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Re: Packaging SMALT for Debian

Hi Hannes,

just to keep you informed since you considered creating Debian packages
yourself in past discussion:  I first created packages from bambamc
library which hit Debian (unstable) now and later uploaded smalt
packages which is currently in the new queue


waiting to become accepted by our ftpmaster.

Thanks for your helpful comments in the initial package creation


On Wed, Apr 09, 2014 at 09:40:14AM +0100, Hannes Ponstingl wrote:
> Hi Andreas,
> There is no dependency on BioPython. The 'from formats import Cigar'
> line imports the class Cigar from the Python module
> smalt/test/formats.py which should be part of the distribution.
> For output in the binary format BAM and input from BAM/SAM files
> (see samtools.sourceforge.net) SMALT depends on the bambamc library
> https://github.com/gt1/bambamc
> See the README file for installation instructions with this library.
> This is optional though and the build process may give warnings but
> should still complete and produce a binary without this
> functionality.
> Some tests depend on the samtools (samtools.sourceforge.net) binary
> being in the search path, but the ./configure script should set up
> the test suite so that those test do not run if samtools is not
> installed.
> The only other dependency is zlib - but also this should be optional.
> Could you send me the smalt/test/tmp/LOGFILE.* files that should be
> there after the failed test bam_cigar_test.py. That should tell my
> why the test might have failed.
> Kind regards,
> /Hannes
> On 08/04/14 18:38, Andreas Tille wrote:
> >Hi Hannes,
> >
> >many thanks for your quick response.
> >
> >On Tue, Apr 08, 2014 at 04:07:24PM +0100, Hannes Ponstingl wrote:
> >>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.
> >Yes, this is where we are taking the source from.
> >
> >>>  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.
> >The author and homepage are usual metadata in Debian packages.
> >
> >>>  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.
> >>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.
> >OK, this simplifies things.
> >
> >>>  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.
> >I get the tests running now on my workstation installation.  However,
> >when I'm running the build process in a clean chroot (which is mandatory
> >for a package build) I seem to miss some precondition.  I have inspected
> >the *.py sources and guessed from
> >
> >    from formats import Cigar
> >
> >that BioPython is needed.  So I added this to the chroot but the tests
> >are not working better.  So most probably I'm lacking some dependency
> >which is available on my workstation - but which one?
> >
> >Also the last test is failing.  I get:
> >
> >PASS: splitReads_test.py
> >PASS: results_split_test.py
> >PASS: ouform_cigar_test.py
> >PASS: sample_test.py
> >PASS: cigar_test.py
> >PASS: mthread_test.py
> >ERROR when mapping: returned with code 1
> >FAIL: bam_cigar_test.py
> >=================================
> >1 of 7 tests failed
> >Please report to hp3@sanger.ac.uk
> >=================================
> >
> >I think this might also be connected to some missing dependency.
> >
> >>>  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.
> >Thanks - at least the test procedure is started now.
> >>Please let me know if you nee more help.
> >I'm happy about your very constructive response.
> >
> >Kind regards
> >
> >        Andreas.
> >
> -- 
> 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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