Re: [Gmod-ajax] JBrowse 1.15.2 released

[Colin <col...@gm...>]

Hi Vaneet,

The new 1.15.2 now recommends downloading the source code from GitHub
release page if you need to rebuild or use plugins, the "-dev" release was
removed as it doesn't add anything compared to the source distribution


Try the source code download from
https://github.com/GMOD/jbrowse/releases/tag/1.15.2-release and I think it
will work for you


The source code download will have the css directory also. The compiled
releases use scss to compile the css into a "module" so the css directory
is unneeded.



-Colin

On Tue, Aug 21, 2018 at 1:27 PM Vaneet Lotay <van...@uc...>
wrote:

> Hey Colin,
>
>
>
> Having trouble installing this new release of JBrowse.  I ran setup.sh
> script and then ran the npm command (‘npm run build’) as usual but it
> returned with errors.  I’ve attached the npm log file.
>
>
>
> Also I could not find the ‘css’ directory in this release, where is that
> located?  Have those files been reorganized somehow.
>
>
>
> Thanks,
>
>
>
> Vaneet
>
>
>
> *Vaneet Lotay*
>
> *Xenbase Bioinformatician*
>
> *716 ICT Building - University of Calgary*
>
> *2500 University Drive NW*
>
> *Calgary AB T2N 1N4*
>
> *CANADA*
>
>
>
> *From:* Colin [mailto:col...@gm...]
> *Sent:* Thursday, August 16, 2018 4:12 PM
> *To:* gmo...@li...
> *Subject:* [Gmod-ajax] JBrowse 1.15.2 released
>
>
>
> Hi all,
>
>
>
> JBrowse 1.15.2 has been released! This contains a couple nice features
> including estimating feature density directly from the index file of BAM,
> VCF, and other tabix formats. We also updated the website with a new
> blogging and documentation platform! Please try it out and give us feedback.
>
> Enjoy browsing!
>
> ·         JBrowse-1.15.2.zip
> <https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2.zip> -
> 4.34 MB
>
> ·         JBrowse-1.15.2-desktop-win32-x64.zip
> <https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2-desktop-win32-x64.zip> -
> 69M
>
> ·         JBrowse-1.15.2-desktop-linux-x64.zip
> <https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2-desktop-linux-x64.zip> -
> 67M
>
> ·         JBrowse-1.15.2-desktop-darwin-x64.zip
> <https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2-desktop-darwin-x64.zip> -
> 68M
> Minor improvements
>
> ·         Created "index stats estimation" which overrides the older
> "global stats estimation" that randomly samples genomic regions of BAM,
> VCF, etc to find feature density. This allows initial track load to be
> faster automatically. (issue #1092
> <https://github.com/gmod/jbrowse/issues/1092>, issue #1167
> <https://github.com/gmod/jbrowse/pull/1167>, @cmdcolin
> <https://github.com/cmdcolin>)
>
> ·         Removed the "full" or "dev" releases from the build. If you
> need a "dev" release, you can simply download the JBrowse "source code"
> link from the GitHub releases page, or use a git clone of the JBrowse
> repository. This will behave the same as the "dev" release. (issue #1160
> <https://github.com/gmod/jbrowse/issues/1160>, issue #1170
> <https://github.com/gmod/jbrowse/pull/1170>, @cmdcolin
> <https://github.com/cmdcolin>)
>
> ·         JBrowse now uses a new binary-file caching and fetching backend
> based on the http-range-fetcher
> <https://www.npmjs.com/package/http-range-fetcher> andtenacious-fetch
> <https://www.npmjs.com/package/tenacious-fetch> npm modules. Users may
> see slightly higher performance when viewing indexed binary formats such as
> BAM, CRAM, 2bit, etc. (issue #1155
> <https://github.com/gmod/jbrowse/issues/1155>, issue #1175
> <https://github.com/gmod/jbrowse/issues/1175>, issue #1165
> <https://github.com/gmod/jbrowse/pull/1165>, @rbuels
> <https://github.com/rbuels>)
>
> ·         Updated the main jbrowse.org website to use the docusaurus
> platform. The main docs for the website are now moved from the GMOD.org
> server to jbrowse.org. You can find the latest documentation in the
> header bar. We hope you will enjoy this upgrade! There is also a new quick
> start guide based on setting up JBrowse with indexed file formats. (issue
> #1153 <https://github.com/gmod/jbrowse/issues/1153>, issue #1137
> <https://github.com/gmod/jbrowse/issues/1137>, issue #1173
> <https://github.com/gmod/jbrowse/pull/1173>, @cmdcolin
> <https://github.com/cmdcolin>)
> Bug fixes
>
> ·         Added a more robust HTML processing in Util.js. Thanks to
> @hkmoon <https://github.com/hkmoon> for the idea and implementation. (issue
> #1169 <https://github.com/gmod/jbrowse/pull/1169>, @hkmoon
> <https://github.com/hkmoon>)
>
> ·         Remove utils/jb_run.js from the minified release (issue #1161
> <https://github.com/gmod/jbrowse/issues/1161>, issue #1160
> <https://github.com/gmod/jbrowse/issues/1160>, @cmdcolin
> <https://github.com/cmdcolin>)
>
> ·         Fixes issue where navigating away from genome browser and
> returning would not remember the location. Thanks to Vaneet Lotay for
> reporting. (issue #1168 <https://github.com/gmod/jbrowse/issues/1168>,
> @cmdcolin <https://github.com/cmdcolin>)
>
> ·         Fixes off-by-one in the display of the size of the genomic
> region being viewed. Thanks to @sammyjava <https://github.com/sammyjava>for
> the bug report! (issue #1176 <https://github.com/gmod/jbrowse/issues/1176>
> , @cmdcolin <https://github.com/cmdcolin>)
>