How to Downgrade GBrowse
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How to Downgrade GBrowse
by Ajendrex
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Hello,
Is there any way to safely downgrade GBrowse? I have GBrowse installed, version 1.993, but it is not working well (not showing "overview" neither "Details", plus errors like "The landmark named chrI:80,000..120,000 is not recognized. See the help pages for suggestions" just after installation), so I want to perform a GBrowse downgrade (to version 1.69, the one I understand is more stable). Could anyone tell me how to do this? Basically, I want to know how to UNINSTALL GBrowse :) which I installed with CPAN (as far as I know, cpan does not have an "uninstall" instruction). Thanks! |
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Re: How to Downgrade GBrowse
by Scott Cain-4
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Hi,
All of the prereqs should be safe--Bio::Graphics and BioPerl can stay as is. To install GBrowse 1.69, you can download the source and do "perl Makefile.PL; make, sudo make install UNINST=1". That UNINST=1 part is important, as it will remove the perl libraries that are specific to GBrowse2. You can do the same thing with an anonymous checkout of the cvs "stable" branch, which is what will be the 1.70 release soon. Scott On Mon, Jun 8, 2009 at 2:57 PM, Ajendrex<ajendrex@...> wrote: > > Hello, > > Is there any way to safely downgrade GBrowse? I have GBrowse installed, > version 1.993, but it is not working well (not showing "overview" > neither "Details", plus errors like "The landmark named > chrI:80,000..120,000 is not recognized. See the help pages for > suggestions" just after installation), so I want to perform a GBrowse > downgrade (to version 1.69, the one I understand is more stable). Could > anyone tell me how to do this? > > Basically, I want to know how to UNINSTALL GBrowse :) which I installed > with CPAN (as far as I know, cpan does not have an "uninstall" > instruction). > > Thanks! > -- > View this message in context: http://www.nabble.com/How-to-Downgrade-GBrowse-tp23930030p23930030.html > Sent from the gmod-gbrowse mailing list archive at Nabble.com. > > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > 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 ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: How to Downgrade GBrowse
by Ajendrex
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Hi Scott!
Thank you for your quick answer. I have only one question more, Do the GBrowse 1.69 installation actually remove GBrowse 1.993? Anyway, I'm going to install GBrowse 1.69 and figure it out :P
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Re: How to Downgrade GBrowse
by Scott Cain-4
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No, the cgi scripts would remain, as would the configuration files.
Scott On Mon, Jun 8, 2009 at 3:16 PM, Ajendrex<ajendrex@...> wrote: > > Hi Scott! > > Thank you for your quick answer. I have only one question more, Do the > GBrowse 1.69 installation actually remove GBrowse 1.993? > > Anyway, I'm going to install GBrowse 1.69 and figure it out :P > > > Scott Cain-4 wrote: >> >> Hi, >> >> All of the prereqs should be safe--Bio::Graphics and BioPerl can stay >> as is. To install GBrowse 1.69, you can download the source and do >> "perl Makefile.PL; make, sudo make install UNINST=1". That UNINST=1 >> part is important, as it will remove the perl libraries that are >> specific to GBrowse2. You can do the same thing with an anonymous >> checkout of the cvs "stable" branch, which is what will be the 1.70 >> release soon. >> >> Scott >> >> >> On Mon, Jun 8, 2009 at 2:57 PM, Ajendrex<ajendrex@...> wrote: >>> >>> Hello, >>> >>> Is there any way to safely downgrade GBrowse? I have GBrowse installed, >>> version 1.993, but it is not working well (not showing "overview" >>> neither "Details", plus errors like "The landmark named >>> chrI:80,000..120,000 is not recognized. See the help pages for >>> suggestions" just after installation), so I want to perform a GBrowse >>> downgrade (to version 1.69, the one I understand is more stable). Could >>> anyone tell me how to do this? >>> >>> Basically, I want to know how to UNINSTALL GBrowse :) which I installed >>> with CPAN (as far as I know, cpan does not have an "uninstall" >>> instruction). >>> >>> Thanks! >>> -- >>> View this message in context: >>> http://www.nabble.com/How-to-Downgrade-GBrowse-tp23930030p23930030.html >>> Sent from the gmod-gbrowse mailing list archive at Nabble.com. >>> >>> >>> ------------------------------------------------------------------------------ >>> Crystal Reports - New Free Runtime and 30 Day Trial >>> Check out the new simplified licensing option that enables unlimited >>> royalty-free distribution of the report engine for externally facing >>> server and web deployment. >>> http://p.sf.net/sfu/businessobjects >>> _______________________________________________ >>> 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 >> >> ------------------------------------------------------------------------------ >> Crystal Reports - New Free Runtime and 30 Day Trial >> Check out the new simplified licensing option that enables unlimited >> royalty-free distribution of the report engine for externally facing >> server and web deployment. >> http://p.sf.net/sfu/businessobjects >> _______________________________________________ >> Gmod-gbrowse mailing list >> Gmod-gbrowse@... >> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >> >> > > -- > View this message in context: http://www.nabble.com/How-to-Downgrade-GBrowse-tp23930030p23930366.html > Sent from the gmod-gbrowse mailing list archive at Nabble.com. > > > ------------------------------------------------------------------------------ > Crystal Reports - New Free Runtime and 30 Day Trial > Check out the new simplified licensing option that enables unlimited > royalty-free distribution of the report engine for externally facing > server and web deployment. > http://p.sf.net/sfu/businessobjects > _______________________________________________ > 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 ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: How to Downgrade GBrowse
by Lincoln Stein-3
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Hi,
The example yeast installation did not work at all? Did you see any error messages during installation? lincoln On Mon, Jun 8, 2009 at 2:57 PM, Ajendrex <ajendrex@...> 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@...> ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Gmod-gbrowse mailing list Gmod-gbrowse@... https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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Re: How to Downgrade GBrowse
by Ajendrex
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Hello lincoln,
During GBrowse installation a big number of messages appear to the screen, I supose many of them were error, as usual in Perl :S However, now, in the apache log files (error_log and acces_log) there is not one line about anything regarding GBrowse... Oh!, wait a moment... I did a resize of the image to 1024 (width) and I have the following message, I think it is for you... [error_log apache] [Sun Jun 07 07:36:10 2009] [notice] Apache/2.2.11 (Ubuntu) PHP/5.2.6-3ubuntu4.1 with Suhosin-Patch mod_perl/2.0.4 Perl/v5.10.0 configured -- resuming normal operations [Mon Jun 08 12:45:15 2009] [error] [client 127.0.0.1] BUG: working around no ref defined bug; tell Lincoln bug is not fixed at /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser/Render.pm line 2396., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/?name=Sequence:YBR037C;dbid= [Mon Jun 08 12:45:16 2009] [error] [client 127.0.0.1] Use of uninitialized value in concatenation (.) or string at /usr/local/lib/perl/5.10.0/Bio/Graphics/Browser/Render.pm line 2405., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/?name=Sequence:YBR037C;dbid= [Mon Jun 08 12:45:17 2009] [error] [client 127.0.0.1] Illegal division by zero at /usr/local/lib/perl/5.10.0/Bio/Graphics/Panel.pm line 237., referer: http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/?name=Sequence:YBR037C;dbid= [Mon Jun 08 12:45:17 2009] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gb2/gbrowse/yeast_advanced/?name=Sequence:YBR037C;dbid=
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