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

[jana]

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