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

The two files have different content. Only the former imports the six module and the former is used by fastq_trimmer_by_quality (as you see in the python stack trace).

The former is already installed in a fresh clone of galaxy (I have checked for 16.07 and 16.10).

The Dependency Resolver Details show that fastq_trimmer_by_quality requires galaxy_sequence_utils 1.0.1, but I can not find this version in my galaxy installation after installing fastq_trimmer_by_quality (find . -iname "galaxy_sequence_utils").

If I install galaxy_sequence_utils 1.0.1 manually (only available from TS) the 1.0.0 version in the database/dependencies/galaxy_sequence_utils is replaced by 1.0.1 (which seems also odd to me - shouldn't both versions be available?).

Anyway, it makes no difference to the python import error if this version is installed or not, since still the version in lib/ is used.

what version of Galaxy are you running?

I am using galaxy 16.10.

The tool you have installed seems to support only new Galaxies that have
Conda dependency resolution enabled. We are currently in the middle of
the transition of the Galaxy's ecosystem to this new dependency manager
so there are rough edges here and there - sorry about that. You can read
details about Conda and dependency resolution
here: https://docs.galaxyproject.org/en/master/admin/conda_faq.html

Since Galaxy 16.07 you can switch the `conda_auto_init` in Galaxy's
config to True and after restart Galaxy will install Conda itself.

I'm using the default dependency_resolvers_conf.xml (ie I don't have the file). Furthermore I have set:

conda_auto_install = True
conda_auto_init = True
conda_copy_dependencies = True

Therefore I recommend you (with Galaxy newer than 16.07) to uninstall
the tool, install Conda (with conda_auto_init) and install the tool
again. That will install the needed dependency for the tool. If you have
older Galaxy please update it.

I did uncheck the checkbox for TS dependencies during the tool installation. I was wondering that galaxy_sequence_utils is not shown as installed in "Manage installed tools". It seems to make no difference if I install it manually or not.

Cheers,
Matthias

Please let us know about any questions you have and thanks for using Galaxy.

Martin

On Fri, Feb 10, 2017 at 10:38 AM Peter Cock <p.j.a.c...@googlemail.com
<mailto:p.j.a.c...@googlemail.com>> wrote:

    On Fri, Feb 10, 2017 at 3:26 PM, Matthias Bernt <m.be...@ufz.de
    <mailto:m.be...@ufz.de>> wrote:
    > Dear galaxy-dev list,
    >
    > I'm currently trying to introduce myself to the galaxy server, i.e.,
    > learning how to use and administer a galaxy server.
    >
    > I have installed galaxy following this excellent tutorial:
    >
    > https://github.com/martenson/dagobah-training
    >
    > Then I tried the tool "FASTQ Quality Trimmer by sliding window"
    which is
    > mentioned in NGS101-6 tutorial. I installed the tool from tool
    shed, but I
    > get a python error (the Admin panel shows that all dependencies are
    > installed):
    >
    > Traceback (most recent call last):
    >   File
    >
    
"/home/berntm/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/25c24379693a/fastq_trimmer_by_quality/fastq_trimmer_by_quality.py
    
<http://toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/25c24379693a/fastq_trimmer_by_quality/fastq_trimmer_by_quality.py>",
    > line 3, in <module>
    >     from galaxy_utils.sequence.fastq import fastqReader, fastqWriter
    >   File "/home/berntm/galaxy/lib/galaxy_utils/sequence/fastq.py",
    line 7, in
    > <module>
    >     from six import Iterator, string_types
    > ImportError: No module named six
    >
    > Do you have an idea what could be wrong? I guess that this is to
    little
    > information, but I did not know which kind of additional
    information would
    > be helpful.

    This appears to be a missing dependency on the Python module "six"
    which is used to help write code which will work under both Python 2
    and Python 3.

    This is likely a recent regression - hopefully one of the Galaxy team
    can comment on this, likely the Tool Shed definition for this tool needs
    a minor tweak (and then you can apply the update via the Galaxy
    Admin controls within your browser).

    > Another question: At my institution quite a lot of NGS projects
    are carried
    > out. After a project is finished all methods and data are stored
    to a long
    > term read only tape archive. For the future the idea is to use
    galaxy. Which
    > options are there to implement such a project life cycle with galaxy?

    Not that I personally am aware of, no. There are optional disk quotas to
    encourage users to remove (delete) old data.

    > A last general question: would it be better to send a separate
    mail to the
    > list when I have multiple questions?

    Yes please, with useful email subjects would be best.

    Peter
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