[Debian-med-packaging] Preliminary package of the NCBI SRA SDK: help needed.

[Charles Plessy]

Le Mon, Dec 20, 2010 at 05:36:46PM +0100, Andreas Tille a écrit :
> On Mon, Dec 20, 2010 at 08:45:30PM +0900, Charles Plessy wrote:
> > For the record, the tools built with the current draft package fail with errors like:
> > 
> > "sra-stat int: schema not found while opening table within virtual database module"
> > 
> > I have not figured out is it is a problem with dynamic building.
> 
> I can not confirm reproduce this problem.  After adding libxml2-dev
> Build-Depends I was able to build the package (which contains a lot of
> lintian problems, but anyway a package was builded).

Hi Andreas,

the errors show up with the programs when trying to use them for something else
than just displaying the help message. You can try with this data for instance,
with programs like sra-stat:

  $ sra-stat
  missing source table
  
  Usage: sra-stat [ options ] table [ column-spec... ]
      run with option '--help' for help
  $ wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/BySample/sra/SRS/SRS001/SRS001798/SRR006565/SRR006565.sra
  $ sra-stat SRR006565.sra 
  2010-12-21 15:15:00 sra-stat int: schema not found while opening table within virtual database module  - failed to open SRATable 'SRR006565.sra'

Here is a typical result obtained from the static binaries that are distributed
by the NCBI (http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software):

  $ /home/karl/src/sratoolkit.2.0b5-centos_linux64/sra-stat SRR006565.sra 
  SRR006565.sra||2145126:77224536:77224536|0:0|0:0|0:0

By the way, I acknowledge that the package is still very far from being
uploadable to Debian (see debian/control).

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Strasbourg, France