From 4faf0283f431df691c87a19067697ba3708bbb44 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Fri, 1 Mar 2024 21:10:37 +0000 Subject: [PATCH] Built site for JBrowseR: 0.10.2@5d1185a --- LICENSE.html | 26 ++++++++--------- articles/creating-urls.html | 40 ++++++++++++------------- articles/custom-browser-tutorial.html | 8 ++--- articles/json-tutorial.html | 42 +++++++++++++-------------- authors.html | 4 +-- index.html | 1 + news/index.html | 2 +- pkgdown.yml | 4 +-- reference/track_data_frame.html | 2 +- 9 files changed, 65 insertions(+), 64 deletions(-) diff --git a/LICENSE.html b/LICENSE.html index 252f8f5..64fcaf2 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -129,19 +129,19 @@

9. Accepting Warranty o

APPENDIX: How to apply the Apache License to your work

To apply the Apache License to your work, attach the following boilerplate notice, with the fields enclosed by brackets [] replaced with your own identifying information. (Don’t include the brackets!) The text should be enclosed in the appropriate comment syntax for the file format. We also recommend that a file or class name and description of purpose be included on the same “printed page” as the copyright notice for easier identification within third-party archives.

-
Copyright [yyyy] [name of copyright owner]
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-  http://www.apache.org/licenses/LICENSE-2.0
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-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
+
Copyright [yyyy] [name of copyright owner]
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+  http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
diff --git a/articles/creating-urls.html b/articles/creating-urls.html index 8750044..bb42818 100644 --- a/articles/creating-urls.html +++ b/articles/creating-urls.html @@ -153,26 +153,26 @@

Hosting options

Here is an example CORS configuration for an S3 bucket:

-
[
-    {
-        "AllowedHeaders": [
-            "*"
-        ],
-        "AllowedMethods": [
-            "GET"
-        ],
-        "AllowedOrigins": [
-            "*"
-        ],
-        "ExposeHeaders": [
-            "Accept-Ranges",
-            "Content-Range",
-            "Content-Encoding",
-            "Content-Length"
-        ],
-        "MaxAgeSeconds": 3000
-    }
-]
+
[
+    {
+        "AllowedHeaders": [
+            "*"
+        ],
+        "AllowedMethods": [
+            "GET"
+        ],
+        "AllowedOrigins": [
+            "*"
+        ],
+        "ExposeHeaders": [
+            "Accept-Ranges",
+            "Content-Range",
+            "Content-Encoding",
+            "Content-Length"
+        ],
+        "MaxAgeSeconds": 3000
+    }
+]

One other note is that if you use S3 and are planning on using shinyapps.io to deploy your app, you should locate your bucket in Amazon’s AWS US-East region. Currently, shinyapps.io is hosted entirely diff --git a/articles/custom-browser-tutorial.html b/articles/custom-browser-tutorial.html index f0f1431..39a4d66 100644 --- a/articles/custom-browser-tutorial.html +++ b/articles/custom-browser-tutorial.html @@ -142,10 +142,10 @@

Preparing an assemblysars-cov2.fa.

With these steps taken, we are going to compress and index the assembly, for best performance. The necessary commands are:

-
# 1. compresses sars-cov2.fa to sars-cov2.fa.gz
-# 2. generates sars-cov2.fa.gz.fai and sars-cov2.fa.gz.gzi
-bgzip sars-cov2.fa
-samtools faidx sars-cov2.fa.gz
+
# 1. compresses sars-cov2.fa to sars-cov2.fa.gz
+# 2. generates sars-cov2.fa.gz.fai and sars-cov2.fa.gz.gzi
+bgzip sars-cov2.fa
+samtools faidx sars-cov2.fa.gz

For the rest of the tutorial code, we are going to use the following already hosted results of these commands:

+

JBrowseR is an R package that provides a simple and clean interface to JBrowse 2 for R users. Using JBrowseR, you can: