I have setup the JBrowse to run, and played with "trackList.json" for appearances. Cool! http://i.animalgenome.org/jbrowse/?data=data/cattle (http://i.animalgenome.org/jbrowse/?data=data/cattle) I ran "prepare-refseqs.pl" and "flatfile-to-json.pl" for the setup. I tried to see some sample configure but see "tracks.conf" is empty -- I didn't find related introductory info and wonder what's the difference between "trackList.json" and "tracks.conf"? It seems they both control track configurations. Does one reference the other? A separate and simpler question: how can I have the pull-down list of all chromosomes sorted? Thanks in advance, Zhiliang
I have setup the JBrowse to run, and played with "trackList.json" for appearances. Cool! http://i.animalgenome.org/jbrowse/?data=data/cattle (http://i.animalgenome.org/jbrowse/?data=data/cattle) I ran "prepare-refseqs.pl" and "flatfile-to-json.pl" for the setup. I tried to see some sample configure but see "tracks.conf" is empty -- I didn't find related introductory info and wonder what's the difference between "trackList.json" and "tracks.conf"? It seems they both control track configurations. Does one reference the other? A separate and simpler question: how can I have the pull-down list of all chromosomes sorted? Thanks in advance, Zhiliang
tracks.conf is a configuration file that follows the GBrowse conf file format. If you've used GBrowse before you'll find that very familiar. I think there are some example tracks.conf texts in the JBrowse configuration guide that you can follow. You can also specify which configuration file JBrowse reads by changing this configuration in the main 'jbrowse.conf' file, asking JBrowse to read either one of them (trackList.json and tracks.conf) or both. In terms of sorting chr names, I think you'll have to change fasta IDs to reflect the order you want. I know sometimes it's not perfect that chr10 comes after chr1 instead of chr9. Ke On Thu, Sep 25, 2014 at 12:14 AM, Zhiliang Hu wrote: > I have setup the JBrowse to run, and played with "trackList.json" for > appearances. Cool! http://i.animalgenome.org/jbrowse/?data=data/cattle (http://i.animalgenome.org/jbrowse/?data=data/cattle) > > I ran "prepare-refseqs.pl" and "flatfile-to-json.pl" for the setup. I > tried to see some sample configure but see "tracks.conf" is empty -- I > didn't find related introductory info and wonder what's the difference > between "trackList.json" and "tracks.conf"? It seems they both control > track configurations. Does one reference the other? > > A separate and simpler question: how can I have the pull-down list of all > chromosomes sorted? > > Thanks in advance, > > Zhiliang > > > > -----------------------------------------------------------------------------> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > > http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk (http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk) > _______________________________________________ > Gmod-ajax mailing list > Gmod-ajax@... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax (https://lists.sourceforge.net/lists/listinfo/gmod-ajax) >
-- Ke Jiang, Ph.D. Post-doctoral Fellow Delbruck Laboratory Cold Spring Harbor Laboratory Cold Spring Harbor, NY 11724
In addition to what Ke said, the best description of the difference between tracks.conf and trackList.json formats is actually in the release notes for jbrowse 1.11.0 http://jbrowse.org/jbrowse-1-11-0/ (http://jbrowse.org/jbrowse-1-11-0/) The command line programs primarily work with trackList.json files. Also, the dropdown menu for refseqs can be configured here (by default the dropdown is limited to 30 refseqs, but you can configure it to show more, and configure the sort, etc.) http://gmod.org/wiki/JBrowse_Configuration_Guide#Reference_Sequence_Selector_Configuration (http://gmod.org/wiki/JBrowse_Configuration_Guide#Reference_Sequence_Selector_Configuration) Note that jbrowse.conf/jbrowse_conf.json is where you can add the refseq configurations. -Colin On Thu, Sep 25, 2014 at 9:26 AM, Ke Jiang wrote: > tracks.conf is a configuration file that follows the GBrowse conf file > format. If you've used GBrowse before you'll find that very familiar. I > think there are some example tracks.conf texts in the JBrowse configuration > guide that you can follow. You can also specify which configuration file > JBrowse reads by changing this configuration in the main 'jbrowse.conf' > file, asking JBrowse to read either one of them (trackList.json and > tracks.conf) or both. > > In terms of sorting chr names, I think you'll have to change fasta IDs to > reflect the order you want. I know sometimes it's not perfect that chr10 > comes after chr1 instead of chr9. > > Ke > > On Thu, Sep 25, 2014 at 12:14 AM, Zhiliang Hu wrote: >> >> I have setup the JBrowse to run, and played with "trackList.json" for >> appearances. Cool! http://i.animalgenome.org/jbrowse/?data=data/cattle (http://i.animalgenome.org/jbrowse/?data=data/cattle) >> >> I ran "prepare-refseqs.pl" and "flatfile-to-json.pl" for the setup. I >> tried to see some sample configure but see "tracks.conf" is empty -- I >> didn't find related introductory info and wonder what's the difference >> between "trackList.json" and "tracks.conf"? It seems they both control >> track configurations. Does one reference the other? >> >> A separate and simpler question: how can I have the pull-down list of all >> chromosomes sorted? >> >> Thanks in advance, >> >> Zhiliang >> >> >> >> ----------------------------------------------------------------------------->> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer >> Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports >> Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper >> Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer >> >> http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk (http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk) >> _______________________________________________ >> Gmod-ajax mailing list >> Gmod-ajax@... >> https://lists.sourceforge.net/lists/listinfo/gmod-ajax (https://lists.sourceforge.net/lists/listinfo/gmod-ajax) > > > > > -> Ke Jiang, Ph.D. > Post-doctoral Fellow > Delbruck Laboratory > Cold Spring Harbor Laboratory > Cold Spring Harbor, NY 11724 > > > -----------------------------------------------------------------------------> Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk (http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk) > _______________________________________________ > Gmod-ajax mailing list > Gmod-ajax@... > https://lists.sourceforge.net/lists/listinfo/gmod-ajax (https://lists.sourceforge.net/lists/listinfo/gmod-ajax) >
On 2014-09-25 19:27, Colin wrote: > In addition to what Ke said, the best description of the difference > between tracks.conf and trackList.json formats is actually in the > release notes for jbrowse 1.11.0 > http://jbrowse.org/jbrowse-1-11-0/ (http://jbrowse.org/jbrowse-1-11-0/) It would be great if this text could be added to the wiki page. I was also looking there for info about the configuration file format and how the .conf format can be transformed into json and vice versa. It took me some time until I finally found the release announcement with the description. Regards, Marcel
