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Re: Packaging SMALT for Debian

Hi Hannes,

On Wed, Apr 09, 2014 at 09:40:14AM +0100, Hannes Ponstingl wrote:
> 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.

OK, I found the issue since my minimal chroot did not contained zlib.
> 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.

Yep, see my other mail.

> 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.

Samtools is available in Debian and does not seem to be the problem.
> 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.

It just gave me the hint to bambamc. :-)
Kind regards



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