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 <[email protected]
<mailto:[email protected]>> wrote:
On Fri, Feb 10, 2017 at 3:26 PM, Matthias Bernt <[email protected]
<mailto:[email protected]>> 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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