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    Nikhil Reddy
    @nikhilRP
    I was wondering if there is a way to load ‘.adam’ files from NFS rather than HDFS
    Frank Austin Nothaft
    @fnothaft
    hi @nikhilRP !
    that shouldn’t be a problem. are you on a cluster where NFS is mounted globally?
    if you’re on a single node (without HDFS mounted) you can just give the normal file system path
    if you’re on a cluster with NFS mounted on all nodes, i think giving the global nfs path will work. alternatively, i’m pretty sure that giving the path prefaced with file:// should work.
    for writing tests for ADAM, we typically put the test file in /tests/resources and then load the file from the classpath
    This message was deleted
    Nikhil Reddy
    @nikhilRP
    @fnothaft yeah I noticed that. But you don’t load “.adam” files at all in tests
    Frank Austin Nothaft
    @fnothaft
    yeah, we normally load from the legacy text formats
    the reason we do that is to avoid checking in binary files
    Nikhil Reddy
    @nikhilRP
    aaah ok. understood
    Frank Austin Nothaft
    @fnothaft
    where we do use .adam files in tests, we load the legacy text file, save it to disk in a temporary directory as a .adam, and then load the converted temp file
    yeah, it just makes it easier to track diffs if we have to change the test collateral
    Nikhil Reddy
    @nikhilRP
    got it
    I thought the primary reason you guys maintain a jenkins server is that you have HDFS mounted
    Frank Austin Nothaft
    @fnothaft
    oh, nope!
    we maintain a jenkins server for spark
    since jenkins is already up for spark, it makes sense to use for adam as well
    we’re in the process of bringing up a large regression test cluster, which we will submit jobs to from jenkins
    Nikhil Reddy
    @nikhilRP
    interesting
    might make sense for you guys to maintain a jenkins server.
    I’m so used to using travis CI just because I don’t have to maintain one extra server
    Frank Austin Nothaft
    @fnothaft
    yeah
    i use travis for a lot of my personal stuff
    jenkins is nice because you can pretty much go wild with customization
    and for the regression testing stuff that we’re setting up
    that’s actually really useful
    Nikhil Reddy
    @nikhilRP
    yeah it’s convenient
    Ok I have some headless browser tests ready for mango.
    Frank Austin Nothaft
    @fnothaft
    e.g., the cluster is set up for dbgap data, so it is kind of hidden away, so we do special hijinks so that jenkins can talk to it
    Nikhil Reddy
    @nikhilRP
    makes sense.
    dbgap and HIPPA are just a pain to deal with
    Frank Austin Nothaft
    @fnothaft
    yeah...
    Nikhil Reddy
    @nikhilRP
    so those headless browser (selenium) tests run fine on my computer for now
    shall i create a pull request and then we can integrate saucelabs driver so that they can run on jenkins
    does that sound good? or you have a better idea?
    Frank Austin Nothaft
    @fnothaft
    that would be wonderful!
    i can get the driver integrated tomorrow, probably
    i’m going to need to drop in a sec; dinner time
    Nikhil Reddy
    @nikhilRP
    cool
    Frank Austin Nothaft
    @fnothaft
    but yeah, just push the PR when you are ready, and i will work to get it set up in jenkins!
    Nikhil Reddy
    @nikhilRP
    enjoy your dinner
    sounds good
    shibuvp
    @shibuvp
    pls give working command of bigdatagenomics/mango
    shibuvp
    @shibuvp
    im getting this error while running mango " java.io.FileNotFoundException: " how to solve this?
    salimbakker
    @salimbakker
    How to change default port and localhost
    Kapeel
    @Kapeel
    hi, I am trying to run Mango notebook on docker on Mac. I used the steps described here:http://bdg-mango.readthedocs.io/en/latest/docker/docker-examples.html
    but when copy paste the notebook URL nothing shows up
    http://0.0.0.0:8888/?token=76279d546798ede3e376b309c982dc9ba070e7b50bd63604
    this was my docker run command
    docker run -p 8080:8080 --entrypoint=/opt/cgl-docker-lib/mango/bin/mango-notebook quay.io/ucsc_cgl/mango:latest -- --ip=0.0.0.0 --allow-root
    jonathan MERCIER
    @bioinfornatics
    Hi, I am experiencing a strange bug with mango described in issue #422 . If any developer is here, i am ready to discuss. thanks