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:
http://blends.debian.org/med/tasks/bio
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
readstats.
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
Andreas.
--
http://fam-tille.de
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