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 h...@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: h...@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. > > > -- > 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/5345076e.5080...@sanger.ac.uk > > -- 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/20140417095857.gb27...@an3as.eu
