On Mon, Feb 13, 2017 at 9:17 AM, Matthias Bernt <m.be...@ufz.de> wrote:
> Dear Martin,
>
> Thanks for your input. Before answering the raised questions I would like to
> add some more information that I just found:
>
> I've noticed something odd (to me) which is maybe the source of the problem.
> My galaxy installation has galaxy_utils installed twice:
>
> - lib/galaxy_utils/sequence/fastq.py
>
> -
> database/dependencies/galaxy_sequence_utils/1.0.0/devteam/package_galaxy_utils_1_0/8882f14715b5/lib/python/galaxy_sequence_utils-1.0.0-py2.7.egg/galaxy_utils/sequence/fastq.py
>

Something like that is to be expected right now as this is in
transition, see also:

http://dev.list.galaxyproject.org/Tools-using-Galaxy-s-Python-library-td4670472.html

In the next release of Galaxy, there will not be a copy of the code at
lib/galaxy_utils/sequence/fastq.py - see this pull request for the change
https://github.com/galaxyproject/galaxy/pull/3551

Originally tools were allowed to access Galaxy's internal Python code,
here lib/galaxy_utils/sequence/fastq.py - but that is changing. In the
next Galaxy release tools should explicitly depend on the new
packaged version of Galaxy's sequence_utils - that's where the
second copy you've seen comes from:

https://github.com/galaxyproject/sequence_utils

This does now import six as part of work to make sure it can be
used on Python 2 and Python 3:

https://github.com/galaxyproject/sequence_utils/blob/master/galaxy_utils/sequence/sequence.py

Galaxy itself will depend on the now separate sequence_utils
package.

--

As to what is going wrong in your situation, I'm hoping one of the
Galaxy developers working on this can help.

Peter
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