On Fri, Feb 10, 2017 at 3:26 PM, Matthias Bernt <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",
> 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.

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