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GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
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124 stars 85 forks source link

handleJbrowse does not seem to download plugins #1000

Closed hexylena closed 8 years ago

hexylena commented 8 years ago 
[hxr@leda:~/work/apollo]1$ gradle :installJBrowsePlugins                                                                                     (master) 

<snip>

:evaluateJBrowseConfigs UP-TO-DATE
:installJBrowse
installing jbrowse [git:[url:https://github.com/GMOD/jbrowse, branch:master, alwaysPull:true, alwaysRecheck:true], plugins:[WebApollo:[included:true], RegexSequenceSearch:[included:true], HideTrackLabels:[included:true], GCContent:[git:https://github.com/cmdcolin/gccontent, branch:master, alwaysPull:true]]]
using bower to update: jbrowse-download
bower jDataView#*           not-cached git://github.com/rbuels/jDataView.git#*
bower jDataView#*              resolve git://github.com/rbuels/jDataView.git#*

<snip>

Evaluating plugin GCContent=[git:https://github.com/cmdcolin/gccontent, branch:master, alwaysPull:true]
Plugin is supplied by git
Cloning 'https://github.com/cmdcolin/gccontent' into 'jbrowse-download/plugins/GCContent'
using bower to install: cmdcolin/gccontent#master
bower gccontent#master      not-cached git://github.com/cmdcolin/gccontent.git#master
bower gccontent#master         resolve git://github.com/cmdcolin/gccontent.git#master
bower gccontent#master        checkout master
bower gccontent#master        resolved git://github.com/cmdcolin/gccontent.git#7badc321e2
bower gccontent#master         install gccontent#7badc321e2

gccontent#7badc321e2 bower_components/gccontent
Bower dependencies already installed.  Type '/usr/local/bin/bower install -f allow-root' to force reinstallation of dependencies.
Installing Perl prerequisites ... done.

Formatting Volvox example data ... done.
To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox.

Formatting Yeast example data ... done.
To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast.

Building and installing legacy wiggle format support (superseded by BigWig tracks) ... done.

Building and installing legacy bam-to-json.pl support (superseded by direct BAM tracks) ... done.
CLONED from https://github.com/cmdcolin/gccontent into jbrowse-download/plugins/GCContent

BUILD SUCCESSFUL

Total time: 11.885 secs
[hxr@leda:~/work/apollo]$                                                                                                                    (master) 
[hxr@leda:~/work/apollo]$ find . -iname 'gccontent'                                                                                          (master)
[hxr@leda:~/work/apollo]$ ls jbrowse-download/plugins/GCContent                                                                             (master) 
ls: klarte ikke å åpne jbrowse-download/plugins/GCContent: Fila eller mappa finnes ikke

It says quite explicitly CLONED from https://github.com/cmdcolin/gccontent into jbrowse-download/plugins/GCContent except there's nothing there. (And given how JBrowse doesn't fail nicely when plugins are missing, this means JBrowse is non-functional in the apollo instance)

nathandunn commented 8 years ago

I think what happened is that it cloned it into bower_components, but at some point it got deleted. I'll take a look at it.

hexylena commented 8 years ago

@nathandunn ok, great. I'm on a2d7fc0e76794e4e0c084a0344f967cdee7987f3.

Btw you're spot on about bower_components getting wiped out. I straced the process and noticed

dump.7533:rmdir("/home/hxr/work/apollo/bower_components/gccontent/css") = 0
dump.7533:rmdir("/home/hxr/work/apollo/bower_components/gccontent/js/Store/SeqFeature") = 0
dump.7533:rmdir("/home/hxr/work/apollo/bower_components/gccontent/js/Store") = 0
dump.7533:rmdir("/home/hxr/work/apollo/bower_components/gccontent/js/View/Track") = 0
dump.7533:rmdir("/home/hxr/work/apollo/bower_components/gccontent/js/View/Dialog") = 0
dump.7533:rmdir("/home/hxr/work/apollo/bower_components/gccontent/js/View") = 0
dump.7533:rmdir("/home/hxr/work/apollo/bower_components/gccontent/js") = 0
dump.7533:rmdir("/home/hxr/work/apollo/bower_components/gccontent/img") = 0
dump.7533:rmdir("/home/hxr/work/apollo/bower_components/gccontent") = 0
dump.7533:rmdir("/home/hxr/work/apollo/bower_components") = 0
nathandunn commented 8 years ago

https://github.com/nathandunn/Apollo/commit/537800a19b5abdebca0742fc61c34306253e088e should fix it. Sorry . . I'd meant to do a pull request.

Let me know if not. And . . 🎂 🎈 🍰 Issue 1000!!!!

hexylena commented 8 years ago

@nathandunn confirmed, that fixes it! :100: (x10)

nathandunn commented 8 years ago

the last commit just removed the bower_components if the directory is empty

hexylena commented 8 years ago

(Would it be possible to get this into gmod/apollo? )