On Mon, Feb 13, 2017 at 9:17 AM, Matthias Bernt <[email protected]> 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
