Respected Sir,
I am very much new to jbrowse, as my professor told to configure jbrowse for one plant genome, i have downloaded JBrowse-1.12.1.zip and installed it by typing ./setup.sh and got below log details in command prompt ************************** ajay@ajay-Precision-Tower-7910[akm] ./setup.sh [ 6:25PM] Installing Perl prerequisites ... done. Formatting Volvox example data ... done. To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox. Formatting Yeast example data ... done. To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast. Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done. Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done. ajay@ajay-Precision-Tower-7910[akm] **** ******************************* Sir now I dont understand how i can call jbrowse in any browser I have tried sever thing like opening the link (http://your.jbrowse.root/index.html?data=sample_data/json/volvox) in browser but it is not working. Kindly help me how I can run jbrowse in browser, I am very much new and dont have much system admin experience. Waiting for your reply and suggestion to solve this problem. Thanks and Warm Regards -- Ajay Kumar Mahato (Research Associate) National Research Centre on Plant Biotechnology (www.nrcpb.org) Indian Agricultural Research Institute, Pusa Campus New- Delhi -110012 Contact No. +91- 9868303571 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
Have you setup a webserver and configured it to point to the directory where you've installed jbrowse? There are also desktop versions you can try: On Fri, Apr 7, 2017 at 6:34 AM, ajay kumar <[hidden email]> wrote:
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Respected Sir, Thanks for your prompt reply, and suggestionI will try the desktop version. Sir I would like to know If I am trying to display, genes, cds, repeat I have to put data in gff3 format?. Also is there any manual with example on jbrowser if yes then please send me the link. I am very much thankful to you Once again Thank you Warm Regards Ajay On Sat, Apr 8, 2017 at 3:29 AM, Eric Yao <[hidden email]> wrote:
-- Ajay Kumar Mahato (Research Associate) National Research Centre on Plant Biotechnology (www.nrcpb.org) Indian Agricultural Research Institute, Pusa Campus New- Delhi -110012 Contact No. +91- 9868303571 ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
Hi Ajay, A good place to start is here: The example shows how to import your gff file among other. On Fri, Apr 7, 2017 at 9:31 PM, ajay kumar <[hidden email]> wrote:
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Respected Sir, I have finished the tutorial. And now able to run jbrowse with my own data set.. But I could not understand how I can change viewing pattern of the track also color of track. Like white to red. Or blue Please help me as I am very much new to this domain. Waitimg.for your kind response. Thanks and Warm Regards Ajay On Apr 11, 2017 1:18 AM, "Eric Yao" <[hidden email]> wrote:
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Hi Ajay, This is the detailed reference for configuration options for your tracks (in trackList.json): http://gmod.org/wiki/JBrowse_Configuration_Guide#Feature_Tracks_.28HTMLFeatures_and_CanvasFeatures.29This configuration in your track config determines whether you are using either CanvasFeatures viewer or HTMLFeatures viewer. "type": "JBrowse/View/Track/HTMLFeatures", On Mon, Apr 10, 2017 at 12:54 PM, ajay kumar <[hidden email]> wrote:
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Hi Ajay, There is also this tutorial that I sometimes give: It tries to go into a little more depth on some topics, like changing how the track looks. Scott On Mon, Apr 10, 2017 at 4:08 PM, Eric Yao <[hidden email]> wrote:
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Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax |
oh, very nice, scott! On Mon, Apr 10, 2017 at 2:27 PM, Scott Cain <[hidden email]> wrote:
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