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 Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140409093420.gi28...@an3as.eu
