Solaris that includes the latest > innovations from Sun and the OpenSource community. Download a copy and > enjoy capabilities such as Networking, Storage and Virtualization. > Go to: http://p.sf.net/sfu/opensolaris-get > _______________________________________________ > 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 ------------------------------------------------------------------------------ OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: Gbrowse 2 installation in CentOS 5
by Scott Cain-4
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OH! CentOS 5! That is related to Fedora and RedHat: you have an
SELinux problem. The easist thing to do is to disable SELinux. If you SysAdmin doesn't want to do that, you have to do (something like) allowing cgis to execute, but I don't know off hand how to do that. Scott On Thu, Jun 4, 2009 at 6:12 PM, Selvaraj, Balamuruganand (B) <BSelvaraj@...> wrote: > Hi, > > I know I must be doing something wrong. > When I check the Apache Error Logs, I get this error > > [Thu Jun 04 17:59:20 2009] [error] [client 127.0.0.1] (13)Permission denied: exec of '/var/www/cgi-bin/gb2/gbrowse2' > failed > [Thu Jun 04 17:59:20 2009] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer http://localhost/gbrowse2 > > Although, the first log points towards Permission access :: My admin is also getting the same error. > > If anybody else, had same problem and solved it, Pl let me know. > > Thanks > -Bala > > > -----Original Message----- > From: Selvaraj, Balamuruganand (B) > Sent: Thursday, June 04, 2009 4:59 PM > To: 'Scott Cain' > Cc: gmod-gbrowse@... > Subject: RE: [Gmod-gbrowse] Gbrowse 2 installation in CentOS 5 > > > Scott, > > Finally, I got the Gbrowse2 installed. I get the automated page with http://localhost/gbrowse2 > However, when I click the Example database I get a blank page > > I checked the configuration files both the Gbrowse.conf and yeast_simple.conf are present in locations > as dictated by the Gbrowse.conf > > I am yet to check the Apache log file. > > ~Bala > > -----Original Message----- > From: Scott Cain [mailto:scott@...] > Sent: Thursday, June 04, 2009 9:53 AM > To: Selvaraj, Balamuruganand (B) > Cc: gmod-gbrowse@... > Subject: Re: [Gmod-gbrowse] Gbrowse 2 installation in CentOS 5 > > Hi Bala, > > Since GBrowse2 is still in development, there are no RPMs for it, so I > don't see how you could use yum to install it. Additionally, since > Bio::Graphics is under active development, RPM production for it is > typically going to lag behind (in fact, I'd be surprised if Allen and > Brian made an RPM for it yet at all). At best, you could get many of > the prereqs with yum. Also, I don't know what you mean when you write > you cannot install GMOD: do you mean GBrowse? > > What I would try for installing GBrowse is to use the cpan shell > (after you use yum to install gd-dev/libgd): > > sudo cpan > cpan> install LDS/GBrowse-1.994.tar.gz > > Scott > > > > On Thu, Jun 4, 2009 at 7:58 AM, Selvaraj, Balamuruganand (B) > <BSelvaraj@...> wrote: >> >> Hi GMOD users, >> >> With installation of Gbrowse 2 not possible with windows, I am trying to >> install it in CentOS 5 using the Biopackages.net. >> >> However, I am facing issues with yum as it cannnot install Bio::Graphics or >> GMOD. >> >> Has anyone tried to install Gbrowse 2 using yum in CentOS 5. >> >> Thanks for your reply >> >> -Bala >> >> ------------------------------------------------------------------------------ >> OpenSolaris 2009.06 is a cutting edge operating system for enterprises >> looking to deploy the next generation of Solaris that includes the latest >> innovations from Sun and the OpenSource community. Download a copy and >> enjoy capabilities such as Networking, Storage and Virtualization. >> Go to: http://p.sf.net/sfu/opensolaris-get >> _______________________________________________ >> 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 > -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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