Blogpost updates

website/blog/2014-05-14-jbrowse-1-11-4-maintenance-release-index.md

@@ -7,9 +7,9 @@ tags: ["News","Software releases"]
 
 I am happy to announce the release of JBrowse 1.11.4. This is the first release after Rob's leave, and it represents the great community effort to keep things going. There are some exciting new developments in this version, including high-resolution rendering of canvas-based tracks and a basic GTF file parser. There are also several important bug fixes, including an update to the setup.sh script in order to maintain compatibility with the latest BioPerl.
 
-*   [JBrowse-1.11.4.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=95) - 5.3M
+*   [JBrowse-1.11.4.zip](http://jbrowse.org/releases/JBrowse-1.11.4.zip) - 4.9M
 file SHA1 08834c1fd3a947971459ddc4482128cdaf80a668
-*   [JBrowse-1.11.4-dev.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=96) - 26M
+*   [JBrowse-1.11.4-dev.zip](http://jbrowse.org/releases/JBrowse-1.11.4-dev.zip) - 26M
 file SHA1 4f6ac7aa339e20e9be3e717fd88bd27a62f40f27
 
 ## Minor improvements
@@ -31,4 +31,4 @@ file SHA1 4f6ac7aa339e20e9be3e717fd88bd27a62f40f27
 *   Fixed a long standing bug with the scrollbar in the dialog box on Chrome and Safari browsers. Thanks to the #dojo irc channel and and Colin Diesh for helping fix this problem ([issue #386](https://github.com/gmod/jbrowse/issues/386)).
 *   Fix a small rendering problem that causes one pixel gap to appear on Safari due to subpixel rendering issues. Thanks to Colin Diesh for the preliminary fix ([issue #341](https://github.com/gmod/jbrowse/issues/341)).
 *   Fix a bug with CanvasFeatures based tracks loading huge amounts of data to generate histograms instead of using pre-generated histograms. Thanks to Daniel Troesser for reporting this on the mailing list and Colin Diesh for the fix ([issue #475](https://github.com/gmod/jbrowse/issues/475)).
- 
+ 

website/blog/2014-09-04-jbrowse-1-11-5-index.md

@@ -7,9 +7,9 @@ tags: ["News","Software releases"]
 
 A new JBrowse release has arrived! JBrowse 1.11.5 incorporates many valuable contributions and feedback from the community which has been overwhelmingly positive. Some notable bugs have been fixed, including a long-standing VCF file parsing bug, a scrolling bug that affected popup boxes for variants on JBrowse 1.11.4, and a patch for setup.sh build errors. There are also some new configuration options for the tracklist and dialog boxes, and the ability to use tablet and touch-screen devices has been fixed!
 
-*   [JBrowse-1.11.5.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=98) - 4.7M
+*   [JBrowse-1.11.5.zip](http://jbrowse.org/releases/JBrowse-1.11.5.zip) - 4.9M
 file SHA1 480a9363c1799713666bed56d6a134af69982c9e
-*   [JBrowse-1.11.5-dev.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=97) - 25.2M
+*   [JBrowse-1.11.5-dev.zip](http://jbrowse.org/releases/JBrowse-1.11.5-dev.zip) - 26M
 file SHA1 8b0040bda792b70a7a100a0f3fc19dcc829819c4
 
 ## Minor improvements
@@ -31,4 +31,4 @@ file SHA1 8b0040bda792b70a7a100a0f3fc19dcc829819c4
 *   Fixed the use of the --refs flag on prepare-refseqs.pl. Thanks to Audrey for finding & fixing this bug ([issue #497](https://github.com/gmod/jbrowse/issues/497)).
 *   Added missing template length flag to the Alignments popup dialogs. Thanks to Kieran Raine for the suggestion and Colin Diesh for the fix ([issue #471](https://github.com/gmod/jbrowse/issues/471)).
 *   Fixed the functionality of the --incremental flag in the generate-names.pl script. Thanks to Richard Hayes and Colin Diesh fixing the issue ([issue #478](https://github.com/gmod/jbrowse/issues/478)).
-*   Fixed legacy bam-to-json.pl support when running setup.sh due to samtools build modifications ([issue #501](https://github.com/gmod/jbrowse/issues/501)).
+*   Fixed legacy bam-to-json.pl support when running setup.sh due to samtools build modifications ([issue #501](https://github.com/gmod/jbrowse/issues/501)).

website/blog/2015-02-12-jbrowse-1-11-6-index.md

@@ -7,9 +7,9 @@ tags: ["News","Software releases"]
 
 I'm pleased to announce JBrowse 1.11.6 is now available! Everybody's feedback, bug reports, pull requests, and feature requests have been invaluable for making this happen. This release includes new UI options for easily setting "Log scale" on wiggle tracks and dynamically changing strandedness on RNA-seq according to multi-segment template flags and splice site (XS) flags. It also includes bug fixes for calculating SNP positions on certain flag combinations in BAM files and for reporting the correct genotypes on certain VCF tracks. Enjoy!
 
-*   [JBrowse-1.11.6.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=99) - 4.7M
+*   [JBrowse-1.11.6.zip](http://jbrowse.org/releases/JBrowse-1.11.6.zip) - 4.9M
 file SHA1 81dd4db6d0dcab261450dab1414e343e106ed6c4
-*   [JBrowse-1.11.6-dev.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=100) - 26M
+*   [JBrowse-1.11.6-dev.zip](http://jbrowse.org/releases/JBrowse-1.11.6-dev.zip) - 26M
 file SHA1 c6d6ff4f68fa3ae0180bdea9c7871f9a5a4dd1d7
 
 ## Minor improvements
@@ -45,4 +45,4 @@ file SHA1 c6d6ff4f68fa3ae0180bdea9c7871f9a5a4dd1d7
 *   Added a bugfix that prevented viewing the details of haploid VCF files. Thanks to Colin Diesh for finding and fixing this bug ([issue #536](https://github.com/gmod/jbrowse/issues/536)).
 *   Added a bugfix for an issue that made browsing very buggy when using private browsing mode in Safari.
 *   Fixed the `shortDescription` option for the mouseover description of tracks in the Hierarchical track list ([issue #553](https://github.com/gmod/jbrowse/issues/553)).
-*   Re-added filter options that were missing for SNPCoverage tracks.
+*   Re-added filter options that were missing for SNPCoverage tracks.

website/blog/2015-12-17-jbrowse-1-12-0-index.md

@@ -7,15 +7,17 @@ tags: ["News","Software releases"]
 
 We are happy to announce JBrowse 1.12.0 release! This new release includes some exciting new features including the ability to load new genomes from FASTA and indexed FASTA formats; in-line refseqs, and server-free desktop applications for Windows and OSX (based on Electron).  New plugins beautifully enhances feature rendering with intron hats and gradients in both HTML and canvas tracks, provide URL links to call up tracks by category URL, among others.  Improvements include the ability to load custom histograms for tracks loaded from flatfile-to-json.pl; a new wiggle track option scoreType: 'avgValue', which helps preserve continuity when zooming in on certain tracks like GC-content; and the ability to specify the set of startCodons and stopCodons in the config.  In addition, several bugs have been addressed.
 
-*   [JBrowse-1.12.0.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=101) - 4.9M
+
+*   [JBrowse-1.12.0.zip](http://jbrowse.org/releases/JBrowse-1.12.0.zip) - 4.9M
 file SHA1 c74adeb9840ae5c9348e59a9054fa93cf68d0402
-*   [JBrowse-1.12.0-dev.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=102) - 26M (development)
+*   [JBrowse-1.12.0-dev.zip](http://jbrowse.org/releases/JBrowse-1.12.0-dev.zip) - 26M
 file SHA1 55c8fa8aa843813ea24a71e1e905c6af80b6db7a
-*   [Docker Image](https://hub.docker.com/r/jbrowse/gmod-jbrowse/)
-*   [JBrowse-1.12.0-desktop-osx.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=103) - 48M (OSX 64bit)
+*   [JBrowse-1.12.0-desktop-osx.zip](http://jbrowse.org/releases/JBrowse-1.12.0-desktop-osx.zip) - 49M (OSX)
 file SHA1 219ae48753c2dc57f341bfed1458ad1f194d3c9f
-*   [JBrowse-1.12.0-desktop-win.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=104) - 49M (Windows 32bit)
+*   [JBrowse-1.12.0-desktop-win.zip](http://jbrowse.org/releases/JBrowse-1.12.0-desktop-win.zip) - 49M (Windows)
 file SHA1 4e3d2098cd6b352caac1b0234a290540ba0ff9a1
+*   [Docker Image](https://hub.docker.com/r/jbrowse/gmod-jbrowse/)
+
 
 ## New features
 
@@ -50,4 +52,4 @@ file SHA1 4e3d2098cd6b352caac1b0234a290540ba0ff9a1
 *   Fixed a bug where the user's --workdir parameter would be deleted which could have unintended side effects if the --workdir was pointing to important data, but this is uncommon ([issue #563](https://github.com/gmod/jbrowse/issues/563)).
 *   Allow falsey values to be used in browser.cookie.
 *   Fix minor issue where sometimes the length field of refSeqs.json was missing.
-*   Fix some issues that occurred when a reference sequence was named '0' ([issue #662](https://github.com/gmod/jbrowse/issues/662), [issue #610](https://github.com/gmod/jbrowse/issues/610)).
+*   Fix some issues that occurred when a reference sequence was named '0' ([issue #662](https://github.com/gmod/jbrowse/issues/662), [issue #610](https://github.com/gmod/jbrowse/issues/610)).

website/blog/2016-03-01-jbrowse-1-12-1-index.md

@@ -7,15 +7,15 @@ tags: ["News","Software releases"]
 
 We are happy to announce JBrowse 1.12.1 release!   This is a maintenance release.
 
-*   [download id="1283"] - 4.9M
+*   [JBrowse-1.12.1.zip](http://jbrowse.org/releases/JBrowse-1.12.1.zip) - 4.9M
 file SHA1 bb917733f768744d703ab7b17b1f80040c055a78
-*   [download id="1285"] - 26M (development)
+*   [JBrowse-1.12.1-dev.zip](http://jbrowse.org/releases/JBrowse-1.12.1-dev.zip) - 26M
 file SHA1 737851bf52c0d537eb1c54b5a4b6a12d6736d2f0
-*   [Docker Image](https://hub.docker.com/r/jbrowse/gmod-jbrowse/)
-*   [download id="1289"] - 48M (OSX 64bit)
+*   [JBrowse-1.12.1-desktop-osx.zip](http://jbrowse.org/releases/JBrowse-1.12.1-desktop-osx.zip) - 49M (OSX)
 file SHA1 d766afe66ccb6eb754d1d329c097a447435d108b
-*   [download id="1287"] - 49M (Windows 32bit)
+*   [JBrowse-1.12.1-desktop-win.zip](http://jbrowse.org/releases/JBrowse-1.12.1-desktop-win.zip) - 49M (Windows)
 file SHA1 22613a35ff5eab9d4f9e151f6a153297fe21cb2d
+*   [Docker Image](https://hub.docker.com/r/jbrowse/gmod-jbrowse/)
 
 ## Minor improvements
 
@@ -25,4 +25,4 @@ file SHA1 22613a35ff5eab9d4f9e151f6a153297fe21cb2d
 
 *   Fix RegexSearch plugin and NeatCanvasFeatures plugin - search track
 loading failure (issue #676)
-*   Fix compat_121.html to access /css directory
+*   Fix compat_121.html to access /css directory

website/blog/2017-05-02-jbrowse-1-12-3-index.md

@@ -13,15 +13,15 @@ In addition, visit the [JBrowse Plugin Registry](https://gmod.github.io/jbrowse-
 
 Enjoy!
 
-*   [download id="1291"]- 5.7MB
+*   [JBrowse-1.12.3.zip](http://jbrowse.org/releases/JBrowse-1.12.3.zip) - 4.9M
 file SHA1 a82b308fe22062c2144efed749e7633c3eeee10a
-*   [download id="1293"] - 28MB (development)
+*   [JBrowse-1.12.3-dev.zip](http://jbrowse.org/releases/JBrowse-1.12.3-dev.zip) - 26M
 file SHA1 e5eda1fe148ed0e5501f31a95f34f77f4f9bd783
-*   [Docker Image](https://hub.docker.com/r/jbrowse/gmod-jbrowse/)
-*   [download id="1289"] - 69M (OSX 64bit)
+*   [JBrowse-1.12.3-desktop-osx.zip](http://jbrowse.org/releases/JBrowse-1.12.3-desktop-osx.zip) - 49M (OSX)
 file SHA1 27eede348c613837b6b0a0cf91ee0ca5557d693b
-*   [download id="1295"] - 61M (Windows 32bit)
+*   [JBrowse-1.12.3-desktop-win.zip](http://jbrowse.org/releases/JBrowse-1.12.3-desktop-win.zip) - 49M (Windows)
 file SHA1 14a8c9a870864462a96d6f52504556e76541e889
+*   [Docker Image](https://hub.docker.com/r/jbrowse/gmod-jbrowse/)
 
 ## Minor improvements
 
@@ -109,4 +109,4 @@ the report ([issue #569](https://github.com/gmod/jbrowse/issues/569)).
 *   Fixed issue where saving GFF3 would fail if the source data
 was in VCF format ([issue #800](https://github.com/gmod/jbrowse/issues/800)).
 *   Fixed issue where there was a mix of plugin declarations
-([issue #866](https://github.com/gmod/jbrowse/issues/866)).
+([issue #866](https://github.com/gmod/jbrowse/issues/866)).

website/blog/2018-02-14-jbrowse-1-12-4-maintenance-release-index.md

@@ -13,9 +13,9 @@ However, there have been a HUGE number of smaller improvements and bugfixes, hav
 
 ## Files for download
 
-*   [JBrowse-1.12.4.zip](https://github.com/GMOD/jbrowse/releases/download/1.12.4-release/JBrowse-1.12.4.zip "download JBrowse-1.12.4.zip") - 5.7M
+*   [JBrowse-1.12.4.zip](https://github.com/GMOD/jbrowse/releases/download/1.12.4-release/JBrowse-1.12.4.zip) - 5.7M
 file SHA1 9c3b88d982ceb86de9999e49ddde631d6b41a28f
-*   [JBrowse-1.12.4-dev.zip](https://github.com/GMOD/jbrowse/releases/download/1.12.4-release/JBrowse-1.12.4-dev.zip "download JBrowse-1.12.4-dev.zip") - 30M
+*   [JBrowse-1.12.4-dev.zip](https://github.com/GMOD/jbrowse/releases/download/1.12.4-release/JBrowse-1.12.4-dev.zip) - 30M
 file SHA1 bb3fa872cbc57055712114e3e01cdcad6776a3b6
 
 ## Minor improvements
@@ -99,4 +99,4 @@ Thanks to [@abretaud](https://github.com/abretaud), [@nathandunn](https://github
 *   Added a `--bigwigCoverage` option to `add-bam-track.pl` to support configuring pregenerated
 coverage histograms from the command line. Thanks to [@loraine](https://github.com/loraine)-gueguen for the suggestion
 and implementation! ([issue #972](https://github.com/gmod/jbrowse/pull/972), [@loraine](https://github.com/loraine)-gueguen)
-*   Improved documentation of the `CategoryURL` plugin. ([issue #985](https://github.com/gmod/jbrowse/pull/985), [@enuggetry](https://github.com/enuggetry))
+*   Improved documentation of the `CategoryURL` plugin. ([issue #985](https://github.com/gmod/jbrowse/pull/985), [@enuggetry](https://github.com/enuggetry))