New website build update (#1347)

Uses travis-ci s3 uploader

.travis.yml

@@ -64,6 +64,7 @@ script:
     MOZ_HEADLESS=1 SELENIUM_BROWSER=firefox NOSEOPTS="-I jasmine" JBROWSE_URL=http://localhost:9000/JBrowse-$RELEASE_VERSION/index.html tests/selenium_tests/travis_wrapper.sh;
   fi
 - set +e
+- website/build.sh
 after_failure:
 - cat setup.log
 before_cache:
@@ -90,10 +91,14 @@ deploy:
     repo: GMOD/jbrowse
     perl: 5.26
     tags: true
-- provider: script
-  script: website/deploy.sh
+- provider: s3
+  access_key_id: $AWS_ACCESS_KEY
+  secret_access_key: $AWS_SECRET_KEY
+  bucket: "jbrowse-org"
   skip_cleanup: true
+  local-dir: website/build/jbrowse/
   on:
     perl: 5.26
+    repo: GMOD/jbrowse
     condition: $TRAVIS_COMMIT_MESSAGE =~ (\[update docs\])
     all_branches: true

docs/tutorial/data_files/volvox-long-reads.fastq.sorted.bam.conf

@@ -1,7 +1,7 @@
 [ tracks . volvox-long_reads ]
 key = BAM - volvox-longreads.bam
 storeClass = JBrowse/Store/SeqFeature/BAM
-urlTemplate = ../../raw/volvox//volvox-long-reads.fastq.sorted.bam
+urlTemplate = ../../raw/volvox/volvox-long-reads.fastq.sorted.bam
 metadata.category = BAM
 metadata.Description = BAM-format alignments of simulated long reads.
 type = JBrowse/View/Track/Alignments2

docs/tutorial/data_files/volvox-long-reads.fastq.sorted.cram.conf

@@ -1,7 +1,7 @@
 [ tracks . volvox-long_reads-cram ]
 key = CRAM - volvox-longreads.cram
 storeClass = JBrowse/Store/SeqFeature/CRAM
-urlTemplate = ../../raw/volvox//volvox-long-reads.fastq.sorted.cram
+urlTemplate = ../../raw/volvox/volvox-long-reads.fastq.sorted.cram
 metadata.category = BAM
 metadata.Description = CRAM-format alignments of simulated long reads.
 type = JBrowse/View/Track/Alignments2

website/build.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+if [ ! -r package.json ]; then
+    echo cannot read version number from ./package.json, aborting website deploy;
+    exit 1;
+fi;
+RELEASE_VERSION=`node -e 'require("fs").readFile("package.json", (e,d)=>console.log(JSON.parse(d).version))'`
+set -e
+set -x
+cd ${0%/*}
+yarn
+yarn build
+cp -R ../img build/jbrowse/docs/assets/img

website/pages/en/demos.js

@@ -17,7 +17,7 @@ class Index extends React.Component {
         <ul>
           <li><a title="Volvox example data" href="/code/latest-release/?loc=ctgA%3A9900..32510&amp;tracks=DNA%2CTranscript%2Cvolvox-sorted-vcf%2Cvolvox-sorted_bam%2Cvolvox_microarray_bw_xyplot%2Cvolvox_microarray_bw_density&amp;data=sample_data%2Fjson%2Fvolvox&amp;highlight=" target="_blank"><i>Volvox mythicus</i> example/test data</a> - the latest JBrowse release, showing the primary test data set used in development.  Includes demonstrations of all major JBrowse track types, including direct display of BAM alignments and coverage, direct display of BigWig data, and more.  This data is made up for demonstration purposes.</li>
           <li><a title="view faceted track selector demo - hit &quot;Select tracks&quot; on the left" href="/code/latest-release/index.html?data=sample_data/json/modencode" target="_blank">Faceted track selection demo</a> - running in the latest JBrowse release with over 1,800 tracks.  Based on a snapshot of the modENCODE track metadata taken from <a href="http://data.modencode.org" target="_blank">http://data.modencode.org</a>.  Note that the actual track data and reference sequences in this track selection demo are just made-up test data.</li>
-          <li><a href="http://jbrowse.org/code/JBrowse-1.12.5/compat_121.html?data=http://jbrowse.org/ucsc/hg19/data/" target="_blank">Human hg19 genes</a> - a demonstration of a large dataset.  From UCSC Genome Database - <a href="https://genome.ucsc.edu" target="_blank">https://genome.ucsc.edu</a></li>
+          <li><a href="http://jbrowse.org/code/JBrowse-1.12.5/compat_121.html?data=/genomes/ucsc_hg19" target="_blank">Human hg19 genes</a> - a demonstration of a large dataset.  From UCSC Genome Database - <a href="https://genome.ucsc.edu" target="_blank">https://genome.ucsc.edu</a></li>
           <li><a title="D. melanogaster JBrowse" href="/code/latest-release/?data=%2Fgenomes%2Fflybase-dmel-5.52-genes&amp;loc=2L%3A10283901..10390066&amp;tracks=DNA%2CGenes" target="_blank"><em>Drosophila melanogaster</em> genes</a> - from FlyBase release 5.52.  Good demonstration of JBrowse 1.12.0 canvas-based gene glyphs.</li>
         </ul>
         <h3>Older instances</h3>

website/pages/en/help.js

@@ -23,7 +23,7 @@ class Help extends React.Component {
         title: 'Join the community',
       },
       {
-        content: "Find out what's new with this project",
+          content: "Find out what's new with this project on the release announcements <a href='http://jbrowse.org/blog'>blog</a> or follow our github",
         title: 'Stay up to date',
       },
     ];