Server error upon Gbrowse2 upgrade
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Server error upon Gbrowse2 upgrade
by joseph franklin
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Hi,
I upgraded from GBrowse-1.993 to GBrowse-1.994 using CPAN in Ubuntu 9.04. These upgrades usually work great, but this time I can't load the browser, and I get apache errors: [Fri Jun 05 10:11:48 2009] [error] [client xx] (13)Permission denied: exec of '/usr/lib/cgi-bin/gb2/gbrowse' failed [Fri Jun 05 10:11:48 2009] [error] [client xx] Premature end of script headers: gbrowse The file permissions for the cgibin/gb2 directory are: -r--r--r-- 1 root root 1119 2009-02-10 07:09 gbgff -r--r--r-- 1 root root 515 2009-06-04 21:59 gbrowse -r--r--r-- 1 root root 17923 2009-06-04 21:59 gbrowse_details -r--r--r-- 1 root root 21468 2009-06-04 21:59 gbrowse_gmap -r--r--r-- 1 root root 20808 2009-06-04 21:59 gbrowse_img I ran the Bio::Graphics::Browser Build reconfig with all defaults, which tested and installed fine--but still the errors. Thanks for any help with this. -Joe ________________________________ Joe Franklin Department of Cell Biology Yale University School of Medicine 295 Congress Ave, BCMM 137 New Haven, CT 06519 USA joseph.franklin@... 407 341 3263 (cell) 203 654 7494 (google voice) ------------------------------------------------------------------------------ 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: Server error upon Gbrowse2 upgrade
by Lincoln Stein
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Sorry, there seems to be a problem with setting the permissions in cgi-bin/gb2. I will check and upload a new version.
Lincoln On Fri, Jun 5, 2009 at 10:33 AM, joseph franklin <joseph.franklin@...> wrote: Hi, -- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ 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: Server error upon Gbrowse2 upgrade
by Bala Selvaraj
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Hi Joe, I am also getting the same error. Scott asked me to disable SELinux. But it is already disabled in my server. I am also not sure how to get rid of this. If you come across anything let me know. Thanks ~Bala -----Original Message----- From: joseph franklin [mailto:joseph.franklin@...] Sent: Friday, June 05, 2009 10:33 AM To: gmod-gbrowse@... Subject: [Gmod-gbrowse] Server error upon Gbrowse2 upgrade Hi, I upgraded from GBrowse-1.993 to GBrowse-1.994 using CPAN in Ubuntu 9.04. These upgrades usually work great, but this time I can't load the browser, and I get apache errors: [Fri Jun 05 10:11:48 2009] [error] [client xx] (13)Permission denied: exec of '/usr/lib/cgi-bin/gb2/gbrowse' failed [Fri Jun 05 10:11:48 2009] [error] [client xx] Premature end of script headers: gbrowse The file permissions for the cgibin/gb2 directory are: -r--r--r-- 1 root root 1119 2009-02-10 07:09 gbgff -r--r--r-- 1 root root 515 2009-06-04 21:59 gbrowse -r--r--r-- 1 root root 17923 2009-06-04 21:59 gbrowse_details -r--r--r-- 1 root root 21468 2009-06-04 21:59 gbrowse_gmap -r--r--r-- 1 root root 20808 2009-06-04 21:59 gbrowse_img I ran the Bio::Graphics::Browser Build reconfig with all defaults, which tested and installed fine--but still the errors. Thanks for any help with this. -Joe ________________________________ Joe Franklin Department of Cell Biology Yale University School of Medicine 295 Congress Ave, BCMM 137 New Haven, CT 06519 USA joseph.franklin@... 407 341 3263 (cell) 203 654 7494 (google voice) ------------------------------------------------------------------------ ------ 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: Server error upon Gbrowse2 upgrade
by Scott Cain-4
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Hi Bala,
Sorry about the SELinux misdirection: it is natural for me to look there for the problem after being bitten by it many times, but I didn't realize that the exec bit wasn't set on cgi scripts. As Lincoln wrote, there is something wrong with the installer. Scott On Fri, Jun 5, 2009 at 11:31 AM, Selvaraj, Balamuruganand (B)<BSelvaraj@...> wrote: > > Hi Joe, > > I am also getting the same error. Scott asked me to disable SELinux. > But it is already disabled in my server. > > I am also not sure how to get rid of this. > If you come across anything let me know. > > Thanks > ~Bala > > > -----Original Message----- > From: joseph franklin [mailto:joseph.franklin@...] > Sent: Friday, June 05, 2009 10:33 AM > To: gmod-gbrowse@... > Subject: [Gmod-gbrowse] Server error upon Gbrowse2 upgrade > > Hi, > > I upgraded from GBrowse-1.993 to GBrowse-1.994 using CPAN in Ubuntu > 9.04. These upgrades usually work great, but this time I can't load > the browser, and I get apache errors: > [Fri Jun 05 10:11:48 2009] [error] [client xx] (13)Permission denied: > exec of '/usr/lib/cgi-bin/gb2/gbrowse' failed > [Fri Jun 05 10:11:48 2009] [error] [client xx] Premature end of script > headers: gbrowse > > The file permissions for the cgibin/gb2 directory are: > -r--r--r-- 1 root root 1119 2009-02-10 07:09 gbgff > -r--r--r-- 1 root root 515 2009-06-04 21:59 gbrowse > -r--r--r-- 1 root root 17923 2009-06-04 21:59 gbrowse_details > -r--r--r-- 1 root root 21468 2009-06-04 21:59 gbrowse_gmap > -r--r--r-- 1 root root 20808 2009-06-04 21:59 gbrowse_img > > I ran the Bio::Graphics::Browser Build reconfig with all defaults, > which tested and installed fine--but still the errors. > > Thanks for any help with this. > > -Joe > > > ________________________________ > Joe Franklin > Department of Cell Biology > Yale University School of Medicine > 295 Congress Ave, BCMM 137 > New Haven, CT 06519 > USA > > joseph.franklin@... > 407 341 3263 (cell) > 203 654 7494 (google voice) > > > ------------------------------------------------------------------------ > ------ > 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 > -- ------------------------------------------------------------------------ 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: Server error upon Gbrowse2 upgrade
by Lincoln Stein-3
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Don't sweat it. This is just something weird that happened when I made the latest distribution. The quick fix is just to make the CGI scripts executable.
Lincoln On Fri, Jun 5, 2009 at 11:31 AM, Selvaraj, Balamuruganand (B) <BSelvaraj@...> wrote:
-- Lincoln D. Stein Director, Informatics and Biocomputing Platform Ontario Institute for Cancer Research 101 College St., Suite 800 Toronto, ON, Canada M5G0A3 416 673-8514 Assistant: Renata Musa <Renata.Musa@...> ------------------------------------------------------------------------------ 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: Server error upon Gbrowse2 upgrade
by Bala Selvaraj
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Thanks Lincoln :)
I will Probably work with previous version as of
now.
------------------------------------------------------------------------------ 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: Server error upon Gbrowse2 upgrade
by Bala Selvaraj
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Joe, Lincoln,
I just set the permission level to 755 for all modules in
cgi-bin and All seems to be working well !
-Bala
From: Lincoln Stein [mailto:lincoln.stein@...] Sent: Friday, June 05, 2009 11:40 AM To: Selvaraj, Balamuruganand (B) Cc: joseph franklin; gmod-gbrowse@... Subject: Re: [Gmod-gbrowse] Server error upon Gbrowse2 upgrade Don't sweat it. This is just something weird that happened when I made the latest distribution. The quick fix is just to make the CGI scripts executable. ------------------------------------------------------------------------------ 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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