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.cock@googlemail.com
> <mailto:p.j.a.cock@googlemail.com>> wrote:
>
>     On Fri, Feb 10, 2017 at 3:26 PM, Matthias Bernt <m.bernt@ufz.de
>     <mailto:m.bernt@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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