Re: Packaging SMALT for Debian
Thanks for your interest in SMALT. I have cleaned up the test routines
for the installation/distribution somewhat with the latest release 0.7.6
which you can download from smalt.sourceforge.net.
There still is no publication describing SMALT - although a number of
high-profile papers have appeared that use it. So if you could mention
smalt.sourceforge.net and my name and affiliation in the citation info.
I would let you know once I have the paper accepted.
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?
Yes, smalt is the only user interface. The other binaries can be used to
generate simulated data and to inspect files ets. They are undocumented
and I should probably remove them from the installation to avoid
confusion. Version 0.7.6 should have been cleaned up somewhat in that
respect. There is no need for a wrapper and smalt does not call any
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
The python scripts are for testing during development except for a
number of installation test drivers *_test.py that are packaged in the
distribution. Please refer to smalt/test/Makefile.am which is also the
test harness (make check). Let me know if you need help with that.
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?
The test suite is run with 'make check' from the distribution (make
dist). Binaries are wrapped with python drivers in smalt/test/*_test.py.
The harness is the automake 'make check' facility.
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
Please let me know if you nee more help.
Hannes Ponstingl, Ph.D.
Sequence Assembly & Analysis Group Tel: +44 (0)1223 834244 x7345
The Wellcome Trust Sanger Institute Fax: +44 (0)1223 494919
Hinxton, Cambridge CB10 1SA, UK. E-mail: firstname.lastname@example.org
The Wellcome Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742969, whose registered
office is 215 Euston Road, London, NW1 2BE.