[Debian-med-packaging] Bug#824402: sra-toolkit: does not load data from fastq files to directory (and probably more problems)

[Andreas Tille]

Hi Jana,

thanks for this bug report.  I admit that sra-toolkit packaging is
lagging behind upstream development.  The reason was a new dependency
(ngs-sdk) which is packaged now.  I tried the latest upstream source but
due to the quite unusual build system (the source is using a configure
script which is something else than an autoconf created script) the new
version does not build as simple.  I hope that once we've managed to get
the package build there are chances that this problem is fixed - if not
we try to contact upstream about this.

Any volunteer to fox the build system is more than welcome.

Kind regards

      Andreas.

On Sun, May 15, 2016 at 04:18:46PM +0200, jana wrote:
> Package: sra-toolkit
> Version: 2.3.5-2+dfsg-1
> Severity: grave
> Justification: renders package unusable
> 
> Dear Maintainer,
> 
> The latf-load binary from sra-toolkit package doesn't load data from fastq
> files to directory - it will ends up with these errors:
> 
> $ latf-load -q PHRED_33 -o Desktop/test Desktop/test.fastq
> 2016-05-15T13:51:17 latf-load.2.3.5 warn: Deprecated argument '-q' may not be
> supported in future releases. Please use '--quality' instead.
> 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory
> within file system module - file="align/align.vschema"
> 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory
> within file system module - failed to parse schema file align/align.vschema
> 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory
> within file system module - accession="test" errors="0" status="failure"
> 2016-05-15T13:51:17 latf-load.2.3.5 err: path not found while opening directory
> within file system module - load failed
> 
> It seems the binary doesn't see the necessary vschema files. There is
> everything fine on the upstream package. The temporary solution is to
> copy/symlink schema directory from upstream package (latest version) to /usr -
> this works fine. I think the problem influence other binaries too, but I don't
> know - didn't try. I tryed this on the clean Debian 8 installation - the
> problem remains.
> 
> 
> 
> -- System Information:
> Debian Release: 8.4
>   APT prefers stable-updates
>   APT policy: (500, 'stable-updates'), (500, 'stable')
> Architecture: i386 (i686)
> 
> Kernel: Linux 3.16.0-4-686-pae (SMP w/1 CPU core)
> Locale: LANG=sk_SK.UTF-8, LC_CTYPE=sk_SK.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: systemd (via /run/systemd/system)
> 
> Versions of packages sra-toolkit depends on:
> ii  libbz2-1.0         1.0.6-7+b3
> ii  libc6              2.19-18+deb8u4
> ii  libxml2            2.9.1+dfsg1-5+deb8u1
> ii  sra-toolkit-libs0  2.3.5-2+dfsg-1
> ii  zlib1g             1:1.2.8.dfsg-2+b1
> 
> sra-toolkit recommends no packages.
> 
> sra-toolkit suggests no packages.
> 
> -- no debconf information
> 
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