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Re: [Gmod-ajax] Jbrowse Set Up Error
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From: Scott C. <sc...@sc...> - 2012-09-11 14:55:21
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Hi Steffi, I don't really know; it's always best to email the mailing list since then you get more eyes looking at the problem. Scott On Tue, Sep 11, 2012 at 4:03 AM, <ste...@gm...> wrote: > Hi, > in the first directory I ran jbrowse, deleting the folder /extlib and running the setup.sh again helped, but in another directory this does not work. > For example, if I try to remove a track with this command: > > bin/remove-track.pl --trackLabel "refGene" --dir hg19/ > > I get this error message: > > , or } expected while parsing object/hash, at character offset 268 (before "//"linkTemplate" : "...") at /var/www/jbrowse2/bin/../src/perl5/JsonFileStorage.pm line 180, <GEN0> line 25. > > Any idea? I am using jbrowse 1.6.1 > > > <quote author='Scott Cain'> > Hi Steffi, > > I'm cc'ing the JBrowse mailing list (confusingly called gmod-ajax--the > list existed before the name of the application). Future replies can > trim of the he...@gm... email address. > > What version of JBrowse are you working with? The last several > versions have done a good job of installing perl prerequisites for > you. I ask because the message "Can't find ....pm" pretty much always > means a prerequisite wasn't installed. If your not using JBrowse > 1.6.1, I'd suggest going to jbrowse.org and getting it. > > Scott > > On Wed, Sep 5, 2012 at 7:08 AM, <ste...@gm...> wrote: >> Installed JSON and JSON::XS again via CPAN. Didn´t work, I get this >> message even while only trying to use the --help parameter: >> >> bin/biodb-to-json.pl --h >> Can't locate Hash/Merge.pm in @INC (@INC contains: >> /var/www/jbrowse/bin/../src/perl5/../../extlib/lib/perl5/x86_64-linux-gnu-thread-multi >> /var/www/jbrowse/bin/../src/perl5/../../extlib/lib/perl5 >> extlib/lib/perl5/x86_64-linux-gnu-thread-multi extlib/lib/perl5 >> /var/www/jbrowse/bin/../src/perl5 /etc/perl /usr/local/lib/perl/5.14.2 >> /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 >> /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at >> /var/www/jbrowse/bin/../src/perl5/GenomeDB.pm line 37. >> BEGIN failed--compilation aborted at >> /var/www/jbrowse/bin/../src/perl5/GenomeDB.pm line 37. >> Compilation failed in require at >> /var/www/jbrowse/bin/../src/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm line 5. >> BEGIN failed--compilation aborted at >> /var/www/jbrowse/bin/../src/perl5/Bio/JBrowse/Cmd/BioDBToJson.pm line 5. >> Compilation failed in require at bin/biodb-to-json.pl line 7. >> BEGIN failed--compilation aborted at bin/biodb-to-json.pl line 7. >> >> >> >> <quote author='Dave Clements, GMOD Help Desk-3'> >> Hi Minh, >> >> I'm CC'ing the JBrowse list as people there may have additional >> suggestions. >> >> My guess is that JSON.pm was not installed on the system, or if it was >> installed, it's in a place that is not in @INC. A common cause of this is >> installing JSON.pm as a regular user, rather than as root. >> >> If you haven't already done so, please install JSON with CPAN. >> >> Dave C. >> >> On Thu, Jul 15, 2010 at 10:09 AM, <bui...@gm...> wrote: >> >>> Hi, >>> I am trying to set up Jbrowse on my Ubuntu Local Server. >>> I follow this guide http://gmod.org/wiki/JBrowse_Tutorial. After I >>> install >>> everything, I run this command in my terminal: >>> "bin/flatfile-to-json.pl" and get the following message. >>> >>> Can't locate JSON.pm in @INC (@INC contains: /var/www/jbrowse/bin/../lib >>> /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 >>> /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 >>> /usr/local/lib/site_perl .) at >>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm >>> line 10. >>> BEGIN failed--compilation aborted at >>> /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 10. >>> Compilation failed in require at >>> /var/www/jbrowse/bin/flatfile-to-json.plline 13. >>> BEGIN failed--compilation aborted at /var/www/jbrowse/bin/ >>> flatfile-to-json.pl line 13. >>> >>> >>> Could you show me how to fix this??? >>> >> >> >> >> -- >> ===> PLEASE KEEP RESPONSES ON THE LIST <=== >> http://gmod.org/wiki/GMOD_News >> http://gmod.org/wiki/ISMB_2010 >> http://gmod.org/wiki/Help_Desk_Feedback >> >> ------------------------------------------------------------------------------ >> This SF.net email is sponsored by Sprint >> What will you do first with EVO, the first 4G phone? >> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first >> _______________________________________________ >> Gmod-ajax mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax >> >> </quote> >> Quoted from: >> http://gmod.827538.n3.nabble.com/Re-Jbrowse-Set-Up-Error-tp970883p970883.html > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain dot > net > GMOD Coordinator (http://gmod.org/) 216-392-3087 > Ontario Institute for Cancer Research > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Gmod-ajax mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax > > </quote> > Quoted from: > http://gmod.827538.n3.nabble.com/Re-Jbrowse-Set-Up-Error-tp4024695p4024695.html -- ------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research |