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Re: Packaging SMALT for Debian

Hi Andreas,

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.
  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?
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.

  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
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 other binaries.
  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 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.
  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.
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.

Please let me know if you nee more help.

Kind regards,

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: hp3@sanger.ac.uk

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.
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