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
https://ftp-master.debian.org/new/smalt_0.7.6-1.html
waiting to become accepted by our ftpmaster.
Thanks for your helpful comments in the initial package creation
Andreas.
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
>
>
>
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