On Mon, Feb 13, 2017 at 9:17 AM, Matthias Bernt <m.bernt@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-td4670... 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/seq... 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