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Packaging SMALT for Debian

Hi Hannes,

I'm writing you on behalf of the Debian Med team which tries to package
software which is relevant in medicine and biology for official Debian.
If you want to get an overview about the biological software we have
included into Debian you can get an overview here:


Since some colleagues of mine have some interest in SMALT and so I went
to this item on our todo list and prepared some packaging.  When doing
so some questions were raised.

 1. Since we always want to honour scientist work we would like to
    add some citation information to the package metadata (you can
    see the result when visiting the page above).  Are there any
    publications about SMALT?

 2. The installation puts a set of binaries next to the main binary
    smalt in the users path (basqcol, fetchseq, ...).  Is it correct
    that in principle only smalt is the user interface and these
    additional binaries are only helpers called by smalt?
    If this is the case I tend to use a wrapper script /usr/bin/smalt
    which calls these exectuables from /usr/lib/smalt.  This would
    avoid potential name space conflicts with generic names like

 3. What is the role of the Python script the installation procedure
    is moving to /usr/share by default.  With the exception of SAM.py
    the scripts seem to belong to a test suite.  Usually in Debian
    Python scripts are installed in a different PATH.  Is SAM.py also
    a user application or just a helper for the smalt binary?

 4. In Debian we try to run any test suite if available but I somehow
    failed to find the documentation how to exactly run the full
    test suite.

Kind regards and thanks for any helpful hint



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