This is my script to rune2e with instrumenting:
As you can see I create an instrumented copy of my js files.
change index.html to reference the instrumented files (with sed)
the script:

#!/bin/bash

BASE_DIR=`dirname $0`
echo ""
echo "Istanbul instrumenting js files"
echo "-------------------------------------------------------------------"
istanbul instrument $BASE_DIR/../app/js -o $BASE_DIR/../app/instrumentjs

echo ""
echo "Building an instrumented index.html"
echo "------------------------------------------------------------------"
cat $BASE_DIR/../app/index.html | sed s/\"js/\"instrumentjs/ >
app/index_e2etest.html

echo ""
echo "Starting node.js local webserver to run the tests"
echo "-------------------------------------------------------------------"
node $BASE_DIR/../scripts/web-server.js > /dev/null 2>&1 &

echo ""
echo "Starting Karma Server (http://karma-runner.github.io)"
echo "-------------------------------------------------------------------"

karma start $BASE_DIR/../config/karma-e2e.conf.js $*

Also: in my karma-e2e.conf I added the following lines:

preprocessors: {
            '../app/instrumentjs/**/*.js': 'coverage'
        },

Setting the coverage plugin to check the instrumented js files we created
before



Twitter:@alonisser <https://twitter.com/alonisser>
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Tel:972-54-6734469


On Tue, Aug 5, 2014 at 12:47 AM, Xiaohui Chen <[email protected]>
wrote:

> I think my problem is the way instrumented files were put on the server.
> You mention you have a special index.html, so I'd like to see how you did
> it.  Please post it if not too much trouble.  I appreciate your help.
>
> Tony
> On Aug 4, 2014 2:09 PM, "alonn" <[email protected]> wrote:
>
>> Since Angular moved to Protractor  I didn't post the working solution -
>> If this is still relevant to you I can post it here
>>
>>
>>
>> Twitter:@alonisser <https://twitter.com/alonisser>
>> LinkedIn Profile <http://www.linkedin.com/in/alonisser>
>> Facebook <https://www.facebook.com/alonisser>
>> *Tech blog:*4p-tech.co.il/blog
>> *Personal Blog:*degeladom.wordpress.com
>> Tel:972-54-6734469
>>
>>
>> On Mon, Aug 4, 2014 at 11:49 PM, Xiaohui Chen <[email protected]>
>> wrote:
>>
>>> Have you got chance to post your solution yet?  Cause I am working on a
>>> similar project but put files instrumented by istanbul on server did not
>>> work.
>>>
>>>
>>> On Thursday, October 31, 2013 12:56:59 AM UTC-7, Alon Nisser wrote:
>>>>
>>>> It can be done (figured it a few days ago) - Also hacky (At least the
>>>> js part, not the html) I'll be posting later the exact process I use, but
>>>> mainly I use istanbul intrument to create an instrumented js folder for my
>>>> app/js, I create (on the fly) an alternative index.html to load this js
>>>> instead of the regular js and changed scenario.js files to use the changed
>>>> index.html instead of the orginial one
>>>> I automated everything in the e2e-tesh.sh.
>>>>
>>>> I hope later today (or tomorrow) I'll have to to post a full solution
>>>>
>>>> On Thursday, October 31, 2013 4:25:43 AM UTC+2, Jack Zhang wrote:
>>>>>
>>>>> Well, thank you for your replay.
>>>>>
>>>>> But we really need a way which can help us measure the coverage of our
>>>>> e2e test in our project. We want a quantifiable report to guarantee the
>>>>> quality of e2e test. If karma can not do this, do you have other 
>>>>> solutions ?
>>>>>
>>>>> Very appreciate for your response.
>>>>>
>>>>> On Thursday, October 31, 2013 2:19:07 AM UTC+8, Daniel Tabuenca wrote:
>>>>>>
>>>>>> I don't believe you can do this with karma for end to end tests.
>>>>>> During normal unit testing the files are served by karma itself so it can
>>>>>> instrument them and fully control things. During end-to-end testing, the
>>>>>> files are being served by your web server.
>>>>>>
>>>>>> If you are looking for javascript coverage, you might want to look at
>>>>>> using Istanbul (the library karma is using for coverage) directly.
>>>>>>
>>>>>> https://github.com/yahoo/istanbul
>>>>>>
>>>>>>
>>>>>> On Wednesday, October 30, 2013 2:52:13 AM UTC-7, Jack Zhang wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> I used angularjs e2e for my project's end2end test i can also run
>>>>>>> that in karma.
>>>>>>>
>>>>>>> I know i can use 'karma-coverage' plugin to measure my code
>>>>>>> coverage, but this is only for unit test.
>>>>>>>
>>>>>>> Now, i want to measure End2End Test coverage which help me know how
>>>>>>> much my test cases have coverage scenario, Anyone can tell me how to
>>>>>>> measure end2end test coverage automatically?
>>>>>>>
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