rbuels

rob@nightshade ~$ echo hihi > foo.txt
rob@nightshade ~$ gzip -c foo.txt > foo.txt.gz
rob@nightshade ~$ gzip -c foo.txt > foo.txt2
rob@nightshade ~$ curl -v --compress http://jbrowse.org/test/foo.txt
* About to connect() to jbrowse.org port 80 (#0)
*   Trying 184.72.219.192... connected
* Connected to jbrowse.org (184.72.219.192) port 80 (#0)
> GET /test/foo.txt HTTP/1.1
> User-Agent: curl/7.21.0 (i686-pc-linux-gnu) libcurl/7.21.0 OpenSSL/0.9.8o zlib/1.2.3.4 libidn/1.18
> Host: jbrowse.org

rbuels

foobar = function( blah, blarg ) {
       // all kinds of javascript in here
# maybe with perl-type comments!
       foo = 42;      
       return foo;
   }; // maybe with or without an ending semicolon

rbuels

#!/usr/bin/env perl
use strict;
use warnings;

use Bio::DB::Taxonomy;

my @gis;
while(<>) {
    chomp;

rbuels

rob@nightshade jbrowse (master $%)$ prove -lr t
t/00.compile.t .............. ok    
t/FastaDatabase.t ........... ok   
t/bam-to-json.pl.t .......... # using temp dir /tmp/4mSzou6L65
t/bam-to-json.pl.t .......... ok   
t/biodb-to-json.pl.t ........ # writing output to /tmp/9WmKQE7M1c
t/biodb-to-json.pl.t ........ ok   
t/draw-basepair-track.pl.t .. # using temp dir /tmp/lGlmDPjaH5
t/draw-basepair-track.pl.t .. 1/? # using temp dir /tmp/Y8MXiXfTAl
t/draw-basepair-track.pl.t .. ok    

rbuels

server {
	listen 80;

	access_log  /var/log/nginx/localhost.access.log;

	location / {
		root   /home/rob/jbrowse;
		index  index.html index.htm;
	}
}

rbuels

{
   "headers" : [
      "start",
      "end",
      "strand",
      "name",
      "alignID",
      "proteinID",
      "subfeatures"
   ],

rbuels

rob@nightshade data_master$ ls tracks/chr1/knownGene/
hist-1000000-0.json   lazyfeatures-27.json  lazyfeatures-4.json   lazyfeatures-72.json
hist-100000-0.json    lazyfeatures-28.json  lazyfeatures-50.json  lazyfeatures-73.json
hist-2000000-0.json   lazyfeatures-29.json  lazyfeatures-51.json  lazyfeatures-74.json
hist-200000-0.json    lazyfeatures-2.json   lazyfeatures-52.json  lazyfeatures-75.json
hist-5000000-0.json   lazyfeatures-30.json  lazyfeatures-53.json  lazyfeatures-76.json
hist-500000-0.json    lazyfeatures-31.json  lazyfeatures-54.json  lazyfeatures-77.json
lazyfeatures-0.json   lazyfeatures-32.json  lazyfeatures-55.json  lazyfeatures-78.json
lazyfeatures-10.json  lazyfeatures-33.json  lazyfeatures-56.json  lazyfeatures-79.json

rbuels

refSeqs = 
[
   {
      "length" : 135534747,
      "name" : "chr10",
      "seqDir" : "seq/chr10",
      "seqChunkSize" : 20000,
      "end" : 135534747,
      "start" : 0
   },

rbuels

trackInfo = 
[
   {
      "url" : "seq/{refseq}/",
      "args" : {
         "chunkSize" : 20000
      },
      "label" : "DNA",
      "type" : "SequenceTrack",
      "key" : "DNA"

rbuels

# Edit this file to specify commands for building this dist.
# See the perldoc for Shipwright::Manual::CustomizeBuild for more
# info.
make: true
test: true
install: mkdir -p %%INSTALL_BASE%%/lib/R; R_LIBS_USER=%%INSTALL_BASE%%/lib/R  R CMD INSTALL -l %%INSTALL_BASE%%/lib/R --no-docs --no-help .
clean: true