QIIME code sprint complete

11 02 2010

The QIIME development team wrapped up our code sprint yesterday, and tested a lot of our changes over the past day. We got a lot of changes pushed in: there were over 140 commits to the SVN repository on 9 Feb alone.

We accomplished our two primary goals: moving all of the command line interface code from the QIIME library files to the QIIME script files, helping us separate the throughly tested QIIME functionality from the lightweight command line wrappers; and modifying the QIIME scripts to standardize the look-and-feel of the command line interfaces. Some of the secondary goals we accomplished were porting the svn documentation to sphinx; moving supporting files (e.g., xml and web templates) to the new Qiime/support_files directory; and adding a uclust OTU picker. This moved us a lot closer to having a solid 1.0 release.

It’s OK to begin doing SVN updates again, but you may run into some bugs over the next week or so. Please post a Sourceforge bug report as you find bugs. (Don’t forget you can request new features via Sourceforge as well.) Remember that if you are primarily interested in having a stable version of QIIME, you should install our latest release, which you can download here. Users of the svn code base have access to the latest features, but are also subject to interface changes and more bugs than users of the stable release. We definitely encourage users who are interested to use the svn code base however, as getting feedback from users helps us find bugs and improve QIIME.

When you next do an ‘svn update’ on QIIME, there are a few things you’ll need to take note of:

  1. You will no longer call the QIIME scripts from the Qiime/qiime directory. Instead, you will now call scripts from the Qiime/scripts directory. For example, you previously may have run the command:
    python Qiime/qiime/align_seqs.py -h

    You will now run:
    python Qiime/scripts/align_seqs.py -h

    For the most part, the script names have stayed the same – only their locations have changed. One notable exception is rarefaction.py, which was split into two scripts:
    Qiime/scripts/single_rarefaction.py
    Qiime/scripts/multiple_rarefactions.py

  2. SVN users who have created custom qiime_config files will need to update those files so script filepaths point to Qiime/scripts, where they previously pointed to Qiime/qiime. For example, I previously had the following line in my qiime_config:
    align_seqs_fp /Users/caporaso/code/Qiime/qiime/align_seqs.py

    This was replaced by:
    align_seqs_fp /Users/caporaso/code/Qiime/scripts/align_seqs.py

    The values that need to be updated correspond to the keys:
    align_seqs_fp
    assign_taxonomy_fp
    pick_otus_fp
    alpha_diversity_fp
    beta_diversity_fp

    Additionally, you’ll need to replace
    rarefaction_fp

    with:
    single_rarefaction_fp

    And the poller_fp key should now point into Qiime/scripts rather than Qiime/qiime/parallel/. Mine now looks like:
    poller_fp /Users/caporaso/code/Qiime/scripts/poller.py

    If this gets confusing, you can look at Qiime/qiime_config, which should help you figure out how these values need to be updated.

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