Hi Matthias,

> 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.

I recommend leaving the box checked so Galaxy will use Conda to install the
dependency.
Is the tool still missing imports after you install it this way?

Currently 'Managed installed repositories' does _not_ show Conda-installed
dependencies - the UI is lacking behind the system's capabilities - our
apologies.


Martin




On Mon, Feb 13, 2017 at 4:17 AM Matthias Bernt <m.be...@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
>
> 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
> >     ___________________________________________________________
> >     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/
> >
>
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