Hi, Trying to use the MultiVariantViewer plugin, I've got the "Grid" type working but when I try switching to the "LDTrack" type it throws the following error:Unable to load undefined?ref=A01&start=24772045&end=24778435&url=http%3A%2F%2Fjbrowse.xxxxx.com%2Fdata%2Fjson%2FGohir_v11%2F%2F..%2F..%2Fraw%2FGohir_v11%2FWGS%2FACH1718_d20.vcf.gz status 404 ------------------------------------------------------------------------------ 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 |
Currently, LDTrack requires the "linkage_server" part of the code to be running. To setup, go into the linkage_server folder, run `npm install`, and then `node index.js`, then set the ldviewer config in trackList.json to point to that node.js microservice (default runs on port 4730)
-Colin On Thu, May 4, 2017 at 10:39 AM, Ke Jiang <[hidden email]> wrote:
------------------------------------------------------------------------------ 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 |
Thanks, Colin! When I read this in the docs, I thought it meant linkage server was an option... This is gonna be hard for me, as I'm not the administrator of the server, but I'll give it a try. "Optionally, LD can be calculated from the VCF files on the server side using plink and rendered as a classic block view." On Thu, May 4, 2017 at 12:23 PM, Colin <[hidden email]> wrote:
------------------------------------------------------------------------------ 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, I gave a try with this and got this error:Unable to load http://localhost:4730?ref=A01&start= [khttp_connect_file] fail to open file (HTTP code: 404). [main] fail to open the data file. Is this because the server couldn't find the calculated LD data? So where are these data calculated and stored so I could go and take a look? Thanks! Ke On Thu, May 4, 2017 at 1:03 PM, Ke Jiang <[hidden email]> wrote:
------------------------------------------------------------------------------ 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 |
The ldserver assumes that it can fetch the tabix VCF similar to how the browser does, so it receives as an argument the URL to the file e.g. the "http%3A%2F%2Fjbrowse. For example, in this case, the url (after urldecoding) says http://jbrowse.xxxxx.com/data/json/Gohir_v11//../../raw/Gohir_v11/WGS/ACH1718_d20.vcf.gz, does this file exist if you visit it manually? -Colin On Wed, May 10, 2017 at 9:38 AM, Ke Jiang <[hidden email]> wrote:
------------------------------------------------------------------------------ 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 |
cc list resolved -Colin On Wed, May 10, 2017 at 10:56 AM, Ke Jiang <[hidden email]> wrote:
------------------------------------------------------------------------------ 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 |
Not quite there yet. I frequently run into complete blank rendering, even in a small interval as big as 10kb. And both "Matrix" and "LDTrack" gave blank rendering. Can't see any error messages on the linkage server side, as well as in the JS console. Any thoughts? On Wed, May 10, 2017 at 11:35 AM, Colin <[hidden email]> wrote:
------------------------------------------------------------------------------ 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 |
Not sure if you already notice but the Matrix and LDTrack tracks are unique track types where you refresh the data in the current view manually using the track menu. Does that help? ![]() -Colin On Wed, May 10, 2017 at 12:05 PM, Ke Jiang <[hidden email]> wrote:
------------------------------------------------------------------------------ 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 |
Free forum by Nabble | Edit this page |