1. Testing seqprep needs some raw run directories which tend to be quite big so aren’t in the main github repo.  These are currently sitting on the system in  /n/informatics/git/testdata/

    The current runs are

    NextSeq150527_NS500422_0126_AH2LC5AFXX
    HiSeq150622_SN343_0517_AC6MUEACXX

    There is also a directory for SampleSheets both correct and flawed in /n/informatics/git/testdata/SampleSheets.

    Make sure you’re on a machine that can see these directories.  Sandy2 is always a good choice.

  2. Check out the iggy code from the git repo.   (I usually put it in /n/informatics/mclamp/test and have to do this from sa01)

    git clone git@github.com:harvardinformatics/IggyTools
    cd IggyTools
    

  3. Setup the environment Ordinarily you would run the setup.sh script if you were going to run seqprep for real.  This sets up the environment with the real environment (the real primary data and analysis directories).  We need to change these defaults before running the tests.

    The main config file for seqprep is usually found in

    ~/.iggytools/iggyseq_settings.yaml

    There is a test version of this file in the git repo in

    IggyTools/tests/data/iggytools_prefs

    To make seqprep read this set an environment variable

    export IGGYPREFDIR=IggyTools/test/data/iggytools_prefs

    You’ll also need to edit the iggyseq_settings.yaml file to change the location of the following :

    PRIMARY_PARENT
    USERS_FILE
    WATCHERS_FILE
    LOGDIR_PARENT
    PROCESSING_PARENT
    FINAL_PARENT
    

  4. Copy over some test files

    cp -r /n/informatics/saved/ /n/informatics/mclamp/test/saved/

  5. Then run

    python IggyTools/iggytools/bin/seqprep

    and it should give you some help text